Abstract
BackgroundMost 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.ResultsWe 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.ConclusionOur 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.
Highlights
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
Bacterial species typically contain large amounts of genetic variation in the form of single nucleotide polymorphisms (SNPs), which originate by mutation and have dynamics that depend on the balance between natural selection and genetic drift [1,2]
Stringent parameters were used to identify high-quality SNPs in a set of two complete R. etli genomes, CFN42 and CIAT652, isolated from México and Costa Rica respectively, and six draft genome sequences from strains isolated in different places of the world: BRASIL5 (Brazil), CIAT894 (Colombia), GR56, IE4771 (México), KIM5 (USA), and 8C-3 and GR56 (Spain) [24]
Summary
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. Species have been genetically defined through the analysis of DNA variation using comparative techniques such as hybridization, the sequencing of gene markers, and (more recently) complete genome sequences [4,5]. It has content [10]. These comparative methods rely on the availability of complete genome sequences and are affected by the quality of the DNA sequencing data, which in the case of draft genomes might not be optimal [10]. One exception was the comparisons made by Richter and Roselló-Mora [10], who suggested that low genome sequence coverage can be sufficient for inferring DNA similarity values comparable to ANI obtained with complete genomes
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