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Comparative Genomic Analysis Confirms Five Genetic Populations of the Select Agent, Rathayibacter toxicus

1
Department of Plant Pathology, Kansas State University, 1712 Claflin Road, 4024 Throckmorton Plant Science Center, Manhattan, KS 66506, USA
2
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
3
Department of Plant and Environmental Protection Sciences, University of Hawai`i at Mānoa, Honolulu, HI 96822, USA
4
Department of Jobs, Precincts and Regions, Microbial Sciences, Pests & Diseases, Agriculture Victoria, AgriBio Centre, La Trobe University, 5 Ring Rd, Bundoora, Victoria 3083, Australia
*
Author to whom correspondence should be addressed.
Microorganisms 2020, 8(3), 366; https://doi.org/10.3390/microorganisms8030366
Received: 14 January 2020 / Revised: 24 February 2020 / Accepted: 3 March 2020 / Published: 5 March 2020
(This article belongs to the Section Environmental Microbiology)
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 ↔ RT-I ↔ RT-II ↔ RT-III ↔ 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. View Full-Text
Keywords: Rathayibacter toxicus; annual ryegrass toxicity; flood plain staggers; Stuart’s range syndrome; comparative genomics; populations Rathayibacter toxicus; annual ryegrass toxicity; flood plain staggers; Stuart’s range syndrome; comparative genomics; populations
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Yasuhara-Bell, J.; Arif, M.; Busot, G.Y.; Mann, R.; Rodoni, B.; Stack, J.P. Comparative Genomic Analysis Confirms Five Genetic Populations of the Select Agent, Rathayibacter toxicus. Microorganisms 2020, 8, 366.

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