Abstract
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.
Highlights
The genus Rathayibacter was described relatively recently [1] and comprises nine species of Gram-positive plant-pathogenic bacteria, including R. agropyri [2,3], R. caricis [4], R. festucae [4], R. iranicus [1], R. oskolensis [5], R. rathayi [1], R. tanaceti [6], R. toxicus [7,8] and R. tritici [1]
A simple analysis of the subsystems between populations would suggest that RT-I is most similar to RT-IV, as is RT-II and RT-III, based on number and types of subsystems
All five R. toxicus populations contain a clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated proteins (Cas) system and vancomycin resistance genes; the CRISPR-Cas system appears most similar to a type I-E CRISPR-Cas system (Escherichia coli-type) [19]
Summary
The genus Rathayibacter was described relatively recently [1] and comprises nine species of Gram-positive plant-pathogenic bacteria, including R. agropyri [2,3], R. caricis [4], R. festucae [4], R. iranicus [1], R. oskolensis [5], R. rathayi [1], R. tanaceti [6], R. toxicus [7,8] and R. tritici [1]. Rathayibacter toxicus [7,8] infects several grass species in the family Poaceae [9], including annual ryegrass (Lolium rigidum) [10], annual beard grass (Polypogon monspeliensis) [11,12], and bent or blown grass (Agrostis avenacea) [12]. Like other Rathayibacter species, R. toxicus is vectored by several species of seed-gall nematodes in the genus Anguina [9,11,12,13,14,15]; the nematode vector determines the plant host that R. toxicus infects. Rathayibacter toxicus-induced toxicities are known in Australia as annual ryegrass toxicity (ARGT), flood plain staggers and Stewart’s Range syndrome [7,10,13,17,25,26]
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