Complete genome sequence of the Medicago microsymbiont Ensifer (Sinorhizobium) medicae strain WSM419

Abstract

Ensifer (Sinorhizobium) medicae is an effective nitrogen fixing microsymbiont of a diverse range of annual Medicago (medic) species. Strain WSM419 is an aerobic, motile, non-spore forming, Gram-negative rod isolated from a M. murex root nodule collected in Sardinia, Italy in 1981. WSM419 was manufactured commercially in Australia as an inoculant for annual medics during 1985 to 1993 due to its nitrogen fixation, saprophytic competence and acid tolerance properties. Here we describe the basic features of this organism, together with the complete genome sequence, and annotation. This is the first report of a complete genome sequence for a microsymbiont of the group of annual medic species adapted to acid soils. We reveal that its genome size is 6,817,576 bp encoding 6,518 protein-coding genes and 81 RNA only encoding genes. The genome contains a chromosome of size 3,781,904 bp and 3 plasmids of size 1,570,951 bp, 1,245,408 bp and 219,313 bp. The smallest plasmid is a feature unique to this medic microsymbiont.

The Structure and Evolution of Beta-Rhizobial Symbiotic Genes Deduced from Their Complete Genomes

“…T was found to be more closely related to Methylobacterium nodulans (Alphaproteobacteria) based on its DNA and amino acid sequences, but its nifH sequence is closer to free-living Burkholderia (Betaproteobacteria) (Figure 3) [6,7,63]. As stated earlier, in contrast to STM678 T , which nodulates papilionoideae, in our complete genome study we found that B. tuberum sv.…”

“…The analysis showed that the nifH and nodA sequences of another B. tuberum strain (CCGE1002), which was isolated from Mimosa occidentalis in Mexico, and which belongs to the mimosae symbiovar of B. tuberum, were grouped within clades of Beta-rhizobial genes. Indeed, [63] that the nodA aa sequence of CCGE1002 clustered with Beta-rhizobial genes, which is consistent with relationships deduced using nodIJ sequences. However, the partial sequences are inaccurate in some aspects, and in the present study, we have found that there is little interaction between the two rhizobial clades, and we further suggest that the nod genes of Alpha-and (Mimosa-nodulating) Beta-rhizobia evolved independently, but we also lend support to the concept that lateral gene transfer has occurred in some clusters.…”

“…Previous reports have discussed the origin of Rhizobia using partial sequences of symbiosis genes but the present study is the first to examine them in terms of whole genome sequences [13,30,31,[77][78][79][80]. Using partial sequences, [63] supposed that the nodIJ genes originated from gene duplication in a lineage of the Betaproteobacterial family, and suggested that Betaproteobacteria symbiosis genes were transferred to Alphaproteobacteria, but made no conclusions about the evolutionary origin of symbiotic nitrogen fixation. After examining the ACC deaminase (acds) genes among Alpha-and Beta-rhizobia from the Cape Fynbos, recombination and horizontal transfer of nodulation genes (HGT) were suggested [14,81].…”

“…With regard to transfer of symbiotic genes between the two classes of Rhizobia, [63] used complete genome sequences to study the origin of the rhizobial nodulation genes nodIJ, and showed that the entire nodIJ clade is included in the Burkholderiaceae DRA-ATPase/permease gene family, suggesting that the nodIJ genes originated from gene duplication in a lineage of the Betaproteobacterial class, and further suggests that Betaproteobacterial symbiosis genes were originally transferred to Alphaproteobacteria. However, the nodIJ sequences of B. tuberum STM678…”

“…T were not included in the clade of β-rhizobial genes used in the study of [63], and yet there are discrepancies between the nodA and nodIJ phylogenies based on their partial sequences. In this study, we attempt to elucidate the evolutionary origin of nodulation and nitrogen-fixation genes by comparing structural maps of symbiotic regions between Alpha-and Beta-rhizobia, and we analyze phylogenies constructed using nodA and nifH sequences, and then examine the B. tuberum symbiosis genes based on complete genomes.…”