Conserved Symbiotic Plasmid DNA Sequences in the Multireplicon Pangenomic Structure of Rhizobium etli

Abstract

Strains of the same bacterial species often show considerable genomic variation. To examine the extent of such variation in Rhizobium etli, the complete genome sequence of R. etli CIAT652 and the partial genomic sequences of six additional R. etli strains having different geographical origins were determined. The sequences were compared with each other and with the previously reported genome sequence of R. etli CFN42. DNA sequences common to all strains constituted the greater part of these genomes and were localized in both the chromosome and large plasmids. About 700 to 1,000 kb of DNA that did not match sequences of the complete genomes of strains CIAT652 and CFN42 was unique to each R. etli strain. These sequences were distributed throughout the chromosome as individual genes or chromosomal islands and in plasmids, and they encoded accessory functions, such as transport of sugars and amino acids, or secondary metabolism; they also included mobile elements and hypothetical genes. Sequences corresponding to symbiotic plasmids showed high levels of nucleotide identity (about 98 to 99%), whereas chromosomal sequences and the sequences with matches to other plasmids showed lower levels of identity (on average, about 90 to 95%). We concluded that R. etli has a pangenomic structure with a core genome composed of both chromosomal and plasmid sequences, including a highly conserved symbiotic plasmid, despite the overall genomic divergence.

Rhizobial communities in symbiosis with legumes: genetic diversity, competition and interactions with host plants

“…Core genes were found on different plasmid replicons, and not only on chromids. They were maintained in syntenic blocks and revealed high level of nucleotide identity of homologous segments, also in the case of symbiosis-related genes located on pSyms [30]. Thus, the architecture of rhizobial genomes and the classification of replicons as plasmids/chromids or symbiotic/nonsymbiotic plasmids seem to be of minor importance [30,32].…”

“…plasmids) is not straightforward. Although chromosomes of strains are classified into the same species, they may differ substantially with the percentage of unique genes reaching up to 40% of the genome [23,30]. Therefore, the `pan-genome' concept arose, which assumes that the genome of a particular species can be defined only after the analysis of genomes of numerous strains.…”

Rhizobial plasmids — replication, structure and biological role

“…On the contrary, the "accessory" component of the genome has a lower content of G+C, different nucleotide composition from the core, and comprises mainly plasmids. Plasmids are prototypically accessory elements composed of genes from different evolutionary origin; they lack synteny even in closely related species, except for genes involved in plasmid replication and symbiotic properties [17,55,83]. The accessory component is significant to the cell, however, very variable, and has an apparently mosaic structure.…”

“…Concomitantly, a considerable number of core genes are dispersed between plasmids. They are often maintained in the syntenic blocks and have a high level of nucleotide sequence identity among the homologous segments [55]. In Sfr GR64, a chimeric transmissible plasmid with segments from two Rhe plasmids and Sfr chromosome was detected [123].…”

“…Due to difficulties encountered in exact localization of the "rhizobial core genome," a pan-genomic concept was employed for R. etli strains [55]. A pangenome "determines the core genome, which consists of genes shared by all the strains studied and probably encoding functions related to the basic biology and phenotypes of the species" [132].…”