Data from: Comparative genomics of 43 strains of Xanthomonas citri pv. citri reveals the evolutionary events giving rise to pathotypes with different host ranges

Background: The identification of factors involved in the host range
definition and evolution is a pivotal challenge in the goal to predict and
prevent the emergence of plant bacterial disease. To trace the evolution
and find molecular differences between three pathotypes of Xanthomonas
citri pv. citri that may explain their distinctive host ranges, 42 strains
of X. citri pv. citri and one outgroup strain, Xanthomonas citri pv.
bilvae were sequenced and compared. Results: The strains from each
pathotype form monophyletic clades, with a short branch shared by the Aw
and A pathotypes. Pathotype-specific recombination was detected in seven
regions of the alignment. Using Ancestral Character Estimation, 426 SNPs
were mapped to the four branches at the base of the A, A*, Aw and A/Aw
clades. Several genes containing pathotype-specific nonsynonymous
mutations have functions related to pathogenicity. The A pathotype is
enriched for SNP-containing genes involved in defense mechanisms, while A*
is significantly depleted for genes that are involved in transcription.
The pathotypes differ by four gene islands that largely coincide with
regions of recombination and include genes with a role in virulence. Both
A* and Aw are missing genes involved in defense mechanisms. In contrast to
a recent study, we find that there are an extremely small number of
pathotype-specific gene presences and absences. Conclusions: The three
pathotypes of X. citri pv. citri that differ in their host ranges largely
show genomic differences related to recombination, horizontal gene
transfer and single nucleotide polymorphism. We detail the phylogenetic
relationship of the pathotypes and provide a set of candidate genes
involved in pathotype-specific evolutionary events that could explain to
the differences in host range and pathogenicity between them.