We report the generation of a non‑invasive, pathogen‑responsive reporter system in Arabidopsis thaliana by placing the PR1 promoter upstream of the betalain‑producing RUBY cassette. Two independent transgenic lines showed robust, dose‑dependent red pigmentation accumulation in response to flg22 (a flagellin-derived peptide) and salicylic acid (a defense-signaling molecule that induces PR1) in both seedling and adult tissues. This reporter provides a simple, low‑cost visual readout of defense activation without the need for destructive sampling or specialized instrumentation. Seeds have been deposited at ABRC, and the plasmid has been made available through Addgene.
","acknowledgements":"We appreciate the support provided by Maeriam Hajjaj and Hope Gruszewski (Virginia Polytechnic Institute and State University). We thank Dr. Yunde Zhao (University of California San Diego) for kindly providing the pHDE-RUBY vector.
","authors":[{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["writing_reviewEditing","conceptualization","investigation"],"email":"lolamcmullan@vt.edu","firstName":"Lola O.","lastName":"McMullan","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["conceptualization","formalAnalysis","investigation","writing_reviewEditing"],"email":"jstaylo8@ncsu.edu","firstName":"Joseph S. ","lastName":"Taylor","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["investigation","writing_reviewEditing"],"email":"rhanlon@vt.edu","firstName":"Regina","lastName":"Hanlon","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["investigation","writing_reviewEditing"],"email":"taldin@vt.edu","firstName":"Alex T.","lastName":"Harris","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["conceptualization","writing_reviewEditing"],"email":"jshuman@vt.edu","firstName":"Joel","lastName":"Shuman","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["conceptualization","fundingAcquisition","supervision","writing_reviewEditing"],"email":"dschmale@vt.edu","firstName":"David G.","lastName":"Schmale III","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["conceptualization","supervision","fundingAcquisition","writing_originalDraft"],"email":"bastiaan@vt.edu","firstName":"Bastiaan O. R. ","lastName":"Bargmann","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0000-0001-8406-5036"}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":null},"extendedData":[],"funding":"Research in the Bargmann lab is supported by U.S. National Science Foundation (United States) IOS 2348321, USDA National Institute of Food and Agriculture, HATCH project VA-160262, and Multistate S-009 project VA-136423. Research in the Schmale lab is supported by the Center for Emerging, Zoonotic, and Arthropod-borne Pathogens (CeZAP) at Virginia Tech. L.O.M. and J.S.T. were supported by the Virginia Tech George Washington Carver Program.
","image":{"url":"https://portal.micropublication.org/uploads/b34629e870f07a8fd06b004e4a93873b.jpg"},"imageCaption":"A. Schematic of the PR1::RUBY construct. A 1,334 bp fragment of the Arabidopsis PR1 promoter was cloned into the SpeI site of pHDE‑RUBY, placing the betalain biosynthetic cassette (CYP76AD1–2A–DODA–2A–glucosyltransferase) under pathogen‑responsive transcriptional control. B. One‑week‑old seedlings of two independent transgenic lines (1.6 and 2.4) grown in 24‑well plates (five seedlings per well) showed dose‑dependent betalain accumulation after 48 h treatment with flg22 (0–5 µM) or salicylic acid (SA) (0–100 µM). C. Four‑week‑old soil‑grown plants (line 2.4) 48 h after treatment with 5 µL droplets of mock solution (0.05% Silwet), 1 µM flg22, or 50 µM SA to each leaf.
","imageTitle":"Pathogen‑responsive PR1::RUBY reporter activation in Arabidopsis
","methods":"Construct assembly
A 1,334 bp fragment upstream of the Arabidopsis thaliana PR1 coding sequence was amplified using primers proPR1_SpeI_Fwd TGACTGACTAGTACGTAATAATATCCTATGGTGTC and proPR1_SpeI_Rev TGACTGACTAGTCATTTTTCTAAGTTGATAATGGTTATTG (based on (Pape et al., 2010)) and cloned into the SpeI site of pHDE‑RUBY (He et al., 2020), placing the RUBY betalain biosynthetic cassette under PR1 promoter control. The pHDE_PR1::RUBY vector is available through Addgene (…).
Plant transformation and growth conditions
The construct was transformed into A. thaliana Col‑0 using Agrobacterium tumefaciens GV3101 via floral dip. T1 plants were selected, and two independent single‑locus lines (1.6 and 2.4) were advanced for characterization. Seeds for both lines are available through the ABRC stock center (https://abrc.osu.edu/; CS74214 - pHDE_PR1::RUBY 1.6 and CS74215 - pHDE_PR1::RUBY 2.4). Seedlings were grown in ½ MS medium (2.2 g/L Murashige and Skoog salts) supplemented with 1% sucrose, incubated in a plant growth chamber (Percival, Perry, IA, USA) at 22 °C with an 18 h light/6 h dark regime at 75 µmol m−2 s−1 PAR. Soil-grown plants were incubated in a plant growth chamber (Conviron, Pembina, ND, USA) at 22 °C with an 18 h light/6 h dark regime at 150 µmol m−2 s−1 PAR.
Elicitation assays
Five seedlings were grown in each well of a 24‑well plate containing 500 µL liquid ½ MS + sucrose medium. After one week, medium in the wells was replaced with 500 µL liquid ½ MS + sucrose supplemented with flg22 (0, 0.008, 0.04, 0.2, 1, or 5 µM) or salicylic acid (0, 6.25, 12.5, 25, 50, or 100 µM). Plates were incubated for 48 h and imaged using a flatbed document scanner. Four‑week‑old soil‑grown plants were treated by applying 5 µL droplets of 0.05% Silwet (mock), Silwet plus 1 µM flg22, or Silwet plus 50 µM SA to each leaf. Plants were imaged after 48 h using a digital camera.
","reagents":"","patternDescription":"Description
Plant immune responses are highly dynamic, spatially heterogeneous, and often difficult to monitor without destructive sampling or specialized equipment. The Arabidopsis thaliana PATHOGENESIS‑RELATED 1 (PR1) promoter is one of the most widely used molecular markers of salicylic acid (SA)–dependent defense activation (Ward et al., 1991), yet most PR1 reporters rely on fluorescent or enzymatic outputs that require microscopy, substrate addition, and/or tissue disruption. To provide a simple, low‑cost, and non‑invasive alternative, we engineered a visible pathogen‑responsive reporter by placing a 1,334 bp PR1 promoter fragment upstream of the RUBY betalain biosynthetic cassette (He et al., 2020) (Figure 1A). RUBY produces red betalain pigments that accumulate without additional substrates and are easily detected by eye, making it an attractive reporter for rapid screening, phenotyping, and educational applications.
We cloned the PR1 promoter into pHDE‑RUBY, generating a PR1::RUBY construct that links immune activation to betalain production. Using Agrobacterium tumefaciens GV3101, we transformed Arabidopsis thaliana Col‑0 and selected two independent single‑locus lines (lines 1.6 and 2.4). Both lines exhibited robust and reproducible reporter activation in response to flg22 (a flagellin-derived peptide) and SA. In a 24‑well plate assay, one‑week‑old seedlings treated for 48 h with flg22 (0–5 µM) (Felix et al., 1999) and SA (0–100 µM) showed clear, dose‑dependent accumulation of red pigmentation, with no obvious signal in untreated controls (Figure 1B). Line 2.4 displayed slightly higher sensitivity, but both lines responded similarly across the full concentration range. SA elicited the strongest overall activation, consistent with its role as a central regulator of PR1 expression (Chen et al., 2020).
To test reporter performance in mature tissues, we applied 5 µL droplets of mock solution (0.05% Silwet only), 1 µM flg22, or 50 µM SA to individual leaves of four‑week‑old soil‑grown plants. After 48 h, flg22 and SA treatments induced visible betalain accumulation, whereas mock‑treated leaves remained green (Figure 1C). These results demonstrate that PR1::RUBY reliably reports immune activation in both seedlings and adult plants, and that betalain accumulation provides a clear, easily interpretable visual output.
This reporter system offers several advantages for the plant research community. First, it enables rapid, non‑destructive monitoring of defense activation without specialized imaging equipment. Second, it is suitable for high‑throughput screening in multi‑well formats. Third, it provides an intuitive visual readout that is accessible for research, teaching, and outreach. Future work will evaluate reporter activation during infection with well-characterized Arabidopsis pathogens, such as Pseudomonas syringae and Hyaloperonospora arabidopsidis(Cameron et al., 1999; Marco et al., 2014). Because the RUBY cassette functions across diverse plant species, the construct may also be adaptable beyond Arabidopsis. To our knowledge, this is the first report of PR1::RUBY reporter in use, although we did find mention of such a construct elsewhere (https://2021.igem.org/Team:Duesseldorf/Proof_Of_Concept). To facilitate broad use, the PR1::RUBY plasmid was deposited at Addgene, and the transgenic Arabidopsis lines were made available through the Arabidopsis Biological Resource Center (ABRC).
","references":[{"reference":"CAMERON RK, PAIVA NL, LAMB CJ, DIXON RA. 1999. Accumulation of salicylic acid and PR-1 gene transcripts in relation to the systemic acquired resistance (SAR) response induced by Pseudomonas syringae pv. tomato in Arabidopsis. Physiological and Molecular Plant Pathology 55: 121-130.
","pubmedId":"","doi":"10.1006/pmpp.1999.0214"},{"reference":"Chen J, Clinton M, Qi G, Wang D, Liu F, Fu ZQ. 2020. Reprogramming and remodeling: transcriptional and epigenetic regulation of salicylic acid-mediated plant defense. Journal of Experimental Botany 71: 5256-5268.
","pubmedId":"","doi":"10.1093/jxb/eraa072"},{"reference":"Felix G, Duran JD, Volko S, Boller T. 1999. Plants have a sensitive perception system for the most conserved domain of bacterial flagellin. The Plant Journal 18: 265-276.
","pubmedId":"","doi":"10.1046/j.1365-313X.1999.00265.x"},{"reference":"He Y, Zhang T, Sun H, Zhan H, Zhao Y. 2020. A reporter for noninvasively monitoring gene expression and plant transformation. Horticulture Research 7: 10.1038/s41438-020-00390-1.
","pubmedId":"","doi":"10.1038/s41438-020-00390-1"},{"reference":"Marco F, Busó E, Carrasco P. 2014. Overexpression of SAMDC1 gene in Arabidopsis thaliana increases expression of defense-related genes as well as resistance to Pseudomonas syringae and Hyaloperonospora arabidopsidis. Frontiers in Plant Science 5: 10.3389/fpls.2014.00115.
","pubmedId":"","doi":"10.3389/fpls.2014.00115"},{"reference":"Pape S, Thurow C, Gatz C. 2010. The Arabidopsis PR-1 Promoter Contains Multiple Integration Sites for the Coactivator NPR1 and the Repressor SNI1. Plant Physiology 154: 1805-1818.
","pubmedId":"","doi":"10.1104/pp.110.165563"},{"reference":"Ward ER, Uknes SJ, Williams SC, Dincher SS, Wiederhold DL, Alexander DC, et al., Ryals. 1991. Coordinate Gene Activity in Response to Agents That Induce Systemic Acquired Resistance.. The Plant Cell : 1085-1094.
","pubmedId":"","doi":"10.1105/tpc.3.10.1085"}],"title":"A Non‑Invasive Pathogen‑Responsive RUBY Reporter Enables Visible Monitoring of PR1 Activation
","reviews":[],"curatorReviews":[]},{"id":"0a30c37f-6d99-4418-9494-e697ce1db4d6","decision":"revise","abstract":"We report the generation of a non‑invasive, pathogen‑responsive reporter system in Arabidopsis thaliana by placing the PR1 promoter upstream of the betalain‑producing RUBY cassette. Two independent transgenic lines showed robust, dose‑dependent red pigmentation accumulation in response to flg22 (a flagellin-derived peptide) and salicylic acid (a defense-signaling molecule that induces PR1) in both seedling and adult tissues. This reporter provides a simple, low‑cost visual readout of defense activation without the need for destructive sampling or specialized instrumentation. Seeds have been deposited at ABRC, and the plasmid has been made available through Addgene.
","acknowledgements":"We appreciate the support provided by Maeriam Hajjaj and Hope Gruszewski (Virginia Polytechnic Institute and State University). We thank Dr. Yunde Zhao (University of California San Diego) for kindly providing the pHDE-RUBY vector.
","authors":[{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["writing_reviewEditing","conceptualization","investigation"],"email":"lolamcmullan@vt.edu","firstName":"Lola O.","lastName":"McMullan","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["conceptualization","formalAnalysis","investigation","writing_reviewEditing"],"email":"jstaylo8@ncsu.edu","firstName":"Joseph S. ","lastName":"Taylor","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["investigation","writing_reviewEditing"],"email":"rhanlon@vt.edu","firstName":"Regina","lastName":"Hanlon","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["investigation","writing_reviewEditing"],"email":"taldin@vt.edu","firstName":"Alex T.","lastName":"Harris","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["conceptualization","writing_reviewEditing"],"email":"jshuman@vt.edu","firstName":"Joel","lastName":"Shuman","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["conceptualization","fundingAcquisition","supervision","writing_reviewEditing"],"email":"dschmale@vt.edu","firstName":"David G.","lastName":"Schmale III","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["conceptualization","supervision","fundingAcquisition","writing_originalDraft"],"email":"bastiaan@vt.edu","firstName":"Bastiaan O. R. ","lastName":"Bargmann","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0000-0001-8406-5036"}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":null},"extendedData":[],"funding":"Research in the Bargmann lab is supported by U.S. National Science Foundation (United States) IOS 2348321, USDA National Institute of Food and Agriculture, HATCH project VA-160262, and Multistate S-009 project VA-136423. Research in the Schmale lab is supported by the Center for Emerging, Zoonotic, and Arthropod-borne Pathogens (CeZAP) at Virginia Tech. L.O.M. and J.S.T. were supported by the Virginia Tech George Washington Carver Program.
","image":{"url":"https://portal.micropublication.org/uploads/b34629e870f07a8fd06b004e4a93873b.jpg"},"imageCaption":"A. Schematic of the PR1::RUBY construct. A 1,334 bp fragment of the Arabidopsis PR1 promoter was cloned into the SpeI site of pHDE‑RUBY, placing the betalain biosynthetic cassette (CYP76AD1–2A–DODA–2A–glucosyltransferase) under pathogen‑responsive transcriptional control. B. One‑week‑old seedlings of two independent transgenic lines (1.6 and 2.4) grown in 24‑well plates (five seedlings per well) showed dose‑dependent betalain accumulation after 48 h treatment with flg22 (0–5 µM) or salicylic acid (SA) (0–100 µM). C. Four‑week‑old soil‑grown plants (line 2.4) 48 h after treatment with 5 µL droplets of mock solution (0.05% Silwet), 1 µM flg22, or 50 µM SA to each leaf.
","imageTitle":"Pathogen‑responsive PR1::RUBY reporter activation in Arabidopsis
","methods":"Construct assembly
A 1,334 bp fragment upstream of the Arabidopsis thaliana PR1 coding sequence was amplified using primers proPR1_SpeI_Fwd TGACTGACTAGTACGTAATAATATCCTATGGTGTC and proPR1_SpeI_Rev TGACTGACTAGTCATTTTTCTAAGTTGATAATGGTTATTG (based on (Pape et al., 2010)) and cloned into the SpeI site of pHDE‑RUBY (He et al., 2020), placing the RUBY betalain biosynthetic cassette under PR1 promoter control. The pHDE_PR1::RUBY vector is available through Addgene (…).
Plant transformation and growth conditions
The construct was transformed into A. thaliana Col‑0 using Agrobacterium tumefaciens GV3101 via floral dip. T1 plants were selected, and two independent single‑locus lines (1.6 and 2.4) were advanced for characterization. Seeds for both lines are available through the ABRC stock center (https://abrc.osu.edu/; CS74214 - pHDE_PR1::RUBY 1.6 and CS74215 - pHDE_PR1::RUBY 2.4). Seedlings were grown in ½ MS medium (2.2 g/L Murashige and Skoog salts) supplemented with 1% sucrose, incubated in a plant growth chamber (Percival, Perry, IA, USA) at 22 °C with an 18 h light/6 h dark regime at 75 µmol m−2 s−1 PAR. Soil-grown plants were incubated in a plant growth chamber (Conviron, Pembina, ND, USA) at 22 °C with an 18 h light/6 h dark regime at 150 µmol m−2 s−1 PAR.
Elicitation assays
Five seedlings were grown in each well of a 24‑well plate containing 500 µL liquid ½ MS + sucrose medium. After one week, medium in the wells was replaced with 500 µL liquid ½ MS + sucrose supplemented with flg22 (0, 0.008, 0.04, 0.2, 1, or 5 µM) or salicylic acid (0, 6.25, 12.5, 25, 50, or 100 µM). Plates were incubated for 48 h and imaged using a flatbed document scanner. Four‑week‑old soil‑grown plants were treated by applying 5 µL droplets of 0.05% Silwet (mock), Silwet plus 1 µM flg22, or Silwet plus 50 µM SA to each leaf. Plants were imaged after 48 h using a digital camera.
","reagents":"","patternDescription":"Description
Plant immune responses are highly dynamic, spatially heterogeneous, and often difficult to monitor without destructive sampling or specialized equipment. The Arabidopsis thaliana PATHOGENESIS‑RELATED 1 (PR1) promoter is one of the most widely used molecular markers of salicylic acid (SA)–dependent defense activation (Ward et al., 1991), yet most PR1 reporters rely on fluorescent or enzymatic outputs that require microscopy, substrate addition, and/or tissue disruption. To provide a simple, low‑cost, and non‑invasive alternative, we engineered a visible pathogen‑responsive reporter by placing a 1,334 bp PR1 promoter fragment upstream of the RUBY betalain biosynthetic cassette (He et al., 2020) (Figure 1A). RUBY produces red betalain pigments that accumulate without additional substrates and are easily detected by eye, making it an attractive reporter for rapid screening, phenotyping, and educational applications.
We cloned the PR1 promoter into pHDE‑RUBY, generating a PR1::RUBY construct that links immune activation to betalain production. Using Agrobacterium tumefaciens GV3101, we transformed Arabidopsis thaliana Col‑0 and selected two independent single‑locus lines (lines 1.6 and 2.4). Both lines exhibited robust and reproducible reporter activation in response to flg22 (a flagellin-derived peptide) and SA. In a 24‑well plate assay, one‑week‑old seedlings treated for 48 h with flg22 (0–5 µM) (Felix et al., 1999) and SA (0–100 µM) showed clear, dose‑dependent accumulation of red pigmentation, with no obvious signal in untreated controls (Figure 1B). Line 2.4 displayed slightly higher sensitivity, but both lines responded similarly across the full concentration range. SA elicited the strongest overall activation, consistent with its role as a central regulator of PR1 expression (Chen et al., 2020).
To test reporter performance in mature tissues, we applied 5 µL droplets of mock solution (0.05% Silwet only), 1 µM flg22, or 50 µM SA to individual leaves of four‑week‑old soil‑grown plants. After 48 h, flg22 and SA treatments induced visible betalain accumulation, whereas mock‑treated leaves remained green (Figure 1C). These results demonstrate that PR1::RUBY reliably reports immune activation in both seedlings and adult plants, and that betalain accumulation provides a clear, easily interpretable visual output.
This reporter system offers several advantages for the plant research community. First, it enables rapid, non‑destructive monitoring of defense activation without specialized imaging equipment. Second, it is suitable for high‑throughput screening in multi‑well formats. Third, it provides an intuitive visual readout that is accessible for research, teaching, and outreach. Future work will evaluate reporter activation during infection with well-characterized Arabidopsis pathogens, such as Pseudomonas syringae and Hyaloperonospora arabidopsidis(Cameron et al., 1999; Marco et al., 2014). Because the RUBY cassette functions across diverse plant species, the construct may also be adaptable beyond Arabidopsis. To our knowledge, this is the first report of PR1::RUBY reporter in use, although we did find mention of such a construct elsewhere (https://2021.igem.org/Team:Duesseldorf/Proof_Of_Concept). To facilitate broad use, the PR1::RUBY plasmid was deposited at Addgene, and the transgenic Arabidopsis lines were made available through the Arabidopsis Biological Resource Center (ABRC).
","references":[{"reference":"CAMERON RK, PAIVA NL, LAMB CJ, DIXON RA. 1999. Accumulation of salicylic acid and PR-1 gene transcripts in relation to the systemic acquired resistance (SAR) response induced by Pseudomonas syringae pv. tomato in Arabidopsis. Physiological and Molecular Plant Pathology 55: 121-130.
","pubmedId":"","doi":"10.1006/pmpp.1999.0214"},{"reference":"Chen J, Clinton M, Qi G, Wang D, Liu F, Fu ZQ. 2020. Reprogramming and remodeling: transcriptional and epigenetic regulation of salicylic acid-mediated plant defense. Journal of Experimental Botany 71: 5256-5268.
","pubmedId":"","doi":"10.1093/jxb/eraa072"},{"reference":"Felix G, Duran JD, Volko S, Boller T. 1999. Plants have a sensitive perception system for the most conserved domain of bacterial flagellin. The Plant Journal 18: 265-276.
","pubmedId":"","doi":"10.1046/j.1365-313X.1999.00265.x"},{"reference":"He Y, Zhang T, Sun H, Zhan H, Zhao Y. 2020. A reporter for noninvasively monitoring gene expression and plant transformation. Horticulture Research 7: 10.1038/s41438-020-00390-1.
","pubmedId":"","doi":"10.1038/s41438-020-00390-1"},{"reference":"Marco F, Busó E, Carrasco P. 2014. Overexpression of SAMDC1 gene in Arabidopsis thaliana increases expression of defense-related genes as well as resistance to Pseudomonas syringae and Hyaloperonospora arabidopsidis. Frontiers in Plant Science 5: 10.3389/fpls.2014.00115.
","pubmedId":"","doi":"10.3389/fpls.2014.00115"},{"reference":"Pape S, Thurow C, Gatz C. 2010. The Arabidopsis PR-1 Promoter Contains Multiple Integration Sites for the Coactivator NPR1 and the Repressor SNI1. Plant Physiology 154: 1805-1818.
","pubmedId":"","doi":"10.1104/pp.110.165563"},{"reference":"Ward ER, Uknes SJ, Williams SC, Dincher SS, Wiederhold DL, Alexander DC, et al., Ryals. 1991. Coordinate Gene Activity in Response to Agents That Induce Systemic Acquired Resistance.. The Plant Cell : 1085-1094.
","pubmedId":"","doi":"10.1105/tpc.3.10.1085"}],"title":"A Non-Invasive Pathogen‑Responsive RUBY Reporter Enables Visible Monitoring of PR1 Activation
","reviews":[],"curatorReviews":[]},{"id":"0010fe74-3e42-4cdc-808c-b2b6304f8c2f","decision":"revise","abstract":"We report the generation of a non‑invasive, pathogen‑responsive reporter system in Arabidopsis thaliana by placing the PR1 promoter upstream of the betalain‑producing RUBY cassette. Two independent transgenic lines showed robust, dose‑dependent red pigmentation accumulation in response to flg22 (a flagellin-derived peptide) and salicylic acid (a defense-signaling molecule that induces PR1) in both seedling and adult tissues. This reporter provides a simple, low‑cost visual readout of defense activation without the need for destructive sampling or specialized instrumentation. Seeds have been deposited at ABRC, and the plasmid has been made available through Addgene.
","acknowledgements":"We appreciate the support provided by Maeriam Hajjaj and Hope Gruszewski (Virginia Polytechnic Institute and State University). We thank Dr. Yunde Zhao (University of California San Diego) for kindly providing the pHDE-RUBY vector.
","authors":[{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["writing_reviewEditing","conceptualization","investigation"],"email":"lolamcmullan@vt.edu","firstName":"Lola O.","lastName":"McMullan","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["conceptualization","formalAnalysis","investigation","writing_reviewEditing"],"email":"jstaylo8@ncsu.edu","firstName":"Joseph S. ","lastName":"Taylor","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["investigation","writing_reviewEditing"],"email":"rhanlon@vt.edu","firstName":"Regina","lastName":"Hanlon","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["investigation","writing_reviewEditing"],"email":"taldin@vt.edu","firstName":"Alex T.","lastName":"Harris","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["conceptualization","writing_reviewEditing"],"email":"jshuman@vt.edu","firstName":"Joel","lastName":"Shuman","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["conceptualization","fundingAcquisition","supervision","writing_reviewEditing"],"email":"dschmale@vt.edu","firstName":"David G.","lastName":"Schmale III","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["conceptualization","supervision","fundingAcquisition","writing_originalDraft"],"email":"bastiaan@vt.edu","firstName":"Bastiaan O. R. ","lastName":"Bargmann","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0000-0001-8406-5036"}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":null},"extendedData":[],"funding":"Research in the Bargmann lab is supported by U.S. National Science Foundation (United States) IOS 2348321, USDA National Institute of Food and Agriculture, HATCH project VA-160262, and Multistate S-009 project VA-136423. Research in the Schmale lab is supported by the Center for Emerging, Zoonotic, and Arthropod-borne Pathogens (CeZAP) at Virginia Tech. L.O.M. and J.S.T. were supported by the Virginia Tech George Washington Carver Program.
","image":{"url":"https://portal.micropublication.org/uploads/b34629e870f07a8fd06b004e4a93873b.jpg"},"imageCaption":"A. Schematic of the PR1::RUBY construct. A 1,334 bp fragment of the Arabidopsis PR1 promoter was cloned into the SpeI site of pHDE‑RUBY, placing the betalain biosynthetic cassette (CYP76AD1–2A–DODA–2A–glucosyltransferase) under pathogen‑responsive transcriptional control. B. One‑week‑old seedlings of two independent transgenic lines (1.6 and 2.4) grown in 24‑well plates (five seedlings per well) showed dose‑dependent betalain accumulation after 48 h treatment with flg22 (0–5 µM) or salicylic acid (SA) (0–100 µM). C. Four‑week‑old soil‑grown plants (line 2.4) 48 h after treatment with 5 µL droplets of mock solution (0.05% Silwet), 1 µM flg22, or 50 µM SA to each leaf.
","imageTitle":"Pathogen‑responsive PR1::RUBY reporter activation in Arabidopsis
","methods":"Construct assembly
A 1,334 bp fragment upstream of the Arabidopsis thaliana PR1 coding sequence was amplified using primers proPR1_SpeI_Fwd TGACTGACTAGTACGTAATAATATCCTATGGTGTC and proPR1_SpeI_Rev TGACTGACTAGTCATTTTTCTAAGTTGATAATGGTTATTG (based on (Pape et al., 2010)) and cloned into the SpeI site of pHDE‑RUBY (He et al., 2020), placing the RUBY betalain biosynthetic cassette under PR1 promoter control. The pHDE_PR1::RUBY vector is available through Addgene (…).
Plant transformation and growth conditions
The construct was transformed into A. thaliana Col‑0 using Agrobacterium tumefaciens GV3101 via floral dip. T1 plants were selected, and two independent single‑locus lines (1.6 and 2.4) were advanced for characterization. Seeds for both lines are available through the ABRC stock center (https://abrc.osu.edu/; CS74214 - pHDE_PR1::RUBY 1.6 and CS74215 - pHDE_PR1::RUBY 2.4). Seedlings were grown in ½ MS medium (2.2 g/L Murashige and Skoog salts) supplemented with 1% sucrose, incubated in a plant growth chamber (Percival, Perry, IA, USA) at 22 °C with an 18 h light/6 h dark regime at 75 µmol m−2 s−1 PAR. Soil-grown plants were incubated in a plant growth chamber (Conviron, Pembina, ND, USA) at 22 °C with an 18 h light/6 h dark regime at 150 µmol m−2 s−1 PAR.
Elicitation assays
Five seedlings were grown in each well of a 24‑well plate containing 500 µL liquid ½ MS + sucrose medium. After one week, medium in the wells was replaced with 500 µL liquid ½ MS + sucrose supplemented with flg22 (0, 0.008, 0.04, 0.2, 1, or 5 µM) or salicylic acid (0, 6.25, 12.5, 25, 50, or 100 µM). Plates were incubated for 48 h and imaged using a flatbed document scanner. Four‑week‑old soil‑grown plants were treated by applying 5 µL droplets of 0.05% Silwet (mock), Silwet plus 1 µM flg22, or Silwet plus 50 µM SA to each leaf. Plants were imaged after 48 h using a digital camera.
","reagents":"","patternDescription":"Description
Plant immune responses are highly dynamic, spatially heterogeneous, and often difficult to monitor without destructive sampling or specialized equipment. The Arabidopsis thaliana PATHOGENESIS‑RELATED 1 (PR1) promoter is one of the most widely used molecular markers of salicylic acid (SA)–dependent defense activation (Ward et al., 1991), yet most PR1 reporters rely on fluorescent or enzymatic outputs that require microscopy, substrate addition, and/or tissue disruption. To provide a simple, low‑cost, and non‑invasive alternative, we engineered a visible pathogen‑responsive reporter by placing a 1,334 bp PR1 promoter fragment upstream of the RUBY betalain biosynthetic cassette (He et al., 2020) (Figure 1A). RUBY produces red betalain pigments that accumulate without additional substrates and are easily detected by eye, making it an attractive reporter for rapid screening, phenotyping, and educational applications.
We cloned the PR1 promoter into pHDE‑RUBY, generating a PR1::RUBY construct that links immune activation to betalain production. Using Agrobacterium tumefaciens GV3101, we transformed Arabidopsis thaliana Col‑0 and selected two independent single‑locus lines (lines 1.6 and 2.4). Both lines exhibited robust and reproducible reporter activation in response to flg22 (a flagellin-derived peptide) and SA. In a 24‑well plate assay, one‑week‑old seedlings treated for 48 h with flg22 (0–5 µM) (Felix et al., 1999) and SA (0–100 µM) showed clear, dose‑dependent accumulation of red pigmentation, with no obvious signal in untreated controls (Figure 1B). Line 2.4 displayed slightly higher sensitivity, but both lines responded similarly across the full concentration range. SA elicited the strongest overall activation, consistent with its role as a central regulator of PR1 expression (Chen et al., 2020).
To test reporter performance in mature tissues, we applied 5 µL droplets of mock solution (0.05% Silwet only), 1 µM flg22, or 50 µM SA to individual leaves of four‑week‑old soil‑grown plants. After 48 h, flg22 and SA treatments induced visible betalain accumulation, whereas mock‑treated leaves remained green (Figure 1C). These results demonstrate that PR1::RUBY reliably reports immune activation in both seedlings and adult plants, and that betalain accumulation provides a clear, easily interpretable visual output.
This reporter system offers several advantages for the plant research community. First, it enables rapid, non‑destructive monitoring of defense activation without specialized imaging equipment. Second, it is suitable for high‑throughput screening in multi‑well formats. Third, it provides an intuitive visual readout that is accessible for research, teaching, and outreach. Future work will evaluate reporter activation during infection with well-characterized Arabidopsis pathogens, such as Pseudomonas syringae and Hyaloperonospora arabidopsidis(Cameron et al., 1999; Marco et al., 2014). Because the RUBY cassette functions across diverse plant species, the construct may also be adaptable beyond Arabidopsis. To our knowledge, this is the first report of PR1::RUBY reporter in use, although we did find mention of such a construct elsewhere (https://2021.igem.org/Team:Duesseldorf/Proof_Of_Concept). To facilitate broad use, the PR1::RUBY plasmid was deposited at Addgene, and the transgenic Arabidopsis lines were made available through the Arabidopsis Biological Resource Center (ABRC).
","references":[{"reference":"CAMERON RK, PAIVA NL, LAMB CJ, DIXON RA. 1999. Accumulation of salicylic acid and PR-1 gene transcripts in relation to the systemic acquired resistance (SAR) response induced by Pseudomonas syringae pv. tomato in Arabidopsis. Physiological and Molecular Plant Pathology 55: 121-130.
","pubmedId":"","doi":"10.1006/pmpp.1999.0214"},{"reference":"Chen J, Clinton M, Qi G, Wang D, Liu F, Fu ZQ. 2020. Reprogramming and remodeling: transcriptional and epigenetic regulation of salicylic acid-mediated plant defense. Journal of Experimental Botany 71: 5256-5268.
","pubmedId":"","doi":"10.1093/jxb/eraa072"},{"reference":"Felix G, Duran JD, Volko S, Boller T. 1999. Plants have a sensitive perception system for the most conserved domain of bacterial flagellin. The Plant Journal 18: 265-276.
","pubmedId":"","doi":"10.1046/j.1365-313X.1999.00265.x"},{"reference":"He Y, Zhang T, Sun H, Zhan H, Zhao Y. 2020. A reporter for noninvasively monitoring gene expression and plant transformation. Horticulture Research 7: 10.1038/s41438-020-00390-1.
","pubmedId":"","doi":"10.1038/s41438-020-00390-1"},{"reference":"Marco F, Busó E, Carrasco P. 2014. Overexpression of SAMDC1 gene in Arabidopsis thaliana increases expression of defense-related genes as well as resistance to Pseudomonas syringae and Hyaloperonospora arabidopsidis. Frontiers in Plant Science 5: 10.3389/fpls.2014.00115.
","pubmedId":"","doi":"10.3389/fpls.2014.00115"},{"reference":"Pape S, Thurow C, Gatz C. 2010. The Arabidopsis PR-1 Promoter Contains Multiple Integration Sites for the Coactivator NPR1 and the Repressor SNI1. Plant Physiology 154: 1805-1818.
","pubmedId":"","doi":"10.1104/pp.110.165563"},{"reference":"Ward ER, Uknes SJ, Williams SC, Dincher SS, Wiederhold DL, Alexander DC, et al., Ryals. 1991. Coordinate Gene Activity in Response to Agents That Induce Systemic Acquired Resistance.. The Plant Cell : 1085-1094.
","pubmedId":"","doi":"10.1105/tpc.3.10.1085"}],"title":"A Non-Invasive Pathogen‑Responsive RUBY Reporter Enables Visible Monitoring of PR1 Activation
","reviews":[{"reviewer":{"displayName":"Nick Kaplinsky"},"openAcknowledgement":false,"status":{"submitted":true}}],"curatorReviews":[]},{"id":"e2fda72b-d515-4e77-a918-e10925c59306","decision":"accept","abstract":"We report the generation of a non‑invasive, pathogen‑responsive reporter system in Arabidopsis thaliana by placing the PR1 promoter upstream of the betalain‑producing RUBY cassette. Two independent transgenic lines showed robust, dose‑dependent red pigmentation accumulation in response to flg22 (a flagellin-derived peptide) and salicylic acid (a defense-signaling molecule that induces PR1) in both seedling and adult tissues. This reporter provides a simple, low‑cost visual readout of defense activation without the need for destructive sampling or specialized instrumentation. Seeds have been deposited at ABRC, and the plasmid has been made available through Addgene.
","acknowledgements":"We appreciate the support provided by Maeriam Hajjaj and Hope Gruszewski (Virginia Polytechnic Institute and State University). We thank Dr. Yunde Zhao (University of California San Diego) for kindly providing the pHDE-RUBY vector.
","authors":[{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["writing_reviewEditing","conceptualization","investigation"],"email":"lolamcmullan@vt.edu","firstName":"Lola O.","lastName":"McMullan","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["conceptualization","formalAnalysis","investigation","writing_reviewEditing"],"email":"jstaylo8@ncsu.edu","firstName":"Joseph S. ","lastName":"Taylor","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["investigation","writing_reviewEditing"],"email":"rhanlon@vt.edu","firstName":"Regina","lastName":"Hanlon","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["investigation","writing_reviewEditing"],"email":"taldin@vt.edu","firstName":"Alex T.","lastName":"Harris","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["conceptualization","writing_reviewEditing"],"email":"jshuman@vt.edu","firstName":"Joel","lastName":"Shuman","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["conceptualization","fundingAcquisition","supervision","writing_reviewEditing"],"email":"dschmale@vt.edu","firstName":"David G.","lastName":"Schmale III","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["conceptualization","supervision","fundingAcquisition","writing_originalDraft"],"email":"bastiaan@vt.edu","firstName":"Bastiaan O. R. ","lastName":"Bargmann","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0000-0001-8406-5036"}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":null},"extendedData":[],"funding":"Research in the Bargmann lab is supported by U.S. National Science Foundation (United States) IOS 2348321, USDA National Institute of Food and Agriculture, HATCH project VA-160262, and Multistate S-009 project VA-136423. Research in the Schmale lab is supported by the Center for Emerging, Zoonotic, and Arthropod-borne Pathogens (CeZAP) at Virginia Tech. L.O.M. and J.S.T. were supported by the Virginia Tech George Washington Carver Program.
","image":{"url":"https://portal.micropublication.org/uploads/da874bb61acc909c970c50bad54a903a.jpg"},"imageCaption":"A. Schematic of the PR1::RUBY construct. A 1,334 bp fragment of the Arabidopsis PR1 promoter was cloned into the SpeI site of pHDE‑RUBY, placing the betalain biosynthetic cassette (CYP76AD1–2A–DODA–2A–glucosyltransferase) under pathogen‑responsive transcriptional control. B. One‑week‑old seedlings of two independent transgenic lines (1.6 and 2.4) grown in 24‑well plates (five seedlings per well) showed dose‑dependent betalain accumulation after 48 h treatment with flg22 (0–5 µM) or salicylic acid (SA) (0–100 µM). Asterisks indicate wells shown in close-up in C. C. Close-up images of the control, 5 µM flg22, and 100 µM SA treatment of line 2.4. D. Four‑week‑old soil‑grown plants (line 2.4) 48 h after treatment with 5 µL droplets of mock solution (0.05% Silwet), 1 µM flg22, or 50 µM SA to each leaf. These results are representative of multiple experiments.
","imageTitle":"Pathogen‑responsive PR1::RUBY reporter activation in Arabidopsis
","methods":"Construct assembly
A 1,334 bp fragment upstream of the Arabidopsis thaliana PR1 coding sequence was amplified using primers proPR1_SpeI_Fwd TGACTGACTAGTACGTAATAATATCCTATGGTGTC and proPR1_SpeI_Rev TGACTGACTAGTCATTTTTCTAAGTTGATAATGGTTATTG (based on (Pape et al., 2010)) and cloned into the SpeI site of pHDE‑RUBY (He et al., 2020), placing the RUBY betalain biosynthetic cassette under PR1 promoter control. The pHDE_PR1::RUBY vector is available through Addgene (https://www.addgene.org/255430/ Plasmid #255430).
Plant transformation and growth conditions
The construct was transformed into A. thaliana Col‑0 using Agrobacterium tumefaciens GV3101 via floral dip. T1 plants were selected, and two independent single‑locus lines (1.6 and 2.4) were advanced for characterization. Seeds for both lines are available through the ABRC stock center (https://abrc.osu.edu/; CS74214 - pHDE_PR1::RUBY 1.6 and CS74215 - pHDE_PR1::RUBY 2.4). Seedlings were grown in ½ MS medium (2.2 g/L Murashige and Skoog salts) supplemented with 1% sucrose, incubated in a plant growth chamber (Percival, Perry, IA, USA) at 22 °C with an 18 h light/6 h dark regime at 75 µmol m−2 s−1 PAR. Soil-grown plants were incubated in a plant growth chamber (Conviron, Pembina, ND, USA) at 22 °C with an 18 h light/6 h dark regime at 150 µmol m−2 s−1 PAR.
Elicitation assays
Five seedlings were grown in each well of a 24‑well plate containing 500 µL liquid ½ MS + sucrose medium. After one week, medium in the wells was replaced with 500 µL liquid ½ MS + sucrose supplemented with flg22 (0, 0.008, 0.04, 0.2, 1, or 5 µM) or salicylic acid (0, 6.25, 12.5, 25, 50, or 100 µM). Plates were incubated for 48 h and imaged using a flatbed document scanner. Four‑week‑old soil‑grown plants were treated by applying 5 µL droplets of 0.05% Silwet (mock), Silwet plus 1 µM flg22, or Silwet plus 50 µM SA to each leaf. Plants were imaged after 48 h using a digital camera.
","reagents":"","patternDescription":"Plant immune responses are highly dynamic, spatially heterogeneous, and often difficult to monitor without destructive sampling or specialized equipment. The Arabidopsis thaliana PATHOGENESIS‑RELATED 1 (PR1) promoter is one of the most widely used molecular markers of salicylic acid (SA)–dependent defense activation (Ward et al., 1991), yet most PR1 reporters rely on fluorescent or enzymatic outputs that require microscopy, substrate addition, and/or tissue disruption. To provide a simple, low‑cost, and non‑invasive alternative, we engineered a visible pathogen‑responsive reporter by placing a 1,334 bp PR1 promoter fragment upstream of the RUBY betalain biosynthetic cassette (He et al., 2020) (Figure 1A). RUBY produces red betalain pigments that accumulate without additional substrates and are easily detected by eye, making it an attractive reporter for rapid screening, phenotyping, and educational applications.
We cloned the PR1 promoter into pHDE‑RUBY, generating a PR1::RUBY construct that links immune activation to betalain production. Using Agrobacterium tumefaciens GV3101, we transformed Arabidopsis thaliana Col‑0 and selected two independent single‑locus lines (lines 1.6 and 2.4; single locus status was determined by examining the segregation ratio of hygromycin resistance in the T2 generation). Both lines exhibited robust and reproducible reporter activation in response to flg22 (a flagellin-derived peptide) and SA. In a 24‑well plate assay, one‑week‑old seedlings treated for 48 h with flg22 (0–5 µM) (Felix et al., 1999) and SA (0–100 µM) showed clear, dose‑dependent accumulation of red pigmentation, with no obvious signal in untreated controls (Figure 1B-C). Line 2.4 displayed slightly higher sensitivity, but both lines responded similarly across the full concentration range. SA elicited the strongest overall activation, consistent with its role as a central regulator of PR1 expression (Chen et al., 2020).
To test reporter performance in mature tissues, we applied 5 µL droplets of mock solution (0.05% Silwet only), 1 µM flg22, or 50 µM SA to individual leaves of four‑week‑old soil‑grown plants. After 48 h, flg22 and SA treatments induced visible betalain accumulation, whereas mock‑treated leaves remained green (Figure 1D). These results demonstrate that PR1::RUBY reliably reports immune activation in both seedlings and adult plants, and that betalain accumulation provides a clear, easily interpretable visual output.
This reporter system offers several advantages for the plant research community. First, it enables rapid, non‑destructive monitoring of defense activation without specialized imaging equipment. Second, it is suitable for high‑throughput screening in multi‑well formats. Third, it provides an intuitive visual readout that is accessible for research, teaching, and outreach. Future work will evaluate reporter activation during infection with well-characterized Arabidopsis pathogens, such as Pseudomonas syringae and Hyaloperonospora arabidopsidis(Cameron et al., 1999; Marco et al., 2014). Because the RUBY cassette functions across diverse plant species, the construct may also be adaptable beyond Arabidopsis. To our knowledge, this is the first report of PR1::RUBY reporter in use, although we did find mention of such a construct elsewhere (https://2021.igem.org/Team:Duesseldorf/Proof_Of_Concept). Future studies incorporating quantitative image analysis or spectrophotometric assays of betalain accumulation will further enable rigorous characterization of reporter sensitivity, dose response, and reproducibility. We envisage its application as a sentinel phytosensor for the presence of plant pathogens. To facilitate broad use, the PR1::RUBY plasmid was deposited at Addgene, and the transgenic Arabidopsis lines were made available through the Arabidopsis Biological Resource Center (ABRC).
","references":[{"reference":"CAMERON RK, PAIVA NL, LAMB CJ, DIXON RA. 1999. Accumulation of salicylic acid and PR-1 gene transcripts in relation to the systemic acquired resistance (SAR) response induced by Pseudomonas syringae pv. tomato in Arabidopsis. Physiological and Molecular Plant Pathology 55: 121-130.
","pubmedId":"","doi":"10.1006/pmpp.1999.0214"},{"reference":"Chen J, Clinton M, Qi G, Wang D, Liu F, Fu ZQ. 2020. Reprogramming and remodeling: transcriptional and epigenetic regulation of salicylic acid-mediated plant defense. Journal of Experimental Botany 71: 5256-5268.
","pubmedId":"","doi":"10.1093/jxb/eraa072"},{"reference":"Felix G, Duran JD, Volko S, Boller T. 1999. Plants have a sensitive perception system for the most conserved domain of bacterial flagellin. The Plant Journal 18: 265-276.
","pubmedId":"","doi":"10.1046/j.1365-313X.1999.00265.x"},{"reference":"He Y, Zhang T, Sun H, Zhan H, Zhao Y. 2020. A reporter for noninvasively monitoring gene expression and plant transformation. Horticulture Research 7: 10.1038/s41438-020-00390-1.
","pubmedId":"","doi":"10.1038/s41438-020-00390-1"},{"reference":"Marco F, Busó E, Carrasco P. 2014. Overexpression of SAMDC1 gene in Arabidopsis thaliana increases expression of defense-related genes as well as resistance to Pseudomonas syringae and Hyaloperonospora arabidopsidis. Frontiers in Plant Science 5: 10.3389/fpls.2014.00115.
","pubmedId":"","doi":"10.3389/fpls.2014.00115"},{"reference":"Pape S, Thurow C, Gatz C. 2010. The Arabidopsis PR-1 Promoter Contains Multiple Integration Sites for the Coactivator NPR1 and the Repressor SNI1. Plant Physiology 154: 1805-1818.
","pubmedId":"","doi":"10.1104/pp.110.165563"},{"reference":"Ward ER, Uknes SJ, Williams SC, Dincher SS, Wiederhold DL, Alexander DC, et al., Ryals. 1991. Coordinate Gene Activity in Response to Agents That Induce Systemic Acquired Resistance.. The Plant Cell : 1085-1094.
","pubmedId":"","doi":"10.1105/tpc.3.10.1085"}],"title":"A Non-Invasive Pathogen‑Responsive RUBY Reporter Enables Visible Monitoring of PR1 Activation
","reviews":[],"curatorReviews":[]},{"id":"4d7e4b87-1012-4695-8274-b55d5cd9a812","decision":"edit","abstract":"We report a non‑invasive, pathogen‑responsive reporter system in Arabidopsis thaliana generated by placing the PR1 promoter upstream of the betalain‑producing RUBY cassette. Two independent transgenic lines showed robust, dose‑dependent red pigmentation accumulation in response to flg22 (a flagellin-derived peptide) and salicylic acid (a defense-signaling molecule that induces PR1) in both seedling and adult tissues. This reporter provides a simple, low‑cost visual readout of defense activation without the need for destructive sampling or specialized instrumentation. Seeds have been deposited at ABRC, and the plasmid has been made available through Addgene.
","acknowledgements":"We appreciate the support provided by Maeriam Hajjaj and Hope Gruszewski (Virginia Polytechnic Institute and State University). We thank Dr. Yunde Zhao (University of California San Diego) for kindly providing the pHDE-RUBY vector.
","authors":[{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["writing_reviewEditing","conceptualization","investigation"],"email":"lolamcmullan@vt.edu","firstName":"Lola O.","lastName":"McMullan","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["conceptualization","formalAnalysis","investigation","writing_reviewEditing"],"email":"jstaylo8@ncsu.edu","firstName":"Joseph S. ","lastName":"Taylor","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["investigation","writing_reviewEditing"],"email":"rhanlon@vt.edu","firstName":"Regina","lastName":"Hanlon","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["investigation","writing_reviewEditing"],"email":"taldin@vt.edu","firstName":"Alex T.","lastName":"Harris","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["conceptualization","writing_reviewEditing"],"email":"jshuman@vt.edu","firstName":"Joel L.","lastName":"Shuman","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["conceptualization","fundingAcquisition","supervision","writing_reviewEditing"],"email":"dschmale@vt.edu","firstName":"David G.","lastName":"Schmale III","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["conceptualization","supervision","fundingAcquisition","writing_originalDraft"],"email":"bastiaan@vt.edu","firstName":"Bastiaan O. R. ","lastName":"Bargmann","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0000-0001-8406-5036"}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":null},"extendedData":[],"funding":"Research in the Bargmann lab is supported by U.S. National Science Foundation (United States) IOS 2348321, USDA National Institute of Food and Agriculture, HATCH project VA-160262, and Multistate S-009 project VA-136423. Research in the Schmale lab is supported by the Center for Emerging, Zoonotic, and Arthropod-borne Pathogens (CeZAP) at Virginia Tech. L.O.M. and J.S.T. were supported by the Virginia Tech George Washington Carver Program.
","image":{"url":"https://portal.micropublication.org/uploads/da874bb61acc909c970c50bad54a903a.jpg"},"imageCaption":"A. Schematic of the PR1::RUBY construct. A 1,334 bp fragment of the Arabidopsis PR1 promoter was cloned into the SpeI site of pHDE‑RUBY, placing the betalain biosynthetic cassette (CYP76AD1–2A–DODA–2A–glucosyltransferase) under pathogen‑responsive transcriptional control. B. One‑week‑old seedlings of two independent transgenic lines (1.6 and 2.4) grown in 24‑well plates (five seedlings per well) showed dose‑dependent betalain accumulation after 48 h treatment with flg22 (0–5 µM) or salicylic acid (SA) (0–100 µM). Asterisks indicate wells shown in close-up in C. C. Close-up images of the control, 5 µM flg22, and 100 µM SA treatment of line 2.4. D. Four‑week‑old soil‑grown plants (line 2.4) 48 h after treatment with 5 µL droplets of mock solution (0.05% Silwet), 1 µM flg22, or 50 µM SA to each leaf. These results are representative of multiple experiments.
","imageTitle":"Pathogen‑responsive PR1::RUBY reporter activation in Arabidopsis
","methods":"Construct assembly
A 1,334 bp fragment upstream of the Arabidopsis thaliana PR1 coding sequence was amplified using primers proPR1_SpeI_Fwd TGACTGACTAGTACGTAATAATATCCTATGGTGTC and proPR1_SpeI_Rev TGACTGACTAGTCATTTTTCTAAGTTGATAATGGTTATTG (based on (Pape et al., 2010)) and cloned into the SpeI site of pHDE‑RUBY (He et al., 2020), placing the RUBY betalain biosynthetic cassette under PR1 promoter control. The pHDE_PR1::RUBY vector is available through Addgene (https://www.addgene.org/255430/: Plasmid #255430).
Plant transformation and growth conditions
The construct was transformed into A. thaliana Col‑0 using Agrobacterium tumefaciens GV3101 via floral dip. T1 plants were selected, and two independent single‑locus lines (1.6 and 2.4) were advanced for characterization. Seeds for both lines are available through the ABRC stock center (https://abrc.osu.edu/; CS74214 - pHDE_PR1::RUBY 1.6 and CS74215 - pHDE_PR1::RUBY 2.4). Seedlings were grown in ½ MS medium (2.2 g/L Murashige and Skoog salts) supplemented with 1% (w/v) sucrose, incubated in a plant growth chamber (Percival, Perry, IA, USA) at 22 °C with an 18 h light/6 h dark regime at 75 µmol m−2 s−1 PAR. Soil-grown plants were incubated in a plant growth chamber (Conviron, Pembina, ND, USA) at 22 °C with an 18 h light/6 h dark regime at 150 µmol m−2 s−1 PAR.
Elicitation assays
Five seedlings were grown in each well of a 24‑well plate containing 500 µL liquid ½ MS + sucrose medium. After one week, medium in the wells was replaced with 500 µL liquid ½ MS + sucrose supplemented with flg22 (0, 0.008, 0.04, 0.2, 1, or 5 µM) or salicylic acid (0, 6.25, 12.5, 25, 50, or 100 µM). Plates were incubated for 48 h and imaged using a flatbed document scanner. Four‑week‑old soil‑grown plants were treated by applying 5 µL droplets of 0.05% (v/v) Silwet (mock), Silwet plus 1 µM flg22, or Silwet plus 50 µM SA to each leaf. Plants were imaged after 48 h using a digital camera.
","reagents":"","patternDescription":"Plant immune responses are highly dynamic, spatially heterogeneous, and often difficult to monitor without destructive sampling or specialized equipment. The Arabidopsis thaliana PATHOGENESIS‑RELATED 1 (PR1) promoter is one of the most widely used molecular markers of salicylic acid (SA)–dependent defense activation (Ward et al., 1991), yet most PR1 reporters rely on fluorescent or enzymatic outputs that require microscopy, substrate addition, and/or tissue disruption. To provide a simple, low‑cost, and non‑invasive alternative, we engineered a visible pathogen‑responsive reporter by placing a 1,334 bp PR1 promoter fragment upstream of the RUBY betalain biosynthetic cassette (He et al., 2020) (Figure 1A). RUBY produces red betalain pigments that accumulate without additional substrates and are easily detected by eye, making it an attractive reporter for rapid screening, phenotyping, and educational applications.
We cloned the PR1 promoter into pHDE‑RUBY, generating a PR1::RUBY construct that links immune activation to betalain production. Using Agrobacterium tumefaciens GV3101, we transformed Arabidopsis thaliana Col‑0 and selected two independent single‑locus lines (lines 1.6 and 2.4; single locus status was determined by examining the segregation ratio of hygromycin resistance in the T2 generation). Both lines exhibited robust and reproducible reporter activation in response to flg22 (a flagellin-derived peptide) and SA. In a 24‑well plate assay, one‑week‑old seedlings treated for 48 h with flg22 (0–5 µM) (Felix et al., 1999) and SA (0–100 µM) showed clear, dose‑dependent accumulation of red pigmentation, with no obvious signal in untreated controls (Figure 1B-C). Line 2.4 displayed slightly higher sensitivity, but both lines responded similarly across the full concentration range. SA elicited the strongest overall activation, consistent with its role as a central regulator of PR1 expression (Chen et al., 2020).
To test reporter performance in mature tissues, we applied 5 µL droplets of mock solution (0.05% Silwet only), 1 µM flg22, or 50 µM SA to individual leaves of four‑week‑old soil‑grown plants. After 48 h, flg22 and SA treatments induced visible betalain accumulation, whereas mock‑treated leaves remained green (Figure 1D). These results demonstrate that PR1::RUBY reliably reports immune activation in both seedlings and adult plants, and that betalain accumulation provides a clear, easily interpretable visual output.
This reporter system offers several advantages for the plant research community. First, it enables rapid, non‑destructive monitoring of defense activation without specialized imaging equipment. Second, it is suitable for high‑throughput screening in multi‑well formats. Third, it provides an intuitive visual readout that is accessible for research, teaching, and outreach. Future work will evaluate reporter activation during infection with well-characterized Arabidopsis pathogens, such as Pseudomonas syringae and Hyaloperonospora arabidopsidis (Cameron et al., 1999; Marco et al., 2014). Because the RUBY cassette functions across diverse plant species, the construct may also be adaptable beyond Arabidopsis. To our knowledge, this is the first report of PR1::RUBY reporter in use, although we did find mention of such a construct on an International Genetically Engineered Machine (iGEM) project website (https://2021.igem.org/Team:Duesseldorf/Proof_Of_Concept). Future studies incorporating quantitative image analysis or spectrophotometric assays of betalain accumulation will further enable rigorous characterization of reporter sensitivity, dose response, and reproducibility. We envisage its application as a sentinel phytosensor for the presence of plant pathogens. To facilitate broad use, the PR1::RUBY plasmid was deposited at Addgene, and the transgenic Arabidopsis lines were made available through the Arabidopsis Biological Resource Center (ABRC).
","references":[{"reference":"Cameron RK, Paiva NL, Lamb CJ, Dixon RA. 1999. Accumulation of salicylic acid and PR-1 gene transcripts in relation to the systemic acquired resistance (SAR) response induced by Pseudomonas syringae pv. tomato in Arabidopsis. Physiol and Mol Plant Pathol 55(2): 121-130.
","pubmedId":"","doi":"10.1006/pmpp.1999.0214"},{"reference":"Chen J, Clinton M, Qi G, Wang D, Liu F, Fu ZQ. 2020. Reprogramming and remodeling: transcriptional and epigenetic regulation of salicylic acid-mediated plant defense. J Exp Bot 71(17): 5256-5268.
","pubmedId":"32060527","doi":"10.1093/jxb/eraa072"},{"reference":"Felix G, Duran JD, Volko S, Boller T. 1999. Plants have a sensitive perception system for the most conserved domain of bacterial flagellin. Plant J 18(3): 265-76.
","pubmedId":"10377992","doi":"10.1046/j.1365-313X.1999.00265.x"},{"reference":"He Y, Zhang T, Sun H, Zhan H, Zhao Y. 2020. A reporter for noninvasively monitoring gene expression and plant transformation. Hortic Res 7(1): 152.
","pubmedId":"33024566","doi":"10.1038/s41438-020-00390-1"},{"reference":"Marco F, Busó E, Carrasco P. 2014. Overexpression of SAMDC1 gene in Arabidopsis thaliana increases expression of defense-related genes as well as resistance to Pseudomonas syringae and Hyaloperonospora arabidopsidis. Front Plant Sci 5: 115.
","pubmedId":"24734036","doi":"10.3389/fpls.2014.00115"},{"reference":"Pape S, Thurow C, Gatz C. 2010. The Arabidopsis PR-1 promoter contains multiple integration sites for the coactivator NPR1 and the repressor SNI1. Plant Physiol 154(4): 1805-18.
","pubmedId":"20935179","doi":"10.1104/pp.110.165563"},{"reference":"Ward ER, Uknes SJ, Williams SC, Dincher SS, Wiederhold DL, Alexander DC, et al., Ryals JA. 1991. Coordinate Gene Activity in Response to Agents That Induce Systemic Acquired Resistance. Plant Cell 3(10): 1085-1094.
","pubmedId":"12324583","doi":"10.1105/tpc.3.10.1085"}],"title":"A Non-Invasive Pathogen‑Responsive RUBY Reporter Enables Visible Monitoring of PR1 Activation
","reviews":[],"curatorReviews":[]},{"id":"52b8b459-e342-4ea6-841a-e45fa2f6ccbc","decision":"edit","abstract":"We report a non‑invasive, pathogen‑responsive reporter system in Arabidopsis thaliana generated by placing the PR1 (AT2G14610) promoter upstream of the betalain‑producing RUBY cassette. Two independent transgenic lines showed robust, dose‑dependent red pigmentation accumulation in response to flg22 (a flagellin-derived peptide) and salicylic acid (a defense-signaling molecule that induces PR1) in both seedling and adult tissues. This reporter provides a simple, low‑cost visual readout of defense activation without the need for destructive sampling or specialized instrumentation. Seeds have been deposited at ABRC, and the plasmid has been made available through Addgene.
","acknowledgements":"We appreciate the support provided by Maeriam Hajjaj and Hope Gruszewski (Virginia Polytechnic Institute and State University). We thank Dr. Yunde Zhao (University of California San Diego) for kindly providing the pHDE-RUBY vector.
","authors":[{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["writing_reviewEditing","conceptualization","investigation"],"email":"lolamcmullan@vt.edu","firstName":"Lola O.","lastName":"McMullan","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["conceptualization","formalAnalysis","investigation","writing_reviewEditing"],"email":"jstaylo8@ncsu.edu","firstName":"Joseph S. ","lastName":"Taylor","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["investigation","writing_reviewEditing"],"email":"rhanlon@vt.edu","firstName":"Regina","lastName":"Hanlon","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["investigation","writing_reviewEditing"],"email":"taldin@vt.edu","firstName":"Alex T.","lastName":"Harris","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["conceptualization","writing_reviewEditing"],"email":"jshuman@vt.edu","firstName":"Joel L.","lastName":"Shuman","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["conceptualization","fundingAcquisition","supervision","writing_reviewEditing"],"email":"dschmale@vt.edu","firstName":"David G.","lastName":"Schmale III","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["conceptualization","supervision","fundingAcquisition","writing_originalDraft"],"email":"bastiaan@vt.edu","firstName":"Bastiaan O. R. ","lastName":"Bargmann","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0000-0001-8406-5036"}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":null},"extendedData":[],"funding":"Research in the Bargmann lab is supported by U.S. National Science Foundation (United States) IOS 2348321, USDA National Institute of Food and Agriculture, HATCH project VA-160262, and Multistate S-009 project VA-136423. Research in the Schmale lab is supported by the Center for Emerging, Zoonotic, and Arthropod-borne Pathogens (CeZAP) at Virginia Tech. L.O.M. and J.S.T. were supported by the Virginia Tech George Washington Carver Program.
","image":{"url":"https://portal.micropublication.org/uploads/da874bb61acc909c970c50bad54a903a.jpg"},"imageCaption":"A. Schematic of the PR1::RUBY construct. A 1,334 bp fragment of the Arabidopsis PR1 promoter (AT2G14610) was cloned into the SpeI site of pHDE‑RUBY, placing the betalain biosynthetic cassette (CYP76AD1–2A–DODA–2A–glucosyltransferase) under pathogen‑responsive transcriptional control. B. One‑week‑old seedlings of two independent transgenic lines (1.6 and 2.4) grown in 24‑well plates (five seedlings per well) showed dose‑dependent betalain accumulation after 48 h treatment with flg22 (0–5 µM) or salicylic acid (SA) (0–100 µM). Asterisks indicate wells shown in close-up in C. C. Close-up images of the control, 5 µM flg22, and 100 µM SA treatment of line 2.4. D. Four‑week‑old soil‑grown plants (line 2.4) 48 h after treatment with 5 µL droplets of mock solution (0.05% Silwet), 1 µM flg22, or 50 µM SA to each leaf. These results are representative of multiple experiments.
","imageTitle":"Pathogen‑responsive PR1::RUBY reporter activation in Arabidopsis
","methods":"Construct assembly
A 1,334 bp fragment upstream of the Arabidopsis thaliana PR1 coding sequence was amplified using primers proPR1_SpeI_Fwd TGACTGACTAGTACGTAATAATATCCTATGGTGTC and proPR1_SpeI_Rev TGACTGACTAGTCATTTTTCTAAGTTGATAATGGTTATTG (based on (Pape et al., 2010)) and cloned into the SpeI site of pHDE‑RUBY (He et al., 2020), placing the RUBY betalain biosynthetic cassette under PR1 promoter control. The pHDE_PR1::RUBY vector is available through Addgene (https://www.addgene.org/255430/: Plasmid #255430).
Plant transformation and growth conditions
The construct was transformed into A. thaliana Col‑0 using Agrobacterium tumefaciens GV3101 via floral dip. T1 plants were selected, and two independent single‑locus lines (1.6 and 2.4) were advanced for characterization. Seeds for both lines are available through the ABRC stock center (https://abrc.osu.edu/; CS74214 - pHDE_PR1::RUBY 1.6 and CS74215 - pHDE_PR1::RUBY 2.4). Seedlings were grown in ½ MS medium (2.2 g/L Murashige and Skoog salts) supplemented with 1% (w/v) sucrose, incubated in a plant growth chamber (Percival, Perry, IA, USA) at 22 °C with an 18 h light/6 h dark regime at 75 µmol m−2 s−1 PAR. Soil-grown plants were incubated in a plant growth chamber (Conviron, Pembina, ND, USA) at 22 °C with an 18 h light/6 h dark regime at 150 µmol m−2 s−1 PAR.
Elicitation assays
Five seedlings were grown in each well of a 24‑well plate containing 500 µL liquid ½ MS + sucrose medium. After one week, medium in the wells was replaced with 500 µL liquid ½ MS + sucrose supplemented with flg22 (0, 0.008, 0.04, 0.2, 1, or 5 µM) or salicylic acid (0, 6.25, 12.5, 25, 50, or 100 µM). Plates were incubated for 48 h and imaged using a flatbed document scanner. Four‑week‑old soil‑grown plants were treated by applying 5 µL droplets of 0.05% (v/v) Silwet (mock), Silwet plus 1 µM flg22, or Silwet plus 50 µM SA to each leaf. Plants were imaged after 48 h using a digital camera.
","reagents":"","patternDescription":"Plant immune responses are highly dynamic, spatially heterogeneous, and often difficult to monitor without destructive sampling or specialized equipment. The Arabidopsis thaliana PATHOGENESIS‑RELATED 1 (PR1) promoter is one of the most widely used molecular markers of salicylic acid (SA)–dependent defense activation (Ward et al., 1991), yet most PR1 reporters rely on fluorescent or enzymatic outputs that require microscopy, substrate addition, and/or tissue disruption. To provide a simple, low‑cost, and non‑invasive alternative, we engineered a visible pathogen‑responsive reporter by placing a 1,334 bp PR1 promoter fragment upstream of the RUBY betalain biosynthetic cassette (He et al., 2020) (Figure 1A). RUBY produces red betalain pigments that accumulate without additional substrates and are easily detected by eye, making it an attractive reporter for rapid screening, phenotyping, and educational applications.
We cloned the PR1 promoter into pHDE‑RUBY, generating a PR1::RUBY construct that links immune activation to betalain production. Using Agrobacterium tumefaciens GV3101, we transformed Arabidopsis thaliana Col‑0 and selected two independent single‑locus lines (lines 1.6 and 2.4; single locus status was determined by examining the segregation ratio of hygromycin resistance in the T2 generation). Both lines exhibited robust and reproducible reporter activation in response to flg22 (a flagellin-derived peptide) and SA. In a 24‑well plate assay, one‑week‑old seedlings treated for 48 h with flg22 (0–5 µM) (Felix et al., 1999) and SA (0–100 µM) showed clear, dose‑dependent accumulation of red pigmentation, with no obvious signal in untreated controls (Figure 1B-C). Line 2.4 displayed slightly higher sensitivity, but both lines responded similarly across the full concentration range. SA elicited the strongest overall activation, consistent with its role as a central regulator of PR1 expression (Chen et al., 2020).
To test reporter performance in mature tissues, we applied 5 µL droplets of mock solution (0.05% Silwet only), 1 µM flg22, or 50 µM SA to individual leaves of four‑week‑old soil‑grown plants. After 48 h, flg22 and SA treatments induced visible betalain accumulation, whereas mock‑treated leaves remained green (Figure 1D). These results demonstrate that PR1::RUBY reliably reports immune activation in both seedlings and adult plants, and that betalain accumulation provides a clear, easily interpretable visual output.
This reporter system offers several advantages for the plant research community. First, it enables rapid, non‑destructive monitoring of defense activation without specialized imaging equipment. Second, it is suitable for high‑throughput screening in multi‑well formats. Third, it provides an intuitive visual readout that is accessible for research, teaching, and outreach. Future work will evaluate reporter activation during infection with well-characterized Arabidopsis pathogens, such as Pseudomonas syringae and Hyaloperonospora arabidopsidis (Cameron et al., 1999; Marco et al., 2014). Because the RUBY cassette functions across diverse plant species, the construct may also be adaptable beyond Arabidopsis. To our knowledge, this is the first report of PR1::RUBY reporter in use, although we did find mention of such a construct on an International Genetically Engineered Machine (iGEM) project website (https://2021.igem.org/Team:Duesseldorf/Proof_Of_Concept). Future studies incorporating quantitative image analysis or spectrophotometric assays of betalain accumulation will further enable rigorous characterization of reporter sensitivity, dose response, and reproducibility. We envisage its application as a sentinel phytosensor for the presence of plant pathogens. To facilitate broad use, the PR1::RUBY plasmid was deposited at Addgene, and the transgenic Arabidopsis lines were made available through the Arabidopsis Biological Resource Center (ABRC).
","references":[{"reference":"Cameron RK, Paiva NL, Lamb CJ, Dixon RA. 1999. Accumulation of salicylic acid and PR-1 gene transcripts in relation to the systemic acquired resistance (SAR) response induced by Pseudomonas syringae pv. tomato in Arabidopsis. Physiol and Mol Plant Pathol 55(2): 121-130.
","pubmedId":"","doi":"10.1006/pmpp.1999.0214"},{"reference":"Chen J, Clinton M, Qi G, Wang D, Liu F, Fu ZQ. 2020. Reprogramming and remodeling: transcriptional and epigenetic regulation of salicylic acid-mediated plant defense. J Exp Bot 71(17): 5256-5268.
","pubmedId":"32060527","doi":"10.1093/jxb/eraa072"},{"reference":"Felix G, Duran JD, Volko S, Boller T. 1999. Plants have a sensitive perception system for the most conserved domain of bacterial flagellin. Plant J 18(3): 265-76.
","pubmedId":"10377992","doi":"10.1046/j.1365-313X.1999.00265.x"},{"reference":"He Y, Zhang T, Sun H, Zhan H, Zhao Y. 2020. A reporter for noninvasively monitoring gene expression and plant transformation. Hortic Res 7(1): 152.
","pubmedId":"33024566","doi":"10.1038/s41438-020-00390-1"},{"reference":"Marco F, Busó E, Carrasco P. 2014. Overexpression of SAMDC1 gene in Arabidopsis thaliana increases expression of defense-related genes as well as resistance to Pseudomonas syringae and Hyaloperonospora arabidopsidis. Front Plant Sci 5: 115.
","pubmedId":"24734036","doi":"10.3389/fpls.2014.00115"},{"reference":"Pape S, Thurow C, Gatz C. 2010. The Arabidopsis PR-1 promoter contains multiple integration sites for the coactivator NPR1 and the repressor SNI1. Plant Physiol 154(4): 1805-18.
","pubmedId":"20935179","doi":"10.1104/pp.110.165563"},{"reference":"Ward ER, Uknes SJ, Williams SC, Dincher SS, Wiederhold DL, Alexander DC, et al., Ryals JA. 1991. Coordinate Gene Activity in Response to Agents That Induce Systemic Acquired Resistance. Plant Cell 3(10): 1085-1094.
","pubmedId":"12324583","doi":"10.1105/tpc.3.10.1085"}],"title":"A Non-Invasive Pathogen‑Responsive RUBY Reporter Enables Visible Monitoring of PR1 Activation
","reviews":[],"curatorReviews":[]},{"id":"96289696-87d6-4e48-8135-7554b6fd77b5","decision":"publish","abstract":"We report a non‑invasive, pathogen‑responsive reporter system in Arabidopsis thaliana generated by placing the PR1 (AT2G14610) promoter upstream of the betalain‑producing RUBY cassette. Two independent transgenic lines showed robust, dose‑dependent red pigmentation accumulation in response to flg22 (a flagellin-derived peptide) and salicylic acid (a defense-signaling molecule that induces PR1) in both seedling and adult tissues. This reporter provides a simple, low‑cost visual readout of defense activation without the need for destructive sampling or specialized instrumentation. Seeds have been deposited at ABRC, and the plasmid has been made available through Addgene.
","acknowledgements":"We appreciate the support provided by Maeriam Hajjaj and Hope Gruszewski (Virginia Polytechnic Institute and State University). We thank Dr. Yunde Zhao (University of California San Diego) for kindly providing the pHDE-RUBY vector.
","authors":[{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["writing_reviewEditing","conceptualization","investigation"],"email":"lolamcmullan@vt.edu","firstName":"Lola O.","lastName":"McMullan","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["conceptualization","formalAnalysis","investigation","writing_reviewEditing"],"email":"jstaylo8@ncsu.edu","firstName":"Joseph S. ","lastName":"Taylor","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["investigation","writing_reviewEditing"],"email":"rhanlon@vt.edu","firstName":"Regina","lastName":"Hanlon","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["investigation","writing_reviewEditing"],"email":"taldin@vt.edu","firstName":"Alex T.","lastName":"Harris","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["conceptualization","writing_reviewEditing"],"email":"jshuman@vt.edu","firstName":"Joel L.","lastName":"Shuman","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["conceptualization","fundingAcquisition","supervision","writing_reviewEditing"],"email":"dschmale@vt.edu","firstName":"David G.","lastName":"Schmale III","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Virginia Polytechnic Institute and State University, Blacksburg, VA, US"],"departments":["School of Plant and Environmental Sciences"],"credit":["conceptualization","supervision","fundingAcquisition","writing_originalDraft"],"email":"bastiaan@vt.edu","firstName":"Bastiaan O. R. ","lastName":"Bargmann","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0000-0001-8406-5036"}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":null},"extendedData":[],"funding":"Research in the Bargmann lab is supported by U.S. National Science Foundation (United States) IOS 2348321, USDA National Institute of Food and Agriculture, HATCH project VA-160262, and Multistate S-009 project VA-136423. Research in the Schmale lab is supported by the Center for Emerging, Zoonotic, and Arthropod-borne Pathogens (CeZAP) at Virginia Tech. L.O.M. and J.S.T. were supported by the Virginia Tech George Washington Carver Program.
","image":{"url":"https://portal.micropublication.org/uploads/da874bb61acc909c970c50bad54a903a.jpg"},"imageCaption":"A. Schematic of the PR1::RUBY construct. A 1,334 bp fragment of the Arabidopsis PR1 promoter (AT2G14610) was cloned into the SpeI site of pHDE‑RUBY, placing the betalain biosynthetic cassette (CYP76AD1–2A–DODA–2A–glucosyltransferase) under pathogen‑responsive transcriptional control. B. One‑week‑old seedlings of two independent transgenic lines (1.6 and 2.4) grown in 24‑well plates (five seedlings per well) showed dose‑dependent betalain accumulation after 48 h treatment with flg22 (0–5 µM) or salicylic acid (SA) (0–100 µM). Asterisks indicate wells shown in close-up in C. C. Close-up images of the control, 5 µM flg22, and 100 µM SA treatment of line 2.4. D. Four‑week‑old soil‑grown plants (line 2.4) 48 h after treatment with 5 µL droplets of mock solution (0.05% Silwet), 1 µM flg22, or 50 µM SA to each leaf. These results are representative of multiple experiments.
","imageTitle":"Pathogen‑responsive PR1::RUBY reporter activation in Arabidopsis
","methods":"Construct assembly
A 1,334 bp fragment upstream of the Arabidopsis thaliana PR1 coding sequence was amplified using primers proPR1_SpeI_Fwd TGACTGACTAGTACGTAATAATATCCTATGGTGTC and proPR1_SpeI_Rev TGACTGACTAGTCATTTTTCTAAGTTGATAATGGTTATTG (based on (Pape et al., 2010)) and cloned into the SpeI site of pHDE‑RUBY (He et al., 2020), placing the RUBY betalain biosynthetic cassette under PR1 promoter control. The pHDE_PR1::RUBY vector is available through Addgene (https://www.addgene.org/255430/: Plasmid #255430).
Plant transformation and growth conditions
The construct was transformed into A. thaliana Col‑0 using Agrobacterium tumefaciens GV3101 via floral dip. T1 plants were selected, and two independent single‑locus lines (1.6 and 2.4) were advanced for characterization. Seeds for both lines are available through the ABRC stock center (https://abrc.osu.edu/; CS74214 - pHDE_PR1::RUBY 1.6 and CS74215 - pHDE_PR1::RUBY 2.4). Seedlings were grown in ½ MS medium (2.2 g/L Murashige and Skoog salts) supplemented with 1% (w/v) sucrose, incubated in a plant growth chamber (Percival, Perry, IA, USA) at 22 °C with an 18 h light/6 h dark regime at 75 µmol m−2 s−1 PAR. Soil-grown plants were incubated in a plant growth chamber (Conviron, Pembina, ND, USA) at 22 °C with an 18 h light/6 h dark regime at 150 µmol m−2 s−1 PAR.
Elicitation assays
Five seedlings were grown in each well of a 24‑well plate containing 500 µL liquid ½ MS + sucrose medium. After one week, medium in the wells was replaced with 500 µL liquid ½ MS + sucrose supplemented with flg22 (0, 0.008, 0.04, 0.2, 1, or 5 µM) or salicylic acid (0, 6.25, 12.5, 25, 50, or 100 µM). Plates were incubated for 48 h and imaged using a flatbed document scanner. Four‑week‑old soil‑grown plants were treated by applying 5 µL droplets of 0.05% (v/v) Silwet (mock), Silwet plus 1 µM flg22, or Silwet plus 50 µM SA to each leaf. Plants were imaged after 48 h using a digital camera.
","reagents":"","patternDescription":"Plant immune responses are highly dynamic, spatially heterogeneous, and often difficult to monitor without destructive sampling or specialized equipment. The Arabidopsis thaliana PATHOGENESIS‑RELATED 1 (PR1, AT2G14610) promoter is one of the most widely used molecular markers of salicylic acid (SA)–dependent defense activation (Ward et al., 1991), yet most PR1 reporters rely on fluorescent or enzymatic outputs that require microscopy, substrate addition, and/or tissue disruption. To provide a simple, low‑cost, and non‑invasive alternative, we engineered a visible pathogen‑responsive reporter by placing a 1,334 bp PR1 promoter fragment upstream of the RUBY betalain biosynthetic cassette (He et al., 2020) (Figure 1A). RUBY produces red betalain pigments that accumulate without additional substrates and are easily detected by eye, making it an attractive reporter for rapid screening, phenotyping, and educational applications.
We cloned the PR1 promoter into pHDE‑RUBY, generating a PR1::RUBY construct that links immune activation to betalain production. Using Agrobacterium tumefaciens GV3101, we transformed Arabidopsis thaliana Col‑0 and selected two independent single‑locus lines (lines 1.6 and 2.4; single locus status was determined by examining the segregation ratio of hygromycin resistance in the T2 generation). Both lines exhibited robust and reproducible reporter activation in response to flg22 (a flagellin-derived peptide) and SA. In a 24‑well plate assay, one‑week‑old seedlings treated for 48 h with flg22 (0–5 µM) (Felix et al., 1999) and SA (0–100 µM) showed clear, dose‑dependent accumulation of red pigmentation, with no obvious signal in untreated controls (Figure 1B-C). Line 2.4 displayed slightly higher sensitivity, but both lines responded similarly across the full concentration range. SA elicited the strongest overall activation, consistent with its role as a central regulator of PR1 expression (Chen et al., 2020).
To test reporter performance in mature tissues, we applied 5 µL droplets of mock solution (0.05% Silwet only), 1 µM flg22, or 50 µM SA to individual leaves of four‑week‑old soil‑grown plants. After 48 h, flg22 and SA treatments induced visible betalain accumulation, whereas mock‑treated leaves remained green (Figure 1D). These results demonstrate that PR1::RUBY reliably reports immune activation in both seedlings and adult plants, and that betalain accumulation provides a clear, easily interpretable visual output.
This reporter system offers several advantages for the plant research community. First, it enables rapid, non‑destructive monitoring of defense activation without specialized imaging equipment. Second, it is suitable for high‑throughput screening in multi‑well formats. Third, it provides an intuitive visual readout that is accessible for research, teaching, and outreach. Future work will evaluate reporter activation during infection with well-characterized Arabidopsis pathogens, such as Pseudomonas syringae and Hyaloperonospora arabidopsidis (Cameron et al., 1999; Marco et al., 2014). Because the RUBY cassette functions across diverse plant species, the construct may also be adaptable beyond Arabidopsis. To our knowledge, this is the first report of PR1::RUBY reporter in use, although we did find mention of such a construct on an International Genetically Engineered Machine (iGEM) project website (https://2021.igem.org/Team:Duesseldorf/Proof_Of_Concept). Future studies incorporating quantitative image analysis or spectrophotometric assays of betalain accumulation will further enable rigorous characterization of reporter sensitivity, dose response, and reproducibility. We envisage its application as a sentinel phytosensor for the presence of plant pathogens. To facilitate broad use, the PR1::RUBY plasmid was deposited at Addgene, and the transgenic Arabidopsis lines were made available through the Arabidopsis Biological Resource Center (ABRC).
","references":[{"reference":"Cameron RK, Paiva NL, Lamb CJ, Dixon RA. 1999. Accumulation of salicylic acid and PR-1 gene transcripts in relation to the systemic acquired resistance (SAR) response induced by Pseudomonas syringae pv. tomato in Arabidopsis. Physiol and Mol Plant Pathol 55(2): 121-130.
","pubmedId":"","doi":"10.1006/pmpp.1999.0214"},{"reference":"Chen J, Clinton M, Qi G, Wang D, Liu F, Fu ZQ. 2020. Reprogramming and remodeling: transcriptional and epigenetic regulation of salicylic acid-mediated plant defense. J Exp Bot 71(17): 5256-5268.
","pubmedId":"32060527","doi":"10.1093/jxb/eraa072"},{"reference":"Felix G, Duran JD, Volko S, Boller T. 1999. Plants have a sensitive perception system for the most conserved domain of bacterial flagellin. Plant J 18(3): 265-76.
","pubmedId":"10377992","doi":"10.1046/j.1365-313X.1999.00265.x"},{"reference":"He Y, Zhang T, Sun H, Zhan H, Zhao Y. 2020. A reporter for noninvasively monitoring gene expression and plant transformation. Hortic Res 7(1): 152.
","pubmedId":"33024566","doi":"10.1038/s41438-020-00390-1"},{"reference":"Marco F, Busó E, Carrasco P. 2014. Overexpression of SAMDC1 gene in Arabidopsis thaliana increases expression of defense-related genes as well as resistance to Pseudomonas syringae and Hyaloperonospora arabidopsidis. Front Plant Sci 5: 115.
","pubmedId":"24734036","doi":"10.3389/fpls.2014.00115"},{"reference":"Pape S, Thurow C, Gatz C. 2010. The Arabidopsis PR-1 promoter contains multiple integration sites for the coactivator NPR1 and the repressor SNI1. Plant Physiol 154(4): 1805-18.
","pubmedId":"20935179","doi":"10.1104/pp.110.165563"},{"reference":"Ward ER, Uknes SJ, Williams SC, Dincher SS, Wiederhold DL, Alexander DC, et al., Ryals JA. 1991. Coordinate Gene Activity in Response to Agents That Induce Systemic Acquired Resistance. Plant Cell 3(10): 1085-1094.
","pubmedId":"12324583","doi":"10.1105/tpc.3.10.1085"}],"title":"A Non-Invasive Pathogen‑Responsive RUBY Reporter Enables Visible Monitoring of PR1 Activation
","reviews":[],"curatorReviews":[]}]}},"species":{"species":[{"value":"acer saccharum","label":"Acer saccharum","imageSrc":"","imageAlt":"","mod":"TreeGenes","modLink":"https://treegenesdb.org","linkVariable":""},{"value":"achillea millefolium","label":"Achillea millefolium","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"acinetobacter baylyi","label":"Acinetobacter baylyi","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"actinobacteria bacterium","label":"Actinobacteria bacterium","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"adelges tsugae","label":"Adelges tsugae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"adenocaulon chilense","label":"Adenocaulon chilense","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"aedes japonicus","label":"Aedes japonicus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"aegorhinus vitulus","label":"Aegorhinus vitulus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"alaimidae","label":"Alaimidae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"allobates femoralis","label":"Allobates femoralis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"alnus glutinosa","label":"Alnus glutinosa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"alosa aestivalis","label":"Alosa aestivalis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"alosa pseudoharengus","label":"Alosa pseudoharengus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"alternaria alternata","label":"Alternaria alternata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"amynthas agrestis","label":"Amynthas Agrestis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ancylostoma caninum","label":"Ancylostoma caninum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ancylostoma ceylanicum","label":"Ancylostoma ceylanicum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"anemone multifida","label":"Anemone multifida","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"anguilla rostrata","label":"Anguilla rostrata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"anisakis simplex","label":"Anisakis simplex","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"anomala albopilosa","label":"Anomala albopilosa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"anthomyiidae sp","label":"Anthomyiidae sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"anthomyiidae sp","label":"Anthomyiidae sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"arabidopsis","label":"Arabidopsis","imageSrc":"arabidopsis.png","imageAlt":"Arabidopsis graphic by Zoe Zorn CC BY 4.0","mod":"TAIR","modLink":"https://arabidopsis.org","linkVariable":""},{"value":"architeuthis dux","label":"Architeuthis dux","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"arion vulgaris","label":"Arion vulgaris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"armeria","label":"Armeria","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"artemia","label":"Artemia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"arthrobacter sp.","label":"Arthrobacter sp.","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ascaridia","label":"Ascaridia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ascaridia galli","label":"Ascaridia galli","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"asparagopsis taxiformis","label":"Asparagopsis taxiformis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"astatotilapia burtoni","label":"Astatotilapia burtoni","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"avena sativa","label":"Avena sativa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"aves","label":"Aves","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacillus","label":"Bacillus (firmicutes)","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacillus cereus","label":"Bacillus cereus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacillus mycoides","label":"Bacillus mycoides","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacillus subtilis","label":"Bacillus subtilis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacillus thuringiensis","label":"Bacillus thuringiensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacillus toyonensis","label":"Bacillus toyonensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacillus wiedmannii","label":"Bacillus wiedmannii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacteria","label":"Bacteria","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacteriophage","label":"Bacteriophage","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bactrocera","label":"Bactrocera sp.","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"batrachospermum gelatinosum","label":"Batrachospermum gelatinosum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"betula lenta","label":"Betula lenta","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"betula nigra","label":"Betula nigra","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bombus dahlbohmii","label":"Bombus dahlbohmii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bombus terrestris","label":"Bombus terrestris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bombyx mori","label":"Bombyx mori","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bos taurus","label":"Bos Taurus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"brachygobius doriae","label":"Brachygobius doriae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"brassica oleracea","label":"Brassica oleracea","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"brassica rapa","label":"Brassica rapa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"brugia malayi","label":"Brugia malayi","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"burkholderia thailandensis","label":"Burkholderia thailandensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"buttiauxella","label":"Buttiauxella","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"caenorhabditis brenneri","label":"Caenorhabditis brenneri","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"caenorhabditis briggsae","label":"Caenorhabditis briggsae","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"c. elegans","label":"Caenorhabditis elegans","imageSrc":"c-elegans.jpg","imageAlt":"C. elegans graphic by Zoe Zorn CC BY 4.0","mod":"WormBase","modLink":"https://wormbase.org","linkVariable":""},{"value":"caenorhabditis inopinata","label":"Caenorhabditis inopinata","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"caenorhabditis japonica","label":"Caenorhabditis japonica","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"caenorhabditis nigoni","label":"Caenorhabditis nigoni","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"caenorhabditis remanei","label":"Caenorhabditis remanei","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"caenorhabditis tropicalis","label":"Caenorhabditis tropicalis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"calidifontibacillus","label":"Calidifontibacillus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"calidifontibacillus erzuremensis","label":"Calidifontibacillus erzuremensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"calliphora sp","label":"Calliphora sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"caltha sagittata","label":"Caltha sagittata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"cambarus latimanus","label":"Cambarus latimanus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"candida albicans","label":"Candida albicans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"canis familiaris","label":"Canis familiaris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"cannabis sativa","label":"Cannabis sativa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"caretta caretta","label":"Caretta caretta","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"cassiopea xamachana","label":"Cassiopea xamachana","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"caulobacter vibrioides","label":"Caulobacter vibrioides","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"cephalopods","label":"Cephalopoda","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"cerastium arvense","label":"Cerastium arvense","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ceriodaphnia","label":"Ceriodaphnia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ceroglossus suturalis","label":"Ceroglossus suturalis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chaetoceros","label":"Chaetoceros","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chamaecrista fasciculata","label":"Chamaecrista fasciculata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chilicola chalcidiformis","label":"Chilicola chalcidiformis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chitinimonas","label":"Chitinimonas","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chlamydomonas reinhardtii","label":"Chlamydomonas reinhardtii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chromobacterium","label":"Chromobacterium","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chrysemys picta","label":"Chrysemys picta","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chrysoperla rufilabris","label":"Chrysoperla rufilabris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"citrus","label":"Citrus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"clavibacter sp.","label":"Clavibacter sp.","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"colinus virginianus","label":"Colinus virginianus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"crassostrea virginica","label":"Crassostrea virginica","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"crithidia fasciculata","label":"Crithidia fasciculata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"cutibacterium acnes","label":"Cutibacterium acnes","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"cyanobacteria","label":"Cyanobacteria","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"daphnia","label":"Daphnia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"daphnia pulex","label":"Daphnia pulex","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"dermacoccus nishinomiyaensis","label":"Dermacoccus nishinomiyaensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"diabrotica virgifera","label":"Diabrotica virgifera","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"diabrotica virgifera virgifera virus 1","label":"Diabrotica virgifera virgifera virus 1","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"d. discoideum","label":"Dictyostelium discoideum","imageSrc":"dicty.png","imageAlt":"D. discoideum","mod":"dictyBase","modLink":"http://dictybase.org","linkVariable":""},{"value":"diptera","label":"Diptera","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"dotocryptus bellicosus","label":"Dotocryptus bellicosus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"drechmeria coniospora","label":"Drechmeria coniospora","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"drosophila","label":"Drosophila","imageSrc":"drosophila.png","imageAlt":"Drosophila graphic by Zoe Zorn CC BY 4.0","mod":"FlyBase","modLink":"https://flybase.org/doi/","linkVariable":"doi"},{"value":"dryopteris campyloptera","label":"Dryopteris campyloptera","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"dryopteris expansa","label":"Dryopteris expansa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"dryopteris intermedia","label":"Dryopteris intermedia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"dugesia dorotocephala","label":"Dugesia dorotocephala","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"elasmobranchii","label":"Elasmobranchii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"embryophyta","label":"Embryophyta","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"enoploteuthis chunii","label":"Enoploteuthis chunii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"enterobacter aerogenes","label":"Enterobacter aerogenes","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"enterococcus raffinosus","label":"Enterococcus raffinosus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"epichloë coenophiala","label":"Epichloë coenophiala","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"equus caballus","label":"Equus caballus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"erigeron sp","label":"Erigeron sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"eristalis","label":"Eristalis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"eruca vesicaria","label":"Eruca vesicaria","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"erwinia carotovora","label":"Erwinia carotovora","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"erythronium americanum","label":"Erythronium americanum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"escherichia coli","label":"Escherichia coli","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"eukaryota","label":"Eukaryotes","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"felis catus","label":"Felis catus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"francisella novicida","label":"Francisella novicida","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"francisella tularensis","label":"Francisella tularensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"fraxinus americana","label":"Fraxinus americana","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"fucus distichus","label":"Fucus distichus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"fungi","label":"Fungi","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"gasteropelecus sp.","label":"Gasteropelecus sp.","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"geranium sp","label":"Geranium sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"girardia","label":"Girardia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"glaucomys volans","label":"Glaucomys volans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"glycine max","label":"Glycine max","imageSrc":"","imageAlt":"","mod":"Soybase","modLink":"https://soybase.org","linkVariable":""},{"value":"glyptemys insculpta","label":"Glyptemys insculpta","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"gossypium hirsutum","label":"Gossypium hirsutum","imageSrc":"","imageAlt":"","mod":"CottonGen","modLink":"https://www.cottongen.org/","linkVariable":""},{"value":"gromphadorhina portentosa","label":"Gromphadorhina portentosa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"gryllodes sigillatus","label":"Gryllodes sigillatus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"haliotis rufescens","label":"Haliotis rufescens","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"hepacivirus hominis","label":"Hepatitis C Virus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"herpes simplex virus type 1","label":"Herpes simplex virus type 1","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"human","label":"Human","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"human coronavirus oc43","label":"Human coronavirus OC43","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"hydra vulgaris","label":"Hydra vulgaris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"hydropsyche sp","label":"Hydropsyche sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"hymenoptera","label":"Hymenoptera","imageSrc":"","imageAlt":"","mod":"Hymenoptera Genome Database","modLink":"https://hymenoptera.elsiklab.missouri.edu/","linkVariable":""},{"value":"hypochaeris radicata","label":"Hypochaeris radicata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"hypodynerus vespiformis","label":"Hypodynerus vespiformis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"iflaviridae","label":"Iflaviridae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"iflavuris","label":"Iflavirus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ipomoea hederacea","label":"Ipomoea hederacea","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ischnomera","label":"Ischnomera","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ischnomera ruficollis","label":"Ischnomera ruficollis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"julidochromis marlieri","label":"Julidochromis marlieri","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"juniperus virginiana","label":"Juniperus virginiana","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"kluyveromyces marxianus","label":"Kluyveromyces marxianus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"l. casei","label":"L. casei","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lacticaseibacillus casei","label":"Lacticaseibacillus casei","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"larentiinae sp","label":"Larentiinae sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"laurus nobilis","label":"Laurus nobilis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lepidoptera","label":"Lepidoptera","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"leucanthemum vulgare","label":"Leucanthemum vulgare","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"linepithema humile","label":"Linepithema humile","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"liometopum occidentale","label":"Liometopum occidentale","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lolium arundinaceum","label":"Lolium arundinaceum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lontra longicaudis","label":"Lontra longicaudis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lumbriculus variegatus","label":"Lumbriculus variegatus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lumbricus terrestris","label":"Lumbricus terrestris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lupinus polyphyllus","label":"Lupinus polyphyllus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lycorma delicatula","label":"Lycorma delicatula","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lynx rufus","label":"Lynx rufus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"magnaporthe oryzae","label":"Magnaporthe oryzae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"mammalia","label":"Mammalia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"manihot esculenta","label":"Manihot esculenta","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"medicago lupulina","label":"Medicago lupulina","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"meloidogyne","label":"Meloidogyne","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"mimus polyglottos","label":"Mimus polyglottos","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bryophyta","label":"Mosses","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"mouse","label":"Mouse","imageSrc":"","imageAlt":"","mod":"MGI","modLink":"https://informatics.jax.org","linkVariable":""},{"value":"m. minutoides","label":"Mus minutoides","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"mycobacterium smegmatis","label":"Mycobacterium smegmatis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"nakaseomyces glabratus","label":"Nakaseomyces glabratus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"nauphoeta cinerea","label":"Nauphoeta cinerea","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"neurospora","label":"Neurospora","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"n. benthamiana","label":"Nicotiana benthamiana","imageSrc":"","imageAlt":"","mod":"Solgenomics Network","modLink":"https://solgenomics.net/organism/Nicotiana_benthamiana/genome","linkVariable":""},{"value":"nicotiana tabacum","label":"Nicotiana tabacum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"noctuidae","label":"Noctuidae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"noctuidae sp","label":"Noctuidae sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"nothobranchius furzeri","label":"Nothobranchius furzeri","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"onchocerca volvulus","label":"Onchocerca volvulus","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"orconectes virilis","label":"Orconectes virilis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ormia ochracea","label":"Ormia ochracea","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"o. sativa","label":"Oryza sativa","imageSrc":"","imageAlt":"","mod":"Gramene","modLink":"https://www.gramene.org/","linkVariable":""},{"value":"other","label":"Other","imageSrc":"","imageAlt":"","mod":null,"modLink":null,"linkVariable":null},{"value":"oxalis enneaphylla","label":"Oxalis enneaphylla","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"paenarthrobacter nicotinovorans","label":"Paenarthrobacter nicotinovorans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"paenarthrobacter nicotinovorans","label":"Paenarthrobacter nicotinovorans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pantoea","label":"Pantoea","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pantoea agglomerans","label":"Pantoea agglomerans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"papaver sp","label":"Papaver sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"paramecium bursaria","label":"Paramecium bursaria","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"partitiviridae","label":"Partitiviridae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pelodiscus sinensis","label":"Pelodiscus sinensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"perezia recurvata","label":"Perezia recurvata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"petromyzon marinus","label":"Petromyzon marinus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"photinus pyralis","label":"Photinus pyralis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"photinus pyralis associated partiti-like virus","label":"Photinus pyralis associated partiti-like virus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"photinus pyralis iflavirus 1","label":"Photinus pyralis iflavirus 1","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"physcomitrium patens","label":"Physcomitrium patens","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pinus strobus","label":"Pinus strobus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pinus taeda","label":"Pinus taeda","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"platycheirus","label":"Platycheirus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"plectus sambesii","label":"Plectus sambesii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pogonomyrmex occidentalis","label":"Pogonomyrmex occidentalis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"poncirus trifoliata","label":"Poncirus trifoliata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"populus deltoides","label":"Populus deltoides","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"potato virus y","label":"Potato virus Y","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"primula magellanica","label":"Primula magellanica","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pristionchus pacificus","label":"Pristionchus pacificus","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"prunus persica","label":"Prunus persica","imageSrc":"","imageAlt":"","mod":"Genome Database for Rosaceae","modLink":"https://www.rosaceae.org/","linkVariable":""},{"value":"psalmopoeus iriminia","label":"Psalmopoeus iriminia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pseudanabaena sp.","label":"Pseudanabaena sp.","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pseudomonas","label":"Pseudomonas","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pseudomonas aeruginosa","label":"Pseudomonas aeruginosa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pseudomonas glycinae","label":"Pseudomonas glycinae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pseudomonas putida","label":"Pseudomonas putida","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pseudomonas syringae","label":"Pseudomonas syringae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pterophyllum scalare","label":"Pterophyllum scalare","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"python regius","label":"Python regius","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"quercus macrocarpa","label":"Quercus macrocarpa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ralstonia solanacearum","label":"Ralstonia solanacearum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ranitomeya imitator","label":"Ranitomeya imitator","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ranunculus peduncularis","label":"Ranunculus peduncularis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"rat","label":"Rat","imageSrc":"","imageAlt":"","mod":"RGD","modLink":"https://rgd.mcw.edu","linkVariable":""},{"value":"rheinheimera","label":"Rheinheimera","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ribes rubrum","label":"Ribes rubrum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"sars-cov-2","label":"SARS-CoV-2","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"s. cerevisiae","label":"Saccharomyces cerevisiae","imageSrc":"yeast.png","imageAlt":"Yeast graphic by Zoe Zorn CC BY 4.0","mod":"SGD","modLink":"https://yeastgenome.org","linkVariable":""},{"value":"saccharomyces paradoxus","label":"Saccharomyces paradoxus ","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"s. uvarum","label":"Saccharomyces uvarum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"schistosoma","label":"Schistosoma","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"schizosaccharomyces japonicus","label":"Schizosaccharomyces japonicus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"s. pombe","label":"Schizosaccharomyces pombe","imageSrc":"pombe.png","imageAlt":"Pombe graphic by Zoe Zorn © Caltech","mod":"PomBase","modLink":"https://www.pombase.org/reference/PMID:","linkVariable":"pmId"},{"value":"schmidtea mediterranea","label":"Schmidtea mediterranea","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"senecio sp","label":"Senecio sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"simocephalus","label":"Simocephalus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"siraitia grosvenorii","label":"Siraitia grosvenorii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"solanum lycopersicum","label":"Solanum lycopersicum","imageSrc":"","imageAlt":"","mod":"Solgenomics Network","modLink":"https://solgenomics.net/organism/1/view/","linkVariable":""},{"value":"sorghum","label":"Sorghum","imageSrc":"","imageAlt":"","mod":"SorghumBase","modLink":"https://www.sorghumbase.org","linkVariable":""},{"value":"spiroplasma eriocheiris","label":"Spiroplasma eriocheiris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"staphylococcus aureus","label":"Staphylococcus aureus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"staphylococcus epidermidis","label":"Staphylococcus epidermidis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"steinernema carpocapsae","label":"Steinernema carpocapsae","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"https://wormbase.org","linkVariable":""},{"value":"steinernema hermaphroditum","label":"Steinernema hermaphroditum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"stenotrophomonas geniculata","label":"Stenotrophomonas geniculata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"stewartia floidana","label":"Stewartia floridana","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"streptococcus gordonii ","label":"Streptococcus gordonii ","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"streptococcus mutans","label":"Streptococcus mutans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":" streptococcus pneumoniae","label":"Streptococcus pneumoniae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"s. purpuratus","label":"Strongylocentrotus purpuratus","imageSrc":"","imageAlt":"","mod":"Echinobase","modLink":"https://www.echinobase.org","linkVariable":""},{"value":"strongyloides ratti","label":"Strongyloides ratti","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"sulfolobus","label":"Sulfolobus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"symphoricarpos albus","label":"Symphoricarpos albus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"syncirsodes","label":"Syncirsodes","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"synechococcus elongatus","label":"Synechococcus elongatus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"syrphidae","label":"Syrphidae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"tarantobelus jeffdanielsi","label":"Tarantobelus jeffdanielsi","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"taraxacum officinale","label":"Taraxacum officinale","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"tatochila theodice","label":"Tatochila theodice","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"tetrahymena","label":"Tetrahymena","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"tetramorium immigrans","label":"Tetramorium immigrans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"tomato brown rugose fruit virus","label":"ToBRFV","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"trachemys scripta","label":"Trachemys scripta","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"tribolium castaneum","label":"Tribolium castaneum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"trichoptera","label":"Trichoptera","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"trichuris muris","label":"Trichuris muris","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"trifolium repens","label":"Trifolium repens","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"trypoxylus dichotomus","label":"Trypoxylus dichotomus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"tsuga canadensis","label":"Tsuga canadensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ulva expansa","label":"Ulva expansa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"universal","label":"Universal","imageSrc":"","imageAlt":"","mod":null,"modLink":null,"linkVariable":null},{"value":"vargula hilgendorfii","label":"Vargula hilgendorfii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"vespula vulgaris","label":"Vespula vulgaris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"virus","label":"Virus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"watasenia scintillans","label":"Watasenia scintillans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"wolbachia pipientis","label":"Wolbachia pipientis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"xenopus","label":"Xenopus","imageSrc":"xenopus.png","imageAlt":"Xenopus graphic by Zoe Zorn CC BY 4.0","mod":"XenBase","modLink":"https://xenbase.org","linkVariable":""},{"value":"xenorhabdus griffiniae","label":"Xenorhabdus griffiniae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"yramea cytheris","label":"Yramea cytheris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"zaprionus indianus","label":"Zaprionus indianus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"zea mays","label":"Zea mays","imageSrc":"","imageAlt":"","mod":"MaizeGDB","modLink":"https://www.maizegdb.org","linkVariable":""},{"value":"zebrafish","label":"Zebrafish","imageSrc":"zebrafish.png","imageAlt":"Zebrafish graphic by Zoe Zorn CC BY 4.0","mod":"ZFIN","modLink":"https://zfin.org","linkVariable":""}]}},"pageContext":{"id":"d37fddbe-5376-4287-9548-9b16d3671634","citedBy":[],"parsedCsv":{"csvHeader":[],"csvData":[]}}}, "staticQueryHashes": ["2114697108"]}