Evolutionary History of the Plant Pathogenic Bacterium Xanthomonas axonopodis

et al. (2013) Evolutionary History of the Plant Pathogenic Bacterium Xanthomonas axonopodis. PLoS ONE 8(3): e58474. doi:10.1371/journal.pone.0058474 Evolutionary History of the Plant Pathogenic Bacterium Xanthomonas axonopodis Nadia Mhedbi-Hajri 0 Ahmed Hajri 0 Tristan Boureau 0 Armelle Darrasse 0 Karine Durand 0 Chrystelle Brin 0 Marion Fischer-Le Saux 0 Charles Manceau 0 Ste phane Poussier 0 Olivier Pruvost 0 Christophe Lemaire 0 Marie-Agne` s Jacques 0 Keith A. Crandall, George Washington University, United States of America 0 1 INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouze , France, 2 Universite d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences , SFR4207 QUASAV, PRES L'UNAM, Angers, France, 3 AgroCampus-Ouest , UMR1345 Institut de Recherche en Horticulture et Semences , Angers, France, 4 CIRAD, UMR PVBMT, Saint Pierre, Cedex Re union , France Deciphering mechanisms shaping bacterial diversity should help to build tools to predict the emergence of infectious diseases. Xanthomonads are plant pathogenic bacteria found worldwide. Xanthomonas axonopodis is a genetically heterogeneous species clustering, into six groups, strains that are collectively pathogenic on a large number of plants. However, each strain displays a narrow host range. We address the question of the nature of the evolutionary processes - geographical and ecological speciation - that shaped this diversity. We assembled a large collection of X. axonopodis strains that were isolated over a long period, over continents, and from various hosts. Based on the sequence analysis of seven housekeeping genes, we found that recombination occurred as frequently as point mutation in the evolutionary history of X. axonopodis. However, the impact of recombination was about three times greater than the impact of mutation on the diversity observed in the whole dataset. We then reconstructed the clonal genealogy of the strains using coalescent and genealogy approaches and we studied the diversification of the pathogen using a model of divergence with migration. The suggested scenario involves a first step of generalist diversification that spanned over the last 25 000 years. A second step of ecology-driven specialization occurred during the past two centuries. Eventually, secondary contacts between hostspecialized strains probably occurred as a result of agricultural development and intensification, allowing genetic exchanges of virulence-associated genes. These transfers may have favored the emergence of novel pathotypes. Finally, we argue that the largest ecological entity within X. axonopodis is the pathovar. - Funding: N. Mhedbi-Hajri and A. Hajri were supported by grants from the Tunisian Government, from CG Maine et Loire and from INRA. This study was funded by the Region Pays de la Loire (Xanthost) and the Plant Health and Environment Department of INRA (SPE 2007-0077-01, AIP Bioressources 2008-077-01). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. . These authors contributed equally to this work. Determining the relative part played by geography and ecological specialization in the reproductive isolation between populations of pathogens is still a great challenge [1], [2]. The extent of isolation between pathogen populations is conditioned by the divergence accumulated in allopatry or by the degree of adaptation to hosts. In complete allopatry, genetic reproductive barriers are less likely to be selected than in sympatry [3], and gene flow remains possible for populations that have diverged for a long time (several million years) [4]. Conversely, specialization on hosts greatly contributes to reproductive isolation and limits gene flow. Host specialization was promoted by plant domestication, which led to a reduction of host genetic variability, and by the development of agriculture, which has uniformized crops and increased host density [5]. More recently, the globalization of agriculture has strongly contributed to breaking natural barriers to dispersal, thereby reducing the geographic isolation and increasing opportunities for gene flow. Subsequent propagation of many pathogens allowed secondary contacts between populations, which have diverged in allopatry [6]. Would such a return to sympatry be sufficient to promote gene flow between these populations of pathogens? The study of the relative importance of gene flow and divergence times between populations occupying different hosts then becomes crucial for understanding evolutionary histories and emergences of pathogens [7], [8]. Unlike for sexual eukaryotes, the classical biological species definition does not apply for prokaryotes, which are asexually reproducing organisms. Bacteria, rather, form ecologically isolated units called ecotypes [9]. The pathovar is an infrasubspecific division that was created to group pathogenic bacteria that display the same symptomatology on the same host range [10]. Would the ecological cohesion of the ecotype concept be found in the pathovar concept? The extent of reproductive isolation among pathovars remains to be clarified, because ecological isolation may be associated with reproductive isolation. Bacteria are mainly clonal but can exchange genes or fragments of their genomes through horizontal gene transfer. Such transfers would be interpreted as recombination events in molecular polymorphism studies. Under the biological species concept for eukaryotes, reproductive isolation can be monitored by a strong decrease in recombination rates between species. In prokaryotes, sequence divergence, as a factor potentially involved in the decrease of recombination efficiency, would play only a little role in the genetic cohesion of bacterial species [11]. Recombination rates are not expected to be homogeneous among loci. Niche-neutral genes such as housekeeping genes are expected to recombine more freely than niche-specifying-genes [12]. For the latter, their transfer into a focus population adapted to a different niche implies a fitness cost resulting in negligible recombination rates. Alternatively, some virulence-associated (VA) genes may act as niche-transcending (NT) genes. NT genes confer a gain of fitness when transferred to a new ecotype (adaptive introgression). The increasing genetic exchanges among strains, due to agricultural globalization, may involve horizontal gene transfer of NT (VA) genes. In the latter case, the emergence of strains with new pathological competences becomes likely. Bacteria belonging to the genus Xanthomonas are collectively responsible for diseases on more than 400 different host plants, among which many are economically important crops [13]. The physiological characteristics of Xanthomonas are very homogeneous. However, the diversity within this genus is highlighted by path (...truncated)