Abblin, Scioto, Natkenzie, and BigHunkinEater are phages that were isolated from soil using the host, Gordonia terrae 3612. They all belong to the DE4 subcluster, and are predicted to by lytic based on their gene content. Their genomes range in size from 58,932-60,002bp and they contain between 89-90 protein-coding genes, of which 34.4-41.1% were assigned a putative function.
","acknowledgements":"We’d like to thank the Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program for sequencing the genomes. We also thank the other SEA-PHAGES students at The Ohio State University who participated in the annotation of these genomes.
","authors":[{"affiliations":["The Ohio State University, Columbus, OH, United States"],"departments":["Biomedical Engineering"],"credit":["investigation","writing_originalDraft"],"email":"allen.3014@osu.edu","firstName":"Lauren","lastName":"Allen","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["The Ohio State University, Columbus, OH, United States"],"departments":["Medicine"],"credit":["investigation","writing_originalDraft"],"email":"carpenter.1205@osu.edu","firstName":"Rachel ","lastName":"Carpenter","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["The Ohio State University, Columbus, OH, United States"],"departments":["Neuroscience"],"credit":["investigation","writing_originalDraft"],"email":"henige.11@osu.edu","firstName":"Sara","lastName":"Henige","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["The Ohio State University, Columbus, OH, United States"],"departments":["Medicine"],"credit":["investigation","writing_originalDraft"],"email":"janikcolette@gmail.com","firstName":"Collette","lastName":"Janik","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["The Ohio State University, Columbus, OH, United States"],"departments":["Neuroscience"],"credit":["investigation","writing_originalDraft"],"email":"mudundi.1@osu.edu","firstName":"Shyla","lastName":"Mundundi","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["The Ohio State University, Columbus, OH, United States"],"departments":["Medicine"],"credit":["investigation","writing_originalDraft"],"email":"ranganathan.47@osu.edu","firstName":"Sandheep","lastName":"Ranganathan","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["The Ohio State University, Columbus, OH, United States"],"departments":["Arts and Sciences"],"credit":["investigation","writing_originalDraft"],"email":"wofford.22@osu.edu","firstName":"Jeila","lastName":"Wofford","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["The Ohio State University, Columbus, OH, United States"],"departments":["Molecular Genetics"],"credit":["investigation","supervision","validation","writing_originalDraft","writing_reviewEditing"],"email":"ball.1766@osu.edu","firstName":"Sarah","lastName":"Ball","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":null}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":"https://portal.micropublication.org/uploads/246463350728937e4df5108519834ae9.csv"},"extendedData":[],"funding":"This project has been supported by the Center for Life Sciences Education, The Ohio State University
","image":{"url":"https://portal.micropublication.org/uploads/e434f645d18eae8dc025bf7a21167f0d.png"},"imageCaption":"(A) BigHunkinEater plaques, Avg. diameter=3-4mm (B) Abblin plaques, Avg. diameter=2-4mm (C) Scioto plaques, Avg. diameter 6-7mm, black dots are artifacts from counting plaques with a marker (D) Natkenzie plaques, Avg. diameter=4-5mm Table: Genome Characteristics of Isolated phages: The sequencing and genome information for four DE4 phages isolated using Gordonia terrae 3612, including read coverage and number of 150 base singe-end reads, genome length, GC content, and number of predicted open reading frames.
","imageTitle":"Representative plaques
","methods":"","reagents":"","patternDescription":"
Gordonia terrae and other members of the genus Gordonia are uncommon human pathogens but do pose a risk, primarily to immunocompromised individuals, and have been known to cause infections in the respiratory tract and soft tissues (Blanc et al., 2007; Pino-Rosa et al., 2023). Since Gordonia terrae has been found to be resistant to several antimicrobials, it is important to develop other possible treatments (Pino-Rosa et al., 2023). To increase our understanding of the genetic diversity of phages capable of infecting members of the genus Gordonia, here we present the discovery and genomic characteristics of 4 phages isolated using G. terrae 3612.
Bacteriophages Abblin, Scioto, Natkenzie, and BigHunkinEater were isolated via direct isolation from soil samples collected in central and eastern Ohio (GPS coordinates presented in Table 1) using standard methods described in the SEA-PHAGES guide (Poxleitner et al., 2018; Zorawik et al. 2024). The soil was suspended in PYCa media and shaken for 1 hour, centrifuged, and the supernatant then filtered through a 0.22mm filter. The filtrate was plated with top agar and incubated at 30°C for 7 days. Individual plaques were purified using three rounds of plaque streaking. Top agar overlay assays produced clear plaques with diameters ranging from 2-7mm (n=5) (Figure 1 A-D).
Phage DNA was extracted from lysates using the Promega Wizard DNA Clean-Up kit and prepared for sequencing using the NEBNext Ultra II FS kit. The genomes of phages Abblin, Scioto and Natkenzie were sequenced using an Illumina MiSeq 1000 sequencer (v3 reagents) and the raw reads were assembled by Newbler v2.9 (Miller et al., 2010) with default settings and Consed v29 (Gordon and Green, 2013) was used to check accuracy, coverage, and genomic termini (Table 1). The genome of BigHunkinEater was sequenced using an Illumina NextSeq 1000 sequencer and the reads were trimmed and filtered by: cutadapt 4.7 (using the option: –nextseq-trim 30) and skewer 0.2.2 (using the options: -q 20 -Q 30 -n -l 50) prior to assembly, as stated above. (Table 1).
Based on a gene content similarity greater than 35% to phages in the Actinobacteriophage Database, all four phages were placed in the DE4 subcluster (Russell & Hatfull, 2017; Pope et al. 2017). The genomes ranged in size from 58,932bp to 60,002bp and had a GC content of 67.7%
Each genome was automatically annotated in PECAAN (Rinehart et al., 2016) using Glimmer v3.02 (Delcher et al., 2007) and GeneMarkS v4.28 (Besemer, 2005). Then, the annotation was refined using BLAST searches against the NCBI Actinobacteriophage Proteins and non-redundant protein sequences databases (Altschul et al., 1990), HHpred searches against the PDB_mmCIF70, SCOPe70, Pfam-A, NCBI_Conserved_Domains databases (Söding et al., 2005), and Phamerator using Actino_draft (Cresawn et al., 2011) and TMHMM databases (Hallgren et al., 2022) . The default setting for each software was used for the annotation. No tRNA genes were identified using Aragorn v1.2.41 (Lanslett, 2004) and tRNAscan-SE v2.012 (Lowe et al., 1997).
The genomes have 89-90 protein coding genes, with an average of 38.8% assigned a putative function (Table 1). The functions identified include both terminase small subunit and terminase large subunit, lysin A, lysin B, portal protein, and RNA ligase, which were all found in each genome.
All predicted genes were transcribed in the forward direction. Additionally, no integrase genes or other functions associated with lysogeny were identified, suggesting that these are lytic phages not capable of establishing lysogeny. Abblin, Scioto and Natkenzie are highly similar; Abblin and Natkenzie share 100 gene content similarity (GCS) whereas Scioto contains one additional gene (41), encoding a putative minor tail protein not present in other cluster DE phages but with homologs present in more distantly related phages (clusters DC and CT, to date). BigHunkinEater is more divergent from these three phages, sharing 79 % GCS.
Nucleotide sequence accession numbers
Abblin is available at GenBank Accession No. PZ492763 and Sequence Read Archive (SRA) No. SRX33845559
Scioto is available at GenBank Accession No. PZ492819 and Sequence Read Archive (SRA) No. SRX33845573
Natkenzie is available at GenBank Accession No. PZ492804 and Sequence Read Archive (SRA) No. SRX33845565
BigHunkinEater is available at GenBank Accession No. PZ492770 and Sequence Read Archive (SRA) No. SRX33845581
","references":[{"reference":"
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. Journal of Molecular Biology 215: 403-410.
","pubmedId":"","doi":"10.1016/S0022-2836(05)80360-2"},{"reference":"Besemer J, Borodovsky M. 2005. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Research 33: W451-W454.
","pubmedId":"","doi":"10.1093/nar/gki487"},{"reference":"Blanc V, Dalle M, Markarian A, Debunne MV, Duplay E, Rodriguez-Nava V, Boiron P. 2007. Gordonia terrae\n : a Difficult-To-Diagnose Emerging Pathogen?. Journal of Clinical Microbiology 45: 1076-1077.
","pubmedId":"","doi":"10.1128/jcm.02394-06"},{"reference":"Cresawn SG, Bogel M, Day N, Jacobs-Sera D, Hendrix RW, Hatfull GF. 2011. Phamerator: a bioinformatic tool for comparative bacteriophage genomics. BMC Bioinformatics 12: 10.1186/1471-2105-12-395.
","pubmedId":"","doi":"10.1186/1471-2105-12-395"},{"reference":"Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23: 673-679.
","pubmedId":"","doi":"10.1093/bioinformatics/btm009"},{"reference":"Gordon D, Green P. 2013. Consed: a graphical editor for next-generation sequencing. Bioinformatics 29: 2936-2937.
","pubmedId":"","doi":"10.1093/bioinformatics/btt515"},{"reference":"Hallgren J, Tsirigos KD, Pedersen MD, Almagro Armenteros JJ, Marcatili P, Nielsen H, Krogh A, Winther O. 2022. DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. : 10.1101/2022.04.08.487609.
","pubmedId":"","doi":"10.1101/2022.04.08.487609"},{"reference":"Laslett D. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Research 32: 11-16.
","pubmedId":"","doi":"10.1093/nar/gkh152"},{"reference":"Lowe TM, Eddy SR. 1997. tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence. Nucleic Acids Research 25: 955-964.
","pubmedId":"","doi":"10.1093/nar/25.5.0955"},{"reference":"Miller JR, Koren S, Sutton G. 2010. Assembly algorithms for next-generation sequencing data. Genomics 95: 315-327.
","pubmedId":"","doi":"10.1016/j.ygeno.2010.03.001"},{"reference":"Pino-Rosa S, Medina-Pascual MaJ, Carrasco G, Garrido N, Villalón P, Valiente Mn, Valdezate S. 2023. Focusing on Gordonia Infections: Distribution, Antimicrobial Susceptibilities and Phylogeny. Antibiotics 12: 1568.
","pubmedId":"","doi":"10.3390/antibiotics12111568 "},{"reference":"Pope WH, Mavrich TN, Garlena RA, Guerrero-Bustamante CA, Jacobs-Sera D, Montgomery MT, et al., Hatfull. 2017. Bacteriophages of\n Gordonia\n spp. Display a Spectrum of Diversity and Genetic Relationships. mBio 8: 10.1128/mbio.01069-17.
","pubmedId":"","doi":"10.1128/mbio.01069-17"},{"reference":"Poxleitner M, Pope W, Jacobs-Sera D, Sivanathan V, Hatfull GF. 2018. HHMI SEA-PHAGES Phage Discovery Guide https://seaphagesphagediscoveryguide.helpdocsonline.com/home
","pubmedId":"","doi":""},{"reference":"Rinehart CA, Gaffney B, Wood JD, Smith S. 2016. PECAAN, a Phage Evidence Collection And Annotation Network. https://discover.kbrinsgd.org/login
","pubmedId":"","doi":""},{"reference":"Russell DA, Hatfull GF. 2016. PhagesDB: the actinobacteriophage database. Bioinformatics 33: 784-786.
","pubmedId":"","doi":"10.1093/bioinformatics/btw711"},{"reference":"Soding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Research 33: W244-W248.
","pubmedId":"","doi":"10.1093/nar/gki408"},{"reference":"Zorawik M, Jacobs-Sera D, Freise AC, SEA-PHAGES, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts. Methods in Molecular Biology,Phage Engineering and Analysis : 273-298.
","pubmedId":"","doi":"10.1007/978-1-0716-3798-2_17"}],"title":"Complete Genome Sequences of four DE4 cluster phages isolated using Gordonia terrae 3612
","reviews":[{"reviewer":{"displayName":"Lee Hughes"},"openAcknowledgement":false,"status":{"submitted":true}}],"curatorReviews":[]},{"id":"715d7441-0262-4a60-9873-7277c08ac358","decision":"accept","abstract":"Abblin, Scioto, Natkenzie, and BigHunkinEater are phages that were isolated from soil using the host, Gordonia terrae 3612. They all belong to the DE4 subcluster, and are predicted to by lytic based on their gene content. Their genomes range in size from 58,932-60,002bp and they contain between 89-90 protein-coding genes, of which 34.4-41.1% were assigned a putative function.
","acknowledgements":"We’d like to thank the Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program for sequencing the genomes. We also thank the other SEA-PHAGES students at The Ohio State University who participated in the annotation of these genomes.
","authors":[{"affiliations":["The Ohio State University, Columbus, OH, United States"],"departments":["Biomedical Engineering"],"credit":["investigation","writing_originalDraft"],"email":"allen.3014@osu.edu","firstName":"Lauren","lastName":"Allen","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["The Ohio State University, Columbus, OH, United States"],"departments":["Medicine"],"credit":["investigation","writing_originalDraft"],"email":"carpenter.1205@osu.edu","firstName":"Rachel ","lastName":"Carpenter","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["The Ohio State University, Columbus, OH, United States"],"departments":["Neuroscience"],"credit":["investigation","writing_originalDraft"],"email":"henige.11@osu.edu","firstName":"Sara","lastName":"Henige","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["The Ohio State University, Columbus, OH, United States"],"departments":["Medicine"],"credit":["investigation","writing_originalDraft"],"email":"janikcolette@gmail.com","firstName":"Collette","lastName":"Janik","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["The Ohio State University, Columbus, OH, United States"],"departments":["Neuroscience"],"credit":["investigation","writing_originalDraft"],"email":"mudundi.1@osu.edu","firstName":"Shyla","lastName":"Mundundi","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["The Ohio State University, Columbus, OH, United States"],"departments":["Medicine"],"credit":["investigation","writing_originalDraft"],"email":"ranganathan.47@osu.edu","firstName":"Sandheep","lastName":"Ranganathan","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["The Ohio State University, Columbus, OH, United States"],"departments":["Arts and Sciences"],"credit":["investigation","writing_originalDraft"],"email":"wofford.22@osu.edu","firstName":"Jeila","lastName":"Wofford","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["The Ohio State University, Columbus, OH, United States"],"departments":["Molecular Genetics"],"credit":["investigation","supervision","validation","writing_originalDraft","writing_reviewEditing"],"email":"ball.1766@osu.edu","firstName":"Sarah","lastName":"Ball","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":null}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":"https://portal.micropublication.org/uploads/246463350728937e4df5108519834ae9.csv"},"extendedData":[],"funding":"This project has been supported by the Center for Life Sciences Education, The Ohio State University
","image":{"url":"https://portal.micropublication.org/uploads/3c21abc31425293e599c0219e0fc5ff3.png"},"imageCaption":"(A) BigHunkinEater plaques, Avg. diameter=3-4mm (n=5) (B) Abblin plaques, Avg. diameter=2-4mm (n=5) (C) Scioto plaques, Avg. diameter 6-7mm (n=5), black dots are artifacts from counting plaques with a marker (D) Natkenzie plaques, Avg. diameter=4-5mm (n=5) Table: Genome Characteristics of Isolated phages: The sequencing and genome information for four DE4 phages isolated using Gordonia terrae 3612, including read coverage and number of 150 base singe-end reads, genome length, GC content, and number of predicted open reading frames.
","imageTitle":"Representative plaques
","methods":"","reagents":"","patternDescription":"
Gordonia terrae and other members of the genus Gordonia are uncommon human pathogens but do pose a risk, primarily to immunocompromised individuals, and have been known to cause infections in the respiratory tract and soft tissues (Blanc et al., 2007; Pino-Rosa et al., 2023). Since Gordonia terrae has been found to be resistant to several antimicrobials, it is important to develop other possible treatments (Pino-Rosa et al., 2023). To increase our understanding of the genetic diversity of phages capable of infecting members of the genus Gordonia, here we present the discovery and genomic characteristics of 4 phages isolated using G. terrae 3612.
Bacteriophages Abblin, Scioto, Natkenzie, and BigHunkinEater were isolated via direct isolation from soil samples collected in central and eastern Ohio (GPS coordinates presented in Table 1) using standard methods described in the SEA-PHAGES guide (Poxleitner et al., 2018; Zorawik et al. 2024). The soil was suspended in PYCa media and shaken for 1 hour, centrifuged, and the supernatant then filtered through a 0.22mm filter. The filtrate was plated with top agar and incubated at 30°C for 7 days. Individual plaques were purified using three rounds of plaque streaking. All plates were incubated at 30°C for 7 days. Top agar overlay assays produced clear plaques with diameters ranging from 2-7mm (n=5) (Figure 1 A-D).
Phage DNA was extracted from lysates using the Promega Wizard DNA Clean-Up kit and prepared for sequencing using the NEBNext Ultra II FS kit. The genomes of phages Abblin, Scioto and Natkenzie were sequenced using an Illumina MiSeq 1000 sequencer (v3 reagents) and the raw reads were assembled by Newbler v2.9 (Miller et al., 2010) with default settings and Consed v29 (Gordon and Green, 2013) was used to check accuracy, coverage, and genomic termini (Table 1). The genome of BigHunkinEater was sequenced using an Illumina NextSeq 1000 sequencer and the reads were trimmed and filtered by: cutadapt 4.7 (using the option: –nextseq-trim 30) and skewer 0.2.2 (using the options: -q 20 -Q 30 -n -l 50) prior to assembly, as stated above. (Table 1).
Based on a gene content similarity greater than 35% to phages in the Actinobacteriophage Database, all four phages were placed in the DE4 subcluster and have circularly permuted genomes (Russell & Hatfull, 2017; Pope et al. 2017). The genomes ranged in size from 58,932bp to 60,002bp and had a GC content of 67.7%.
Each genome was automatically annotated in PECAAN (Rinehart et al., 2016) using Glimmer v3.02 (Delcher et al., 2007) and GeneMarkS v4.28 (Besemer, 2005). Then, the annotation was refined using BLAST searches against the NCBI Actinobacteriophage Proteins and non-redundant protein sequences databases (Altschul et al., 1990), HHpred searches against the PDB_mmCIF70, SCOPe70, Pfam-A, NCBI_Conserved_Domains databases (Söding et al., 2005), and Phamerator using Actino_draft (Cresawn et al., 2011) and TMHMM databases (Hallgren et al., 2022) . The default setting for each software was used for the annotation. No tRNA genes were identified using Aragorn v1.2.41 (Lanslett, 2004) and tRNAscan-SE v2.012 (Lowe et al., 1997).
The genomes have 89-90 protein coding genes, with an average of 38.8% assigned a putative function (Table 1). The functions identified include both terminase small subunit and terminase large subunit, lysin A, lysin B, portal protein, and RNA ligase, which were all found in each genome.
All predicted genes were transcribed in the forward direction. Additionally, no integrase genes or other functions associated with lysogeny were identified, suggesting that these are lytic phages not capable of establishing lysogeny. Abblin, Scioto and Natkenzie are highly similar; Abblin and Natkenzie share 100 gene content similarity (GCS) whereas Scioto contains one additional gene (41), encoding a putative minor tail protein not present in other cluster DE phages but with homologs present in more distantly related phages (clusters DC and CT, to date). BigHunkinEater is more divergent from these three phages, sharing 79 % GCS.
Nucleotide sequence accession numbers
Abblin is available at GenBank Accession No. PZ492763 and Sequence Read Archive (SRA) No. SRX33845559
Scioto is available at GenBank Accession No. PZ492819 and Sequence Read Archive (SRA) No. SRX33845573
Natkenzie is available at GenBank Accession No. PZ492804 and Sequence Read Archive (SRA) No. SRX33845565
BigHunkinEater is available at GenBank Accession No. PZ492770 and Sequence Read Archive (SRA) No. SRX33845581
","references":[{"reference":"
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. Journal of Molecular Biology 215: 403-410.
","pubmedId":"","doi":"10.1016/S0022-2836(05)80360-2"},{"reference":"Besemer J, Borodovsky M. 2005. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Research 33: W451-W454.
","pubmedId":"","doi":"10.1093/nar/gki487"},{"reference":"Blanc V, Dalle M, Markarian A, Debunne MV, Duplay E, Rodriguez-Nava V, Boiron P. 2007. Gordonia terrae\n : a Difficult-To-Diagnose Emerging Pathogen?. Journal of Clinical Microbiology 45: 1076-1077.
","pubmedId":"","doi":"10.1128/jcm.02394-06"},{"reference":"Cresawn SG, Bogel M, Day N, Jacobs-Sera D, Hendrix RW, Hatfull GF. 2011. Phamerator: a bioinformatic tool for comparative bacteriophage genomics. BMC Bioinformatics 12: 10.1186/1471-2105-12-395.
","pubmedId":"","doi":"10.1186/1471-2105-12-395"},{"reference":"Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23: 673-679.
","pubmedId":"","doi":"10.1093/bioinformatics/btm009"},{"reference":"Gordon D, Green P. 2013. Consed: a graphical editor for next-generation sequencing. Bioinformatics 29: 2936-2937.
","pubmedId":"","doi":"10.1093/bioinformatics/btt515"},{"reference":"Hallgren J, Tsirigos KD, Pedersen MD, Almagro Armenteros JJ, Marcatili P, Nielsen H, Krogh A, Winther O. 2022. DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. : 10.1101/2022.04.08.487609.
","pubmedId":"","doi":"10.1101/2022.04.08.487609"},{"reference":"Laslett D. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Research 32: 11-16.
","pubmedId":"","doi":"10.1093/nar/gkh152"},{"reference":"Lowe TM, Eddy SR. 1997. tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence. Nucleic Acids Research 25: 955-964.
","pubmedId":"","doi":"10.1093/nar/25.5.0955"},{"reference":"Miller JR, Koren S, Sutton G. 2010. Assembly algorithms for next-generation sequencing data. Genomics 95: 315-327.
","pubmedId":"","doi":"10.1016/j.ygeno.2010.03.001"},{"reference":"Pino-Rosa S, Medina-Pascual MaJ, Carrasco G, Garrido N, Villalón P, Valiente Mn, Valdezate S. 2023. Focusing on Gordonia Infections: Distribution, Antimicrobial Susceptibilities and Phylogeny. Antibiotics 12: 1568.
","pubmedId":"","doi":"10.3390/antibiotics12111568 "},{"reference":"Pope WH, Mavrich TN, Garlena RA, Guerrero-Bustamante CA, Jacobs-Sera D, Montgomery MT, et al., Hatfull. 2017. Bacteriophages of\n Gordonia\n spp. Display a Spectrum of Diversity and Genetic Relationships. mBio 8: 10.1128/mbio.01069-17.
","pubmedId":"","doi":"10.1128/mbio.01069-17"},{"reference":"Poxleitner M, Pope W, Jacobs-Sera D, Sivanathan V, Hatfull GF. 2018. HHMI SEA-PHAGES Phage Discovery Guide https://seaphagesphagediscoveryguide.helpdocsonline.com/home
","pubmedId":"","doi":""},{"reference":"Rinehart CA, Gaffney B, Wood JD, Smith S. 2016. PECAAN, a Phage Evidence Collection And Annotation Network. https://discover.kbrinsgd.org/login
","pubmedId":"","doi":""},{"reference":"Russell DA, Hatfull GF. 2016. PhagesDB: the actinobacteriophage database. Bioinformatics 33: 784-786.
","pubmedId":"","doi":"10.1093/bioinformatics/btw711"},{"reference":"Soding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Research 33: W244-W248.
","pubmedId":"","doi":"10.1093/nar/gki408"},{"reference":"Zorawik M, Jacobs-Sera D, Freise AC, SEA-PHAGES, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts. Methods in Molecular Biology,Phage Engineering and Analysis : 273-298.
","pubmedId":"","doi":"10.1007/978-1-0716-3798-2_17"}],"title":"Complete Genome Sequences of four DE4 cluster phages isolated using Gordonia terrae 3612
","reviews":[],"curatorReviews":[]},{"id":"412edd36-7cef-48e5-b273-43c6ab7b91f8","decision":"edit","abstract":"Abblin, Scioto, Natkenzie, and BigHunkinEater are phages that were isolated from soil using the host, Gordonia terrae 3612. They all belong to the DE4 subcluster, and are predicted to by lytic based on their gene content. Their genomes range in size from 58,932-60,002bp and they contain between 89-90 protein-coding genes, of which 34.4-41.1% were assigned a putative function.
","acknowledgements":"We’d like to thank the Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program for sequencing the genomes. We also thank the other SEA-PHAGES students at The Ohio State University who participated in the annotation of these genomes.
","authors":[{"affiliations":["The Ohio State University, Columbus, OH, United States"],"departments":["Department of Biomedical Engineering"],"credit":["investigation","writing_originalDraft"],"email":"allen.3014@osu.edu","firstName":"Lauren","lastName":"Allen","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["The Ohio State University, Columbus, OH, United States"],"departments":["College of Medicine"],"credit":["investigation","writing_originalDraft"],"email":"carpenter.1205@osu.edu","firstName":"Rachel ","lastName":"Carpenter","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["The Ohio State University, Columbus, OH, United States"],"departments":["Department of Neuroscience"],"credit":["investigation","writing_originalDraft"],"email":"henige.11@osu.edu","firstName":"Sara","lastName":"Henige","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["The Ohio State University, Columbus, OH, United States"],"departments":["College of Medicine"],"credit":["investigation","writing_originalDraft"],"email":"janikcolette@gmail.com","firstName":"Collette","lastName":"Janik","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["The Ohio State University, Columbus, OH, United States"],"departments":["Department of Neuroscience"],"credit":["investigation","writing_originalDraft"],"email":"mudundi.1@osu.edu","firstName":"Shyla","lastName":"Mundundi","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["The Ohio State University, Columbus, OH, United States"],"departments":["College of Medicine"],"credit":["investigation","writing_originalDraft"],"email":"ranganathan.47@osu.edu","firstName":"Sandheep","lastName":"Ranganathan","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["The Ohio State University, Columbus, OH, United States"],"departments":["College of Arts and Sciences"],"credit":["investigation","writing_originalDraft"],"email":"wofford.22@osu.edu","firstName":"Jeila","lastName":"Wofford","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["The Ohio State University, Columbus, OH, United States"],"departments":["Department of Molecular Genetics"],"credit":["investigation","supervision","validation","writing_originalDraft","writing_reviewEditing"],"email":"ball.1766@osu.edu","firstName":"Sarah","lastName":"Ball","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":null}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":"https://portal.micropublication.org/uploads/246463350728937e4df5108519834ae9.csv"},"extendedData":[],"funding":"This project has been supported by the Center for Life Sciences Education, The Ohio State University
","image":{"url":"https://portal.micropublication.org/uploads/3c21abc31425293e599c0219e0fc5ff3.png"},"imageCaption":"(A) BigHunkinEater plaques, Avg. diameter=3-4mm (n=5) (B) Abblin plaques, Avg. diameter=2-4mm (n=5) (C) Scioto plaques, Avg. diameter 6-7mm (n=5), black dots are artifacts from counting plaques with a marker (D) Natkenzie plaques, Avg. diameter=4-5mm (n=5) Table: Genome Characteristics of Isolated phages: The sequencing and genome information for four DE4 phages isolated using Gordonia terrae 3612, including read coverage and number of 150 base singe-end reads, genome length, GC content, and number of predicted open reading frames.
","imageTitle":"Representative plaques
","methods":"","reagents":"","patternDescription":"
Gordonia terrae and other members of the genus Gordonia are uncommon human pathogens but do pose a risk, primarily to immunocompromised individuals, and have been known to cause infections in the respiratory tract and soft tissues (Blanc et al., 2007; Pino-Rosa et al., 2023). Since Gordonia terrae has been found to be resistant to several antimicrobials, it is important to develop other possible treatments (Pino-Rosa et al., 2023). To increase our understanding of the genetic diversity of phages capable of infecting members of the genus Gordonia, here we present the discovery and genomic characteristics of 4 phages isolated using G. terrae 3612.
Bacteriophages Abblin, Scioto, Natkenzie, and BigHunkinEater were isolated via direct isolation from soil samples collected in central and eastern Ohio (GPS coordinates presented in Table 1) using standard methods described in the SEA-PHAGES guide (Poxleitner et al., 2018; Zorawik et al. 2024). The soil was suspended in PYCa media and shaken for 1 hour, centrifuged, and the supernatant then filtered through a 0.22μm filter. The filtrate was plated with top agar and incubated at 30°C for 7 days. Individual plaques were purified using three rounds of plaque streaking. All plates were incubated at 30°C for 7 days. Top agar overlay assays produced clear plaques with diameters ranging from 2-7mm (n=5) (Figure 1 A-D).
Phage DNA was extracted from lysates using the Promega Wizard DNA Clean-Up kit and prepared for sequencing using the NEBNext Ultra II FS kit. The genomes of phages Abblin, Scioto and Natkenzie were sequenced using an Illumina MiSeq 1000 sequencer (v3 reagents) and the raw reads were assembled by Newbler v2.9 (Miller et al., 2010) with default settings and Consed v29 (Gordon and Green, 2013) was used to check accuracy, coverage, and genomic termini (Table 1). The genome of BigHunkinEater was sequenced using an Illumina NextSeq 1000 sequencer and the reads were trimmed and filtered by: cutadapt 4.7 (using the option: –nextseq-trim 30) and skewer 0.2.2 (using the options: -q 20 -Q 30 -n -l 50) prior to assembly, as stated above. (Table 1).
Based on a gene content similarity greater than 35% to phages in the Actinobacteriophage Database, all four phages were placed in the DE4 subcluster and have circularly permuted genomes (Russell & Hatfull, 2017; Pope et al. 2017). The genomes ranged in size from 58,932bp to 60,002bp and had a GC content of 67.7%.
Each genome was automatically annotated in PECAAN (Rinehart et al., 2016) using Glimmer v3.02 (Delcher et al., 2007) and GeneMarkS v4.28 (Besemer, 2005). Then, the annotation was refined using BLAST searches against the NCBI Actinobacteriophage Proteins and non-redundant protein sequences databases (Altschul et al., 1990), HHpred searches against the PDB_mmCIF70, SCOPe70, Pfam-A, NCBI_Conserved_Domains databases (Söding et al., 2005), and Phamerator using Actino_draft (Cresawn et al., 2011) and TMHMM databases (Hallgren et al., 2022) . The default setting for each software was used for the annotation. No tRNA genes were identified using Aragorn v1.2.41 (Lanslett, 2004) and tRNAscan-SE v2.012 (Lowe et al., 1997).
The genomes have 89-90 protein coding genes, with an average of 38.8% assigned a putative function (Table 1). The functions identified include both terminase small subunit and terminase large subunit, lysin A, lysin B, portal protein, and RNA ligase, which were all found in each genome.
All predicted genes were transcribed in the forward direction. Additionally, no integrase genes or other functions associated with lysogeny were identified, suggesting that these are lytic phages not capable of establishing lysogeny. Abblin, Scioto and Natkenzie are highly similar; Abblin and Natkenzie share 100 gene content similarity (GCS) whereas Scioto contains one additional gene (41), encoding a putative minor tail protein not present in other cluster DE phages but with homologs present in more distantly related phages (clusters DC and CT, to date). BigHunkinEater is more divergent from these three phages, sharing 79 % GCS.
Nucleotide sequence accession numbers
Abblin is available at GenBank Accession No. PZ492763 and Sequence Read Archive (SRA) No. SRX33845559
Scioto is available at GenBank Accession No. PZ492819 and Sequence Read Archive (SRA) No. SRX33845573
Natkenzie is available at GenBank Accession No. PZ492804 and Sequence Read Archive (SRA) No. SRX33845565
BigHunkinEater is available at GenBank Accession No. PZ492770 and Sequence Read Archive (SRA) No. SRX33845581
","references":[{"reference":"
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. Journal of Molecular Biology 215: 403-410.
","pubmedId":"","doi":"10.1016/S0022-2836(05)80360-2"},{"reference":"Besemer J, Borodovsky M. 2005. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Research 33: W451-W454.
","pubmedId":"","doi":"10.1093/nar/gki487"},{"reference":"Blanc V, Dalle M, Markarian A, Debunne MV, Duplay E, Rodriguez-Nava V, Boiron P. 2007. Gordonia terrae\n : a Difficult-To-Diagnose Emerging Pathogen?. Journal of Clinical Microbiology 45: 1076-1077.
","pubmedId":"","doi":"10.1128/jcm.02394-06"},{"reference":"Cresawn SG, Bogel M, Day N, Jacobs-Sera D, Hendrix RW, Hatfull GF. 2011. Phamerator: a bioinformatic tool for comparative bacteriophage genomics. BMC Bioinformatics 12: 10.1186/1471-2105-12-395.
","pubmedId":"","doi":"10.1186/1471-2105-12-395"},{"reference":"Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23: 673-679.
","pubmedId":"","doi":"10.1093/bioinformatics/btm009"},{"reference":"Gordon D, Green P. 2013. Consed: a graphical editor for next-generation sequencing. Bioinformatics 29: 2936-2937.
","pubmedId":"","doi":"10.1093/bioinformatics/btt515"},{"reference":"Hallgren J, Tsirigos KD, Pedersen MD, Almagro Armenteros JJ, Marcatili P, Nielsen H, Krogh A, Winther O. 2022. DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. : 10.1101/2022.04.08.487609.
","pubmedId":"","doi":"10.1101/2022.04.08.487609"},{"reference":"Laslett D. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Research 32: 11-16.
","pubmedId":"","doi":"10.1093/nar/gkh152"},{"reference":"Lowe TM, Eddy SR. 1997. tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence. Nucleic Acids Research 25: 955-964.
","pubmedId":"","doi":"10.1093/nar/25.5.0955"},{"reference":"Miller JR, Koren S, Sutton G. 2010. Assembly algorithms for next-generation sequencing data. Genomics 95: 315-327.
","pubmedId":"","doi":"10.1016/j.ygeno.2010.03.001"},{"reference":"Pino-Rosa S, Medina-Pascual MaJ, Carrasco G, Garrido N, Villalón P, Valiente Mn, Valdezate S. 2023. Focusing on Gordonia Infections: Distribution, Antimicrobial Susceptibilities and Phylogeny. Antibiotics 12: 1568.
","pubmedId":"","doi":"10.3390/antibiotics12111568 "},{"reference":"Pope WH, Mavrich TN, Garlena RA, Guerrero-Bustamante CA, Jacobs-Sera D, Montgomery MT, et al., Hatfull. 2017. Bacteriophages of\n Gordonia\n spp. Display a Spectrum of Diversity and Genetic Relationships. mBio 8: 10.1128/mbio.01069-17.
","pubmedId":"","doi":"10.1128/mbio.01069-17"},{"reference":"Poxleitner M, Pope W, Jacobs-Sera D, Sivanathan V, Hatfull GF. 2018. HHMI SEA-PHAGES Phage Discovery Guide https://seaphagesphagediscoveryguide.helpdocsonline.com/home
","pubmedId":"","doi":""},{"reference":"Rinehart CA, Gaffney B, Wood JD, Smith S. 2016. PECAAN, a Phage Evidence Collection And Annotation Network. https://discover.kbrinsgd.org/login
","pubmedId":"","doi":""},{"reference":"Russell DA, Hatfull GF. 2016. PhagesDB: the actinobacteriophage database. Bioinformatics 33: 784-786.
","pubmedId":"","doi":"10.1093/bioinformatics/btw711"},{"reference":"Soding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Research 33: W244-W248.
","pubmedId":"","doi":"10.1093/nar/gki408"},{"reference":"Zorawik M, Jacobs-Sera D, Freise AC, SEA-PHAGES, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts. Methods in Molecular Biology,Phage Engineering and Analysis : 273-298.
","pubmedId":"","doi":"10.1007/978-1-0716-3798-2_17"}],"title":"Complete Genome Sequences of four DE4 cluster phages isolated using Gordonia terrae 3612
","reviews":[],"curatorReviews":[]},{"id":"fb09459f-45d7-4002-921f-1a5caaa1fca9","decision":"publish","abstract":"Abblin, Scioto, Natkenzie, and BigHunkinEater are phages that were isolated from soil using the host, Gordonia terrae 3612. They all belong to the DE4 subcluster, and are predicted to by lytic based on their gene content. Their genomes range in size from 58,932-60,002bp and they contain between 89-90 protein-coding genes, of which 34.4-41.1% were assigned a putative function.
","acknowledgements":"We’d like to thank the Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program for sequencing the genomes. We also thank the other SEA-PHAGES students at The Ohio State University who participated in the annotation of these genomes.
","authors":[{"affiliations":["The Ohio State University, Columbus, OH, United States"],"departments":["Department of Biomedical Engineering"],"credit":["investigation","writing_originalDraft"],"email":"allen.3014@osu.edu","firstName":"Lauren","lastName":"Allen","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["The Ohio State University, Columbus, OH, United States"],"departments":["College of Medicine"],"credit":["investigation","writing_originalDraft"],"email":"carpenter.1205@osu.edu","firstName":"Rachel ","lastName":"Carpenter","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["The Ohio State University, Columbus, OH, United States"],"departments":["Department of Neuroscience"],"credit":["investigation","writing_originalDraft"],"email":"henige.11@osu.edu","firstName":"Sara","lastName":"Henige","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["The Ohio State University, Columbus, OH, United States"],"departments":["College of Medicine"],"credit":["investigation","writing_originalDraft"],"email":"janikcolette@gmail.com","firstName":"Collette","lastName":"Janik","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["The Ohio State University, Columbus, OH, United States"],"departments":["Department of Neuroscience"],"credit":["investigation","writing_originalDraft"],"email":"mudundi.1@osu.edu","firstName":"Shyla","lastName":"Mundundi","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["The Ohio State University, Columbus, OH, United States"],"departments":["College of Medicine"],"credit":["investigation","writing_originalDraft"],"email":"ranganathan.47@osu.edu","firstName":"Sandheep","lastName":"Ranganathan","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["The Ohio State University, Columbus, OH, United States"],"departments":["College of Arts and Sciences"],"credit":["investigation","writing_originalDraft"],"email":"wofford.22@osu.edu","firstName":"Jeila","lastName":"Wofford","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["The Ohio State University, Columbus, OH, United States"],"departments":["Department of Molecular Genetics"],"credit":["investigation","supervision","validation","writing_originalDraft","writing_reviewEditing"],"email":"ball.1766@osu.edu","firstName":"Sarah","lastName":"Ball","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":null}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":"https://portal.micropublication.org/uploads/246463350728937e4df5108519834ae9.csv"},"extendedData":[],"funding":"This project has been supported by the Center for Life Sciences Education, The Ohio State University
","image":{"url":"https://portal.micropublication.org/uploads/3c21abc31425293e599c0219e0fc5ff3.png"},"imageCaption":"(A) BigHunkinEater plaques, Avg. diameter=3-4mm (n=5) (B) Abblin plaques, Avg. diameter=2-4mm (n=5) (C) Scioto plaques, Avg. diameter 6-7mm (n=5), black dots are artifacts from counting plaques with a marker (D) Natkenzie plaques, Avg. diameter=4-5mm (n=5) Table: Genome Characteristics of Isolated phages: The sequencing and genome information for four DE4 phages isolated using Gordonia terrae 3612, including read coverage and number of 150 base singe-end reads, genome length, GC content, and number of predicted open reading frames.
","imageTitle":"
Representative plaques
","methods":"","reagents":"","patternDescription":"
Gordonia terrae and other members of the genus Gordonia are uncommon human pathogens but do pose a risk, primarily to immunocompromised individuals, and have been known to cause infections in the respiratory tract and soft tissues (Blanc et al., 2007; Pino-Rosa et al., 2023). Since Gordonia terrae has been found to be resistant to several antimicrobials, it is important to develop other possible treatments (Pino-Rosa et al., 2023). To increase our understanding of the genetic diversity of phages capable of infecting members of the genus Gordonia, here we present the discovery and genomic characteristics of 4 phages isolated using G. terrae 3612.
Bacteriophages Abblin, Scioto, Natkenzie, and BigHunkinEater were isolated via direct isolation from soil samples collected in central and eastern Ohio (GPS coordinates presented in Table 1) using standard methods described in the SEA-PHAGES guide (Poxleitner et al., 2018; Zorawik et al. 2024). The soil was suspended in PYCa media and shaken for 1 hour, centrifuged, and the supernatant then filtered through a 0.22μm filter. The filtrate was plated with top agar and incubated at 30°C for 7 days. Individual plaques were purified using three rounds of plaque streaking. All plates were incubated at 30°C for 7 days. Top agar overlay assays produced clear plaques with diameters ranging from 2-7mm (n=5) (Figure 1 A-D).
Phage DNA was extracted from lysates using the Promega Wizard DNA Clean-Up kit and prepared for sequencing using the NEBNext Ultra II FS kit. The genomes of phages Abblin, Scioto and Natkenzie were sequenced using an Illumina MiSeq 1000 sequencer (v3 reagents) and the raw reads were assembled by Newbler v2.9 (Miller et al., 2010) with default settings and Consed v29 (Gordon and Green, 2013) was used to check accuracy, coverage, and genomic termini (Table 1). The genome of BigHunkinEater was sequenced using an Illumina NextSeq 1000 sequencer and the reads were trimmed and filtered by: cutadapt 4.7 (using the option: –nextseq-trim 30) and skewer 0.2.2 (using the options: -q 20 -Q 30 -n -l 50) prior to assembly, as stated above. (Table 1).
Based on a gene content similarity greater than 35% to phages in the Actinobacteriophage Database, all four phages were placed in the DE4 subcluster and have circularly permuted genomes (Russell & Hatfull, 2017; Pope et al. 2017). The genomes ranged in size from 58,932bp to 60,002bp and had a GC content of 67.7%.
Each genome was automatically annotated in PECAAN (Rinehart et al., 2016) using Glimmer v3.02 (Delcher et al., 2007) and GeneMarkS v4.28 (Besemer, 2005). Then, the annotation was refined using BLAST searches against the NCBI Actinobacteriophage Proteins and non-redundant protein sequences databases (Altschul et al., 1990), HHpred searches against the PDB_mmCIF70, SCOPe70, Pfam-A, NCBI_Conserved_Domains databases (Söding et al., 2005), and Phamerator using Actino_draft (Cresawn et al., 2011) and TMHMM databases (Hallgren et al., 2022) . The default setting for each software was used for the annotation. No tRNA genes were identified using Aragorn v1.2.41 (Lanslett, 2004) and tRNAscan-SE v2.012 (Lowe et al., 1997).
The genomes have 89-90 protein coding genes, with an average of 38.8% assigned a putative function (Table 1). The functions identified include both terminase small subunit and terminase large subunit, lysin A, lysin B, portal protein, and RNA ligase, which were all found in each genome.
All predicted genes were transcribed in the forward direction. Additionally, no integrase genes or other functions associated with lysogeny were identified, suggesting that these are lytic phages not capable of establishing lysogeny. Abblin, Scioto and Natkenzie are highly similar; Abblin and Natkenzie share 100 gene content similarity (GCS) whereas Scioto contains one additional gene (41), encoding a putative minor tail protein not present in other cluster DE phages but with homologs present in more distantly related phages (clusters DC and CT, to date). BigHunkinEater is more divergent from these three phages, sharing 79 % GCS.
Nucleotide sequence accession numbers
Abblin is available at GenBank Accession No. PZ492763 and Sequence Read Archive (SRA) No. SRX33845559
Scioto is available at GenBank Accession No. PZ492819 and Sequence Read Archive (SRA) No. SRX33845573
Natkenzie is available at GenBank Accession No. PZ492804 and Sequence Read Archive (SRA) No. SRX33845565
BigHunkinEater is available at GenBank Accession No. PZ492770 and Sequence Read Archive (SRA) No. SRX33845581
","references":[{"reference":"
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. Journal of Molecular Biology 215: 403-410.
","pubmedId":"","doi":"10.1016/S0022-2836(05)80360-2"},{"reference":"Besemer J, Borodovsky M. 2005. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Research 33: W451-W454.
","pubmedId":"","doi":"10.1093/nar/gki487"},{"reference":"Blanc V, Dalle M, Markarian A, Debunne MV, Duplay E, Rodriguez-Nava V, Boiron P. 2007. Gordonia terrae\n : a Difficult-To-Diagnose Emerging Pathogen?. Journal of Clinical Microbiology 45: 1076-1077.
","pubmedId":"","doi":"10.1128/jcm.02394-06"},{"reference":"Cresawn SG, Bogel M, Day N, Jacobs-Sera D, Hendrix RW, Hatfull GF. 2011. Phamerator: a bioinformatic tool for comparative bacteriophage genomics. BMC Bioinformatics 12: 10.1186/1471-2105-12-395.
","pubmedId":"","doi":"10.1186/1471-2105-12-395"},{"reference":"Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23: 673-679.
","pubmedId":"","doi":"10.1093/bioinformatics/btm009"},{"reference":"Gordon D, Green P. 2013. Consed: a graphical editor for next-generation sequencing. Bioinformatics 29: 2936-2937.
","pubmedId":"","doi":"10.1093/bioinformatics/btt515"},{"reference":"Hallgren J, Tsirigos KD, Pedersen MD, Almagro Armenteros JJ, Marcatili P, Nielsen H, Krogh A, Winther O. 2022. DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. : 10.1101/2022.04.08.487609.
","pubmedId":"","doi":"10.1101/2022.04.08.487609"},{"reference":"Laslett D. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Research 32: 11-16.
","pubmedId":"","doi":"10.1093/nar/gkh152"},{"reference":"Lowe TM, Eddy SR. 1997. tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence. Nucleic Acids Research 25: 955-964.
","pubmedId":"","doi":"10.1093/nar/25.5.0955"},{"reference":"Miller JR, Koren S, Sutton G. 2010. Assembly algorithms for next-generation sequencing data. Genomics 95: 315-327.
","pubmedId":"","doi":"10.1016/j.ygeno.2010.03.001"},{"reference":"Pino-Rosa S, Medina-Pascual MaJ, Carrasco G, Garrido N, Villalón P, Valiente Mn, Valdezate S. 2023. Focusing on Gordonia Infections: Distribution, Antimicrobial Susceptibilities and Phylogeny. Antibiotics 12: 1568.
","pubmedId":"","doi":"10.3390/antibiotics12111568 "},{"reference":"Pope WH, Mavrich TN, Garlena RA, Guerrero-Bustamante CA, Jacobs-Sera D, Montgomery MT, et al., Hatfull. 2017. Bacteriophages of\n Gordonia\n spp. Display a Spectrum of Diversity and Genetic Relationships. mBio 8: 10.1128/mbio.01069-17.
","pubmedId":"","doi":"10.1128/mbio.01069-17"},{"reference":"Poxleitner M, Pope W, Jacobs-Sera D, Sivanathan V, Hatfull GF. 2018. HHMI SEA-PHAGES Phage Discovery Guide https://seaphagesphagediscoveryguide.helpdocsonline.com/home
","pubmedId":"","doi":""},{"reference":"Rinehart CA, Gaffney B, Wood JD, Smith S. 2016. PECAAN, a Phage Evidence Collection And Annotation Network. https://discover.kbrinsgd.org/login
","pubmedId":"","doi":""},{"reference":"Russell DA, Hatfull GF. 2016. PhagesDB: the actinobacteriophage database. Bioinformatics 33: 784-786.
","pubmedId":"","doi":"10.1093/bioinformatics/btw711"},{"reference":"Soding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Research 33: W244-W248.
","pubmedId":"","doi":"10.1093/nar/gki408"},{"reference":"Zorawik M, Jacobs-Sera D, Freise AC, SEA-PHAGES, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts. Methods in Molecular Biology,Phage Engineering and Analysis : 273-298.
","pubmedId":"","doi":"10.1007/978-1-0716-3798-2_17"}],"title":"Complete Genome Sequences of four DE4 cluster phages isolated using Gordonia terrae 3612
","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":"aerococcus","label":"Aerococcus","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":"lactobacillus","label":"Lactobacillus","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":"ligilactobacillus","label":"Ligilactobacillus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ligilactobacillus salivarius","label":"Ligilactobacillus salivarius","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"limosilactobacillus","label":"Limosilactobacillus","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":"3c8eff58-cfb5-4159-9eb8-8647f45799c0","citedBy":[],"parsedCsv":{"csvHeader":[{"accessor":"Phage","Header":"Phage"},{"accessor":"GPS coordinates","Header":"GPS coordinates"},{"accessor":"Approximate read coverage","Header":"Approximate read coverage"},{"accessor":"# of 150 base single-end reads","Header":"# of 150 base single-end reads"},{"accessor":"Genome length (bp)","Header":"Genome length (bp)"},{"accessor":"GC content %","Header":"GC content %"},{"accessor":"# of ORFs (% with predicted function)","Header":"# of ORFs (% with predicted function)"}],"csvData":[{"Phage":"Abblin","GPS coordinates":"40.11557 N, 83.17065 W","Approximate read coverage":"759","# of 150 base single-end reads":"318,583","Genome length (bp)":"60,001","GC content %":"67.7","# of ORFs (% with predicted function)":"89 (40.4%)"},{"Phage":"Scioto","GPS coordinates":"40.079576 N, 83.112103 W","Approximate read coverage":"655","# of 150 base single-end reads":"262,015","Genome length (bp)":"60,002","GC content %":"67.7","# of ORFs (% with predicted function)":"90 (41.1%)"},{"Phage":"Natkenzie","GPS coordinates":"40.58 N, 84.33 W","Approximate read coverage":"632","# of 150 base single-end reads":"456,081","Genome length (bp)":"60,001","GC content %":"67.7","# of ORFs (% with predicted function)":"89 (39.3%)"},{"Phage":"BigHunkinEater","GPS coordinates":"39.99639 N, 83.01091 W","Approximate read coverage":"769","# of 150 base single-end reads":"509,639","Genome length (bp)":"58,932","GC content %":"67.7","# of ORFs (% with predicted function)":"90 (34.4%)"}]}}}, "staticQueryHashes": ["2114697108"]}