Whole-Genome Sequences of Xanthomonas euvesicatoria Strains Clarify Taxonomy and Reveal a Stepwise Erosion of Type 3 Effectors

Jeri D Barak; Taca Vancheva; Pierre Lefeuvre; Jeffrey B Jones; Sujan Timilsina; Gerald V Minsavage; Gary E Vallad; Ralf Koebnik

doi:10.3389/fpls.2016.01805

Whole-Genome Sequences of Xanthomonas euvesicatoria Strains Clarify Taxonomy and Reveal a Stepwise Erosion of Type 3 Effectors

Front Plant Sci. 2016 Dec 9:7:1805. doi: 10.3389/fpls.2016.01805. eCollection 2016.

Authors

Jeri D Barak¹, Taca Vancheva², Pierre Lefeuvre³, Jeffrey B Jones⁴, Sujan Timilsina⁴, Gerald V Minsavage⁴, Gary E Vallad⁵, Ralf Koebnik⁶

Affiliations

¹ UMR Interactions - Plantes - Microorganismes - Environnement, IRD-Cirad-Université MontpellierMontpellier, France; Department of Plant Pathology, University of WisconsinMadison, WI, USA.
² UMR Interactions - Plantes - Microorganismes - Environnement, IRD-Cirad-Université MontpellierMontpellier, France; Faculty of Biology, Sofia University St. Kliment OhridskiSofia, Bulgaria.
³ Pôle de Protection des Plantes, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Cirad-Université de la Réunion Saint-Pierre, Ile de la Réunion, France.
⁴ Department of Plant Pathology, University of Florida Gainsville, FL, USA.
⁵ Gulf Coast Research and Education Center, University of Florida Wimauma, FL, USA.
⁶ UMR Interactions - Plantes - Microorganismes - Environnement, IRD-Cirad-Université Montpellier Montpellier, France.

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.

Keywords: HrpX regulon; PIP box; Xanthomonas euvesicatoria; Xanthomonas perforans; cell wall degrading enzymes; comparative genomics; taxonomy; type III effectors.