title: Population genomics of the facultatively mutualistic bacteria Sinorhizobium meliloti and S. medicae.
abstract: The symbiosis between rhizobial bacteria and legume plants has served as a model for investigating the genetics of nitrogen fixation and the evolution of facultative mutualism. We used deep sequence coverage (>100×) to characterize genomic diversity at the nucleotide level among 12 Sinorhizobium medicae and 32 S. meliloti strains. Although these species are closely related and share host plants, based on the ratio of shared polymorphisms to fixed differences we found that horizontal gene transfer (HGT) between these species was confined almost exclusively to plasmid genes. Three multi-genic regions that show the strongest evidence of HGT harbor genes directly involved in establishing or maintaining the mutualism with host plants. In both species, nucleotide diversity is 1.5-2.5 times greater on the plasmids than chromosomes. Interestingly, nucleotide diversity in S. meliloti but not S. medicae is highly structured along the chromosome - with mean diversity (θ(π)) on one half of the chromosome five times greater than mean diversity on the other half. Based on the ratio of plasmid to chromosome diversity, this appears to be due to severely reduced diversity on the chromosome half with less diversity, which is consistent with extensive hitchhiking along with a selective sweep. Frequency-spectrum based tests identified 82 genes with a signature of adaptive evolution in one species or another but none of the genes were identified in both species. Based upon available functional information, several genes identified as targets of selection are likely to alter the symbiosis with the host plant, making them attractive targets for further functional characterization.
authors.affiliation: Department of Plant Biology, University of Minnesota, St Paul, Minnesota, United States of America.
authors.forename: Brendan
authors.initials: B
authors.lastname: Epstein
authors.forename: Antoine
authors.initials: A
authors.lastname: Branca
authors.forename: Joann
authors.initials: J
authors.lastname: Mudge
authors.forename: Arvind K
authors.initials: AK
authors.lastname: Bharti
authors.forename: Roman
authors.initials: R
authors.lastname: Briskine
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Farmer
authors.forename: Masayuki
authors.initials: M
authors.lastname: Sugawara
authors.forename: Nevin D
authors.initials: ND
authors.lastname: Young
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Sadowsky
authors.forename: Peter
authors.initials: P
authors.lastname: Tiffin
mesh_terms: D005075:Biological Evolution; D002876:Chromosomes, Bacterial; D022761:Gene Transfer, Horizontal; D046913:Medicago truncatula / Q000382:microbiology*; D056186:Metagenomics; D009586:Nitrogen Fixation / Q000235:genetics; D010802:Phylogeny; D010957:Plasmids / Q000235:genetics; D011110:Polymorphism, Genetic; D012336:RNA, Ribosomal, 16S / Q000145:classification / Q000235:genetics*; D017422:Sequence Analysis, DNA; D020579:Sinorhizobium / Q000145:classification / Q000235:genetics*; D016962:Sinorhizobium meliloti / Q000145:classification / Q000235:genetics*; D013559:Symbiosis / Q000235:genetics
chemical_list: D012336:RNA, Ribosomal, 16S