Genomes-based phylogeny of the genus Xanthomonas

Luis M Rodriguez-R,Alejandro Grajales,Camilo Salazar,Adriana Bernal,Silvia Restrepo,Mario L Arrieta-Ortiz

doi:10.1186/1471-2180-12-43

Abstract

BackgroundThe genus Xanthomonas comprises several plant pathogenic bacteria affecting a wide range of hosts. Despite the economic, industrial and biological importance of Xanthomonas, the classification and phylogenetic relationships within the genus are still under active debate. Some of the relationships between pathovars and species have not been thoroughly clarified, with old pathovars becoming new species. A change in the genus name has been recently suggested for Xanthomonas albilineans, an early branching species currently located in this genus, but a thorough phylogenomic reconstruction would aid in solving these and other discrepancies in this genus.ResultsHere we report the results of the genome-wide analysis of DNA sequences from 989 orthologous groups from 17 Xanthomonas spp. genomes available to date, representing all major lineages within the genus. The phylogenetic and computational analyses used in this study have been automated in a Perl package designated Unus, which provides a framework for phylogenomic analyses which can be applied to other datasets at the genomic level. Unus can also be easily incorporated into other phylogenomic pipelines.ConclusionsOur phylogeny agrees with previous phylogenetic topologies on the genus, but revealed that the genomes of Xanthomonas citri and Xanthomonas fuscans belong to the same species, and that of Xanthomonas albilineans is basal to the joint clade of Xanthomonas and Xylella fastidiosa. Genome reduction was identified in the species Xanthomonas vasicola in addition to the previously identified reduction in Xanthomonas albilineans. Lateral gene transfer was also observed in two gene clusters.

Highlights

The genus Xanthomonas comprises several plant pathogenic bacteria affecting a wide range of hosts
The automated selection of orthologous genes is consistent with manual selection In order to compare a typical literature-based selection of genes for phylogenetic reconstruction in bacteria with the Unus automated method, using 989 genes in the genomes listed in Table 1, we evaluated the presence of the housekeeping genes used by AMPHORA [41]
A previous Multi Locus Sequence Analysis (MLSA) conducted by Young and collaborators [31] employed four protein-coding genes included in the previous lists plus the tonB-dependent receptor fyuA, present in our selection

Summary

Introduction

The genus Xanthomonas comprises several plant pathogenic bacteria affecting a wide range of hosts. Xanthomonas is a genus in the gamma division of Proteobacteria primarily constituted by pathogens to plants of considerable economic importance These pathogens affect a wide variety of crops, including Citrus spp. A general classification has been established based on polyphasic analysis [6,17], while other analyses helped to clarify the classification in specific clades, mainly using Multi Locus Sequence Analysis (MLSA) and Amplified Fragment Length Polymorphism (AFLP) [18,19] This allowed the development of several typing and characterization tools (e.g., [11,18,19,20,21,22,23,24]), which have revealed the diversity and complexity of the genus [23,24], while showing the limitations of single locus analyses [25]. Genus-wide reclassifications have been proposed [26,27], and frequent sub-specific reclassifications and proposals for new species have been published [19,20,21,28,29,30]

Methods

Results

Discussion

Conclusion