DOI: 10.5061/dryad.8t53k
title: Data from: Comparative genomics of 43 strains of Xanthomonas citri pv. citri reveals the evolutionary events giving rise to pathotypes with different host ranges

description: 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.
description: Xanthomonas citri - 44
 strain Mugsy genome alignmentA multiple genome
 alignment of 44 strains of Xanthomonas citri output from the Mugsy genome
 alignment softwareXanthomonas_citri_44_strain_Mugsy_genome_alignment.mafXanthomonas citri - 44 strain PhyML phylogeny SYM modelA maximum likelihood phylogenetic tree constructed with PhyML from the genome alignment of 44 strains of Xanthomonas citri. Regions of recombination were removed from the alignment as well as gap-containing columns and +/- 20bp from a gap-containing column. The evolutionary model used was SYM, as chosen with jModeltest 2.1.7.Xanthomonas_citri_44_strain_PhyML_phylogeny_SYM_model.nwkXanthomonas citri - 44 strain concatenated genome alignment (recombination, gaps +/- 20nt removed) FASTA formatA FASTA format multiple sequence alignment used for phylogenetic reconstruction. The alignment was constructed by concatenating blocks from a whole genome multiple alignment using the IAPAR 306 strain to order blocks. Regions of recombination detected using RDP were removed, as were gap-containing columns and 20 nt surrounding gap-containing columns.Xanthomonas_citri_44_strain_concatenated_genome_alignment_gaps+20nt_removed_no_recomb.fastaXanthomonas citri - 36 strain PhyML phylogeny GTR model, Reduced A-strain distribution, Contains recombinationA maximum likelihood phylogenetic tree constructed with PhyML from the genome alignment of 36 strains of Xanthomonas citri. The alignment contains regions of recombination and the distibution of A pathotype strains is reduced to only those containing recombination Event 16. The evolutionary model used was GTR.Xanthomonas_citri_36_strain_concatenated_genome_alignment_phylogeny_GTR_model.nwkXanthomonas citri - 36 strain concatenated genome alignment (gaps +/- 20nt removed) FASTA format, Contains recombinationA FASTA format multiple sequence alignment used for phylogenetic reconstruction. The alignment was constructed by concatenating blocks from a whole genome multiple alignment using the IAPAR 306 strain to order blocks. Gap-containing columns and 20 nt surrounding gap-containing columns were removed. The alignment contains regions of recombination and the distibution of A pathotype strains is reduced to only those containing recombination event 16.Xanthomonas_citri_36_strain_concatenated_genome_alignment_gaps+20nt_removed_+recomb.fasta