title: Comparative genomics reveals genes significantly associated with woody hosts in the plant pathogen Pseudomonas syringae.
abstract: The diversification of lineages within Pseudomonas syringae has involved a number of adaptive shifts from herbaceous hosts onto various species of tree, resulting in the emergence of highly destructive diseases such as bacterial canker of kiwi and bleeding canker of horse chestnut. This diversification has involved a high level of gene gain and loss, and these processes are likely to play major roles in the adaptation of individual lineages onto their host plants. In order to better understand the evolution of P. syringae onto woody plants, we have generated de novo genome sequences for 26 strains from the P. syringae species complex that are pathogenic on a range of woody species, and have looked for statistically significant associations between gene presence and host type (i.e. woody or herbaceous) across a phylogeny of 64 strains. We have found evidence for a common set of genes associated with strains that are able to colonize woody plants, suggesting that divergent lineages have acquired similarities in genome composition that may form the genetic basis of their adaptation to woody hosts. We also describe in detail the gain, loss and rearrangement of specific loci that may be functionally important in facilitating this adaptive shift. Overall, our analyses allow for a greater understanding of how gene gain and loss may contribute to adaptation in P. syringae.
authors.affiliation: Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK.|Centre for Ecosystems, Society and Biosecurity, Forest Research, Midlothian EH25 9SY, UK.
authors.forename: Reuben W
authors.initials: RW
authors.lastname: Nowell
authors.affiliation: Centre for Ecosystems, Society and Biosecurity, Forest Research, Midlothian EH25 9SY, UK.
authors.forename: Bridget E
authors.initials: BE
authors.lastname: Laue
authors.affiliation: Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK.|Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK.
authors.forename: Paul M
authors.initials: PM
authors.lastname: Sharp
authors.affiliation: Centre for Ecosystems, Society and Biosecurity, Forest Research, Midlothian EH25 9SY, UK.
authors.forename: Sarah
authors.initials: S
authors.lastname: Green
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D000272:Adipates / Q000378:metabolism; D058947:Bacterial Secretion Systems / Q000235:genetics; D005798:Genes, Bacterial; D023281:Genomics; D054884:Host-Pathogen Interactions / Q000235:genetics*; D016013:Likelihood Functions; D009876:Operon / Q000235:genetics; D010802:Phylogeny; D010935:Plant Diseases / Q000235:genetics / Q000382:microbiology; D044224:Pseudomonas syringae / Q000235:genetics* / Q000472:pathogenicity*; D017422:Sequence Analysis, DNA; D014774:Virulence / Q000235:genetics; D014934:Wood / Q000382:microbiology*
chemical_list: D000272:Adipates; D058947:Bacterial Secretion Systems; C027316:3-oxoadipic acid
keywords: adaptation; genome fluctuation, Pseudomonas syringae; woody hosts