The early events underlying genome evolution in a localized Sinorhizobium meliloti population

Abstract

Background: Population genetic analyses based on genome-wide sequencing data have been carried out for Sinorhizobium medicae and S. meliloti, two closely related bacterial species forming nitrogen-fixing symbioses with plants of the genus Medicago. However, genome coverage was low or the isolates had a broad geographic distribution, making it difficult to interpret the estimated diversity and to unravel the early events underlying population genetic variations and ecological differentiation.

Results: Here, to gain insight into the early genome level variation and diversification within S. meliloti populations, we first used Illumina paired-end reads technology to sequence a new clone of S. meliloti strain GR4, a highly competitive strain for alfalfa nodulation. The Illumina data and the GR4 genome sequence previously obtained with 454 technology were used to generate a high-quality reference genome sequence. We then used Illumina technology to sequence the genomes of 13 S. meliloti isolates representative of the genomic variation within the GR4-type population, obtained from a single field site with a high degree of coverage. The genome sequences obtained were analyzed to determine nucleotide diversity, divergence times, polymorphism and genomic variation. Similar low levels of nucleotide diversity were observed for the chromosome, pSymB and pSymA replicons. The isolates displayed other types of variation, such as indels, recombination events, genomic island excision and the transposition of mobile elements.

Conclusions: Our results suggest that the GR4-type population has experienced a process of demographic expansion and behaves as a stable genotypic cluster of genome-wide similarity, with most of the genome following a clonal pattern of evolution. Although some of genetic variation detected within the GR4-type population is probably due to genetic drift, others might be important in diversification and environmental adaptation.

Keywords: Diversity; Genome-wide sequencing; Genomic islands; Group II introns; Illumina technology; Insertion sequences; Polymorphism; Population genomics; Recombination.

Fig. 1

Distribution of SNPs on the replicons. The names of the replicons are indicated. sSNPs are indicated in blue, nsSNPs in pink and iSNPs are shown in black. Light green and white background, respectively; indicate island and non-island regions in the most likely global assignment of CpG islands to the sequence. To improve their visualization the SNPs are placed out of the sequence

Fig. 2

Phylogeny of GR4-type isolates based on alignments of SNP types. Phylogeny based on all SNPs (370 nt positions). Phylogenetic trees were inferred from Bayesian analyses and posterior probabilities (≥50 %) are indicated at the nodes. The names of the isolates and clades are indicated

Fig. 3

Mismatch distribution analysis for concatenated genes carrying SNPs. Graphs of the mismatch distribution are shown for each replicon and for the two halves of the chromosome. The x-axis shows the observed distribution of pairwise nucleotide differences, with frequency plotted on the y-axis. The values of the moment estimator Tau (τ), and the Raggedness index r and R ₂ statistics are shown

Fig. 4

The maximum clade credibility tree estimated with BEAST 2, based on concatenated genes carrying SNPs. a Chromosome. b pSymB. c pSymA. d All concatenated genes carrying SNPs. Node bars indicate the 95 % credible intervals (95 % HPD) for node ages, and posterior probabilities (>0.5) are indicated (in italics) on the branches. Relevant node ages (years) and clades are indicated. The root of the unrooted tree was placed at the mid-point of the longest distance between two taxa in the tree

Fig. 5

Bayesian skyline plots based on the concatenated genes carrying SNPs for each replicon. a Chromosome. b pSymB. c pSymA. d All concatenated genes carrying SNPs. The median estimates are shown as solid lines, and the blue areas indicate the limits of the 95 % HPD. The vertical line indicates the beginning of the stabilization period. Time (x-axis) is expressed in years ago. The effective population size is indicated on the y-axis

Fig. 6

Pyrimidine/purine dinucleotide CT/GA-rich MRI (mid-range inhomogeneity) region. The identified MRI and flanking sequences in the pSymA of GR4-type isolates and that conserved on the chromosomes of S. meliloti and S. medicae are shown. Residues in color are different from the consensus sequence. The location of the replicon and GenBank accession numbers are shown