title: Genomic lineages of Rhizobium etli revealed by the extent of nucleotide polymorphisms and low recombination.
abstract: BACKGROUND
  Most of the DNA variations found in bacterial species are in the form of single nucleotide polymorphisms (SNPs), but there is some debate regarding how much of this variation comes from mutation versus recombination. The nitrogen-fixing symbiotic bacteria Rhizobium etli is highly variable in both genomic structure and gene content. However, no previous report has provided a detailed genomic analysis of this variation at nucleotide level or the role of recombination in generating diversity in this bacterium. Here, we compared draft genomic sequences versus complete genomic sequences to obtain reliable measures of genetic diversity and then estimated the role of recombination in the generation of genomic diversity among Rhizobium etli.
  
  
  RESULTS
  We identified high levels of DNA polymorphism in R. etli, and found that there was an average divergence of 4% to 6% among the tested strain pairs. DNA recombination events were estimated to affect 3% to 10% of the genomic sample analyzed. In most instances, the nucleotide diversity (π) was greater in DNA segments with recombinant events than in non-recombinant segments. However, this degree of recombination was not sufficiently large to disrupt the congruence of the phylogenetic trees, and further evaluation of recombination in strains quartets indicated that the recombination levels in this species are proportionally low.
  
  
  CONCLUSIONS
  Our data suggest that R. etli is a species composed of separated lineages with low homologous recombination among the strains. Horizontal gene transfer, particularly via the symbiotic plasmid characteristic of this species, seems to play an important role in diversity but the lineages maintain their evolutionary cohesiveness.
authors: Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad N/C Col. Chamilpa, Apdo. Postal 565-A, Cuernavaca 62210, México. jlacosta@ccg.unam.mx
authors: José L
authors: JL
authors: Acosta
authors: Luis E
authors: LE
authors: Eguiarte
authors: Rosa I
authors: RI
authors: Santamaría
authors: Patricia
authors: P
authors: Bustos
authors: Pablo
authors: P
authors: Vinuesa
authors: Esperanza
authors: E
authors: Martínez-Romero
authors: Guillermo
authors: G
authors: Dávila
authors: Víctor
authors: V
authors: González
mesh_terms: D004269:DNA, Bacterial / Q000235:genetics*; D014644:Genetic Variation; D016680:Genome, Bacterial; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic; D042163:Rhizobium etli / Q000235:genetics*
chemical_list: D004269:DNA, Bacterial