Abstract
Multiple species of Xanthomonas cause bacterial spot of tomato (BST) and pepper. We sequenced five Xanthomonas euvesicatoria strains isolated from three continents (Africa, Asia, and South America) to provide a set of representative genomes with temporal and geographic diversity. LMG strains 667, 905, 909, and 933 were pathogenic on tomato and pepper, except LMG 918 elicited a hypersensitive reaction (HR) on tomato. Furthermore, LMG 667, 909, and 918 elicited a HR on Early Cal Wonder 30R containing Bs3. We examined pectolytic activity and starch hydrolysis, two tests which are useful in differentiating X. euvesicatoria from X. perforans, both causal agents of BST. LMG strains 905, 909, 918, and 933 were nonpectolytic while only LMG 918 was amylolytic. These results suggest that LMG 918 is atypical of X. euvesicatoria. Sequence analysis of all the publicly available X. euvesicatoria and X. perforans strains comparing seven housekeeping genes identified seven haplotypes with few polymorphisms. Whole genome comparison by average nucleotide identity (ANI) resulted in values of >99% among the LMG strains 667, 905, 909, 918, and 933 and X. euvesicatoria strains and >99.6% among the LMG strains and a subset of X. perforans strains. These results suggest that X. euvesicatoria and X. perforans should be considered a single species. ANI values between strains of X. euvesicatoria, X. perforans, X. allii, X. alfalfa subsp. citrumelonis, X. dieffenbachiae, and a recently described pathogen of rose were >97.8% suggesting these pathogens should be a single species and recognized as X. euvesicatoria. Analysis of the newly sequenced X. euvesicatoria strains revealed interesting findings among the type 3 (T3) effectors, relatively ancient stepwise erosion of some T3 effectors, additional X. euvesicatoria-specific T3 effectors among the causal agents of BST, orthologs of avrBs3 and avrBs4, and T3 effectors shared among xanthomonads pathogenic against various hosts. The results from this study supports the finding that T3 effector repertoire and host range are fundamental for the study of host—microbe interaction but of little relevance to bacterial speciation.
Highlights
The genus Xanthomonas includes numerous phytopathogenic bacteria
By average nucleotide identity (ANI), we examined the phylogeny of X. euvesicatoria, X. perforans, X. allii, X. alfalfa subsp. citrumelonis, and X. dieffenbachiae, members of Rademaker group 9.2
Since ANI is considered the new standard for species definition, these results suggest that the strains sequenced in this study are X. euvesicatoria and that X. perforans strains should be considered X. euvesicatoria, similar to the findings of others (Young et al, 2008; Constantin et al, 2016)
Summary
The genus Xanthomonas includes numerous phytopathogenic bacteria. While the physiological characteristics of Xanthomonas are quite homogeneous, biological diversity is evident in that the phytopathogenic xanthomonads cause disease on more than 400 hosts, ranging across 11 monocotyledonous, and 57 dicotyledonous families (Leyns et al, 1984). These results suggest differences in the functional type 3 effectors among the LMG strains which we examined following genome sequencing. Results from the comparison of these niche independent genes suggest that a few polymorphisms exist among X. euvesicatoria and X. perforans strains, separating the strains into distinct species is poorly supported by examination of a broad collection of strains.
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