{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,12]],"date-time":"2025-10-12T02:46:09Z","timestamp":1760237169670,"version":"build-2065373602"},"reference-count":168,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2020,3,5]],"date-time":"2020-03-05T00:00:00Z","timestamp":1583366400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Rathayibacter toxicus is a Gram-positive, nematode-vectored bacterium that infects several grass species in the family Poaceae. Unique in its genus, R. toxicus has the smallest genome, possesses a complete CRISPR-Cas system, a vancomycin-resistance cassette, produces tunicamycin, a corynetoxin responsible for livestock deaths in Australia, and is designated a Select Agent in the United States. In-depth, genome-wide analyses performed in this study support the previously designated five genetic populations, with a core genome comprising approximately 80% of the genome for all populations. Results varied as a function of the type of analysis and when using different bioinformatics tools for the same analysis; e.g., some programs failed to identify specific genomic regions that were actually present. The software variance highlights the need to verify bioinformatics results by additional methods; e.g., PCR, mapping genes to genomes, use of multiple algorithms). These analyses suggest the following relationships among populations: RT-IV \u2194 RT-I \u2194 RT-II \u2194 RT-III \u2194 RT-V, with RT-IV and RT-V being the most unrelated. This is the most comprehensive analysis of R. toxicus that included populations RT-I and RT-V. Future studies require underrepresented populations and more recent isolates from varied hosts and geographic locations.<\/jats:p>","DOI":"10.3390\/microorganisms8030366","type":"journal-article","created":{"date-parts":[[2020,3,6]],"date-time":"2020-03-06T07:33:46Z","timestamp":1583480026000},"page":"366","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Comparative Genomic Analysis Confirms Five Genetic Populations of the Select Agent, Rathayibacter toxicus"],"prefix":"10.3390","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5365-8170","authenticated-orcid":false,"given":"Jarred","family":"Yasuhara-Bell","sequence":"first","affiliation":[{"name":"Department of Plant Pathology, Kansas State University, 1712 Claflin Road, 4024 Throckmorton Plant Science Center, Manhattan, KS 66506, USA"},{"name":"Plant Biosecurity Cooperative Research Centre, CRC for National Plant Biosecurity, Level 2, Building 22, Innovation Centre, University Drive, University of Canberra, Bruce, Australian Capital Territory, Canberra 2617, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5887-2050","authenticated-orcid":false,"given":"Mohammad","family":"Arif","sequence":"additional","affiliation":[{"name":"Plant Biosecurity Cooperative Research Centre, CRC for National Plant Biosecurity, Level 2, Building 22, Innovation Centre, University Drive, University of Canberra, Bruce, Australian Capital Territory, Canberra 2617, Australia"},{"name":"Department of Plant and Environmental Protection Sciences, University of Hawai`i at M\u0101noa, Honolulu, HI 96822, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Grethel Y.","family":"Busot","sequence":"additional","affiliation":[{"name":"Department of Plant Pathology, Kansas State University, 1712 Claflin Road, 4024 Throckmorton Plant Science Center, Manhattan, KS 66506, USA"},{"name":"Plant Biosecurity Cooperative Research Centre, CRC for National Plant Biosecurity, Level 2, Building 22, Innovation Centre, University Drive, University of Canberra, Bruce, Australian Capital Territory, Canberra 2617, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rachel","family":"Mann","sequence":"additional","affiliation":[{"name":"Plant Biosecurity Cooperative Research Centre, CRC for National Plant Biosecurity, Level 2, Building 22, Innovation Centre, University Drive, University of Canberra, Bruce, Australian Capital Territory, Canberra 2617, Australia"},{"name":"Department of Jobs, Precincts and Regions, Microbial Sciences, Pests &amp; Diseases, Agriculture Victoria, AgriBio Centre, La Trobe University, 5 Ring Rd, Bundoora, Victoria 3083, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Brendan","family":"Rodoni","sequence":"additional","affiliation":[{"name":"Plant Biosecurity Cooperative Research Centre, CRC for National Plant Biosecurity, Level 2, Building 22, Innovation Centre, University Drive, University of Canberra, Bruce, Australian Capital Territory, Canberra 2617, Australia"},{"name":"Department of Jobs, Precincts and Regions, Microbial Sciences, Pests &amp; Diseases, Agriculture Victoria, AgriBio Centre, La Trobe University, 5 Ring Rd, Bundoora, Victoria 3083, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James P.","family":"Stack","sequence":"additional","affiliation":[{"name":"Department of Plant Pathology, Kansas State University, 1712 Claflin Road, 4024 Throckmorton Plant Science Center, Manhattan, KS 66506, USA"},{"name":"Plant Biosecurity Cooperative Research Centre, CRC for National Plant Biosecurity, Level 2, Building 22, Innovation Centre, University Drive, University of Canberra, Bruce, Australian Capital Territory, Canberra 2617, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2020,3,5]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1099\/00207713-43-1-143","article-title":"Rathayibacter gen. nov., including the species Rathayibacter rathayi comb. nov., Rathayibacter tritici comb. nov., Rathayibacter iranicus comb. nov., and six strains from annual grasses","volume":"43","author":"Zgurskaya","year":"1993","journal-title":"Int. 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