MULTIPLE GENE GENEALOGICAL ANALYSIS OF SINORHIZOBIUMMELILOTI

Abstract

Sinorhizobium meliloti is an economically important bacterium as it forms nodules on and fixes nitrogen for alfalfa, an important agricultural crop. The complete genome of a laboratory strain, Rml021, was published in 2001 and this strain was found to have three replicons: a chromosome with 3.65 million base pairs (MB) and two megaplasmids called pSymA (1.35 MB) and pSymB (1.68 MB). In this study, I sequenced 3 genes from each replicon (9 genes total) for each of 33 natural S. meliloti strains and analyzed the DNA sequence variation. The mean sequence divergence between strains varied significantly among the nine genes, ranging from 0.11% to 5.02%. Overall, the three genes located on the chromosome showed a lower level polymorphism than those on pSymA and pSymB. My population genetic analyses revealed that: (i) within each ofthe nine genes, polymorphic nucleotide sites were in significant linkage disequilibrium (LD); (ii) between genes within a replicon, those on the chromosome were in significant LD while those on the two megaplasmids were in linkage equilibrium (LE); and (iii) between genes on different replicons, a variable proportion showed LD. Gene genealogical analysis indicated a lack of host or geographic pattern for the observed molecular variation. My results suggest a dynamic pattern ofmolecular evolution in the genomes of natural strains ofS. meliloti.