Prevalence of Xanthomonas translucens, which causes cereal leaf streak (CLS) in cereal crops and bacterial wilt in forage and turfgrass species, has increased in many regions in recent years. Because the pathogen is seedborne in economically important cereals, it is a concern for international and interstate germplasm exchange, and thus, reliable and robust protocols for its detection in seed are needed. However, historical confusion surrounding the taxonomy within the species has complicated the development of accurate and reliable diagnostic tools for X. translucens. Therefore, we sequenced genomes of 15 X. translucens strains representing six different pathovars and compared them with additional publicly available X. translucens genome sequences to obtain a genome-based phylogeny for robust classification of this species. Our results reveal three main clusters: one consisting of pathovar cerealis, one consisting of pathovars undulosa and translucens, and a third one consisting of pathovars arrhenatheri, graminis, phlei and poae. Based on genomic differences, diagnostic Loop Mediated Isothermal Amplification (LAMP) primers were developed that clearly distinguish strains that cause disease on cereals, such as pathovars undulosa, translucens, hordei, and secalis, from strains that cause disease on non-cereal hosts, such as pathovars arrhenatheri, cerealis, graminis, phlei and poae. Additional LAMP assays were developed that selectively amplify strains belonging to pathovars cerealis and poae, distinguishing them from other pathovars. These primers will be instrumental in diagnostics when implementing quarantine regulations to limit further geographic spread of X. translucens pathovars.
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