However, the relationships between X albilineans, Xylella and th

However, the relationships between X. albilineans, Xylella and the other Xanthomonas remain unclear. Another shared feature between Xylella fastidiosa and X. albilineans is the reduced genome. The reductions in these genomes were previously shown to be due to independent events [42]. Here we show evidence suggesting that reductive genome evolution

could also affect other clades in the genus such as X. vasicola. The phylogenetic relationship between X. albilineans, Xylella fastidiosa and the rest of the taxa in the genus Xanthomonas is not clear. The genome of X. albilineans is part of the “”early-branching species”" [7], a group of species including X. albilineans and X. sacchari previously found to be basal in the phylogeny of the genus [7, 35]. The species is also a member of the “”hyacinthii”" group, a group of species with major differences in the 16S-23S rDNA Intergenic Spacer (ITS) with respect to the other members of the genus [32]. Pieretti and collaborators [42] suggested that Xylella and X. albilineans form a monophyletic clade, which is basal to the rest of Xanthomonas. This is based on a Maximum Likelihood analysis with seven housekeeping genes. Our analyses with over two hundred genes suggest that X. albilineans

is basal to Xylella and the rest SN-38 mouse of taxa in the genus Xanthomonas. Neither of the analyses obtains a good support value for these nodes. The most straightforward Cetuximab order explanation for this is that certain regions of the genome support one topology and certain others support the second one. This could be due to a considerable Cl-amidine ic50 number of LGT in these genomes.

Alternatively, it could be due to the large amount of changes accumulated in Xylella fastidiosa, as revealed by the length of the corresponding branch (Figure 2b). The phylogenetic tree presented in Figure 2a displays identical topology and similar relative branch lengths as inferred by different optimality criteria (Maximum Likelihood, Bayesian Inference, Maximum Parsimony). The tree supports monophyly in the species X. campestris, X. oryzae and X. vasicola. The clade “”X. axonopodis”" contains the species X. fuscans, X. citri, X. axonopodis and X. euvesicatoria. However, the lower coverage in terms of sequenced genomes of these species makes it difficult to support any further observation beyond the close relatedness within the clade with respect to other species. Interestingly, the phylogeny displays a close relationship between the species X. fuscans and X. citri. In order to compare their similarity in the same framework of MLSA performed for other species of Xanthomonas (e.g., [31]), we constructed a matrix containing 989 loci employed for the phylogenetic inference (Table 2). According to the resulting matrix, a similarity threshold of 99% can differentiate bacteria recognized as belonging to the different pathovars (except in X.

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