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Logo of bmcmicrBioMed Centralsearchsubmit a manuscriptregisterthis articleBMC Microbiology
 
BMC Microbiol. 2012; 12: 43.
Published online Mar 23, 2012. doi:  10.1186/1471-2180-12-43
PMCID: PMC3359215
Genomes-based phylogeny of the genus Xanthomonas
Luis M Rodriguez-R,1,5 Alejandro Grajales,2 Mario L Arrieta-Ortiz,1 Camilo Salazar,3,4 Silvia Restrepo,1 and Adriana Bernalcorresponding author1
1Laboratory of Mycology and Plant Pathology, Biological Sciences Department, Universidad de Los Andes, Cra 1 No 18A-12, Bogotá, Colombia
2Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, 10024-5192 New York, NY, USA
3Smithsonian Tropical Research Institute, Roosvelt Ave. Tupper Building, Panama 0843-03092, Panama
4University of Cambridge, The Old Schools, Trinity Lane, Cambridge CB2 1TN, UK
5Department of Biology, Georgia Institute of Technology, 311 Ferst Drive, 30332 Atlanta, GA, USA
corresponding authorCorresponding author.
Luis M Rodriguez-R: lrr/at/gatech.edu; Alejandro Grajales: alejogr/at/gmail.com; Mario L Arrieta-Ortiz: m-arriet/at/uniandes.edu.co; Camilo Salazar: salazarc/at/si.edu; Silvia Restrepo: srestrep/at/uniandes.edu.co; Adriana Bernal: abernal/at/uniandes.edu.co
Received July 18, 2011; Accepted March 23, 2012.
Abstract
Background
The 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.
Results
Here 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.
Conclusions
Our 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.
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