Xanthomonas citri pv. malvacearum Genome sequencing and assembly. Xanthomonas citri pv. malvacearum

Cotton bacterial blight (CBB), caused by Xanthomonas citri pv. malvacearum (Xcm), significantly limited cotton yields in the early 20th century, but has been controlled by classical resistance genes for more than 50 years. However, the pathogen re-emerged in the southern US in 2011. Differences in virulence were observed among Xcm strains at the molecular and phenotypic level. AR81009 (CFBP2035) was isolated in Argentina in 1981 and is one of the most virulent strains investigated in this study. MS14003 was isolated in Mississippi and causes comparatively slower and diminished leaf symptoms; however, both strains are able to multiply and cause disease on susceptible varieties of cotton. Full genome sequences were generated with Single Molecule Real-Time (SMRT) sequencing. Genomes were assembled using the PacBio Falcon assembler which yielded circular 5Mb genomes and associated plasmids. MS14003 contains three plasmids (52.4, 47.4, and 15.3kb) while AR81009 contains two plasmids (92.6 and 22.9kb). The long reads obtained from SMRT sequencing are able to span whole TAL effectors, allowing for full assemblies of the TAL effectors in each strain. The AR81009 genome encodes twelve TAL effectors that range in size from twelve to twenty three repeat lengths, six of which reside on plasmids. The MS14003 genome encodes eight TAL effectors that range in size from fourteen to twenty eight repeat lengths, seven of which reside on plasmids. The tool AnnoTALE was used to annotate and group TAL effectors based on the identities of the repeat variable diresidues (RVDs) in each gene.