title: Evolutionary dynamics of insertion sequences in relation to the evolutionary histories of the chromosome and symbiotic plasmid genes of Rhizobium etli populations.
abstract: Insertion sequences (IS) are mobile genetic elements that are distributed in many prokaryotes. In particular, in the genomes of the symbiotic nitrogen-fixing bacteria collectively known as rhizobia, IS are fairly abundant in plasmids or chromosomal islands that carry the genes needed for symbiosis. Here, we report an analysis of the distribution and genetic conservation of the IS found in the genome of Rhizobium etli CFN42 in a collection of 87 Rhizobium strains belonging to populations with different geographical origins. We used PCR to generate presence/absence profiles of the 39 IS found in R. etli CFN42 and evaluated whether the IS were located in consistent genomic contexts. We found that the IS from the symbiotic plasmid were frequently present in the analyzed strains, whereas the chromosomal IS were observed less frequently. We then examined the evolutionary dynamics of these strains based on a population genetic analysis of two chromosomal housekeeping genes (glyA and dnaB) and three symbiotic sequences (nodC and the two IS elements). Our results indicate that the IS contained within the symbiotic plasmid have a higher degree of genomic context conservation, lower nucleotide diversity and genetic differentiation, and fewer recombination events than the chromosomal housekeeping genes. These results suggest that the R. etli populations diverged recently in Mexico, that the symbiotic plasmid also had a recent origin, and that the IS elements have undergone a process of cyclic infection and expansion.
authors.affiliation: Centro de Ciencias Genomicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México. llozano@ccg.unam.mx
authors.forename: Luis
authors.initials: L
authors.lastname: Lozano
authors.forename: Ismael
authors.initials: I
authors.lastname: Hernández-González
authors.forename: Patricia
authors.initials: P
authors.lastname: Bustos
authors.forename: Rosa I
authors.initials: RI
authors.lastname: Santamaría
authors.forename: Valeria
authors.initials: V
authors.lastname: Souza
authors.forename: J Peter W
authors.initials: JP
authors.lastname: Young
authors.forename: Guillermo
authors.initials: G
authors.lastname: Dávila
authors.forename: Víctor
authors.initials: V
authors.lastname: González
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D002876:Chromosomes, Bacterial; D016000:Cluster Analysis; D004251:DNA Transposable Elements; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D019143:Evolution, Molecular; D008800:Mexico; D008969:Molecular Sequence Data; D010802:Phylogeny; D010957:Plasmids; D016133:Polymerase Chain Reaction; D011110:Polymorphism, Genetic; D042163:Rhizobium etli / Q000235:genetics*; D017422:Sequence Analysis, DNA; D017385:Sequence Homology
chemical_list: D001426:Bacterial Proteins; D004251:DNA Transposable Elements; D004269:DNA, Bacterial