Search for Ancestral Features in Genomes of Rhizobium leguminosarum bv. viciae Strains Isolated from the Relict Legume Vavilovia formosa

Abstract

Vavilovia formosa is a relict leguminous plant growing in hard-to-reach habitats in the rocky highlands of the Caucasus and Middle East, and it is considered as the putative closest living relative of the last common ancestor (LCA) of the Fabeae tribe. Symbionts of Vavilovia belonging to Rhizobium leguminosarum bv. viciae compose a discrete group that differs from the other strains, especially in the nucleotide sequences of the symbiotically specialised (sym) genes. Comparison of the genomes of Vavilovia strains with the reference group composed of R. leguminosarum bv. viciae strains isolated from Pisum and Vicia demonstrated that the vavilovia strains have a set of genomic features, probably indicating the important stages of microevolution of the symbiotic system. Specifically, symbionts of Vavilovia (considered as an ancestral group) demonstrated a scattered arrangement of sym genes (>90 kb cluster on pSym), with the location of nodT gene outside of the other nod operons, the presence of nodX and fixW, and the absence of chromosomal fixNOPQ copies. In contrast, the reference (derived) group harboured sym genes as a compact cluster (<60 kb) on a single pSym, lacking nodX and fixW, with nodT between nodN and nodO, and possessing chromosomal fixNOPQ copies. The TOM strain, obtained from nodules of the primitive "Afghan" peas, occupied an intermediate position because it has the chromosomal fixNOPQ copy, while the other features, the most important of which is presence of nodX and fixW, were similar to the Vavilovia strains. We suggest that genome evolution from the ancestral to the derived R. leguminosarum bv. viciae groups follows the "gain-and-loss of sym genes" and the "compaction of sym cluster" strategies, which are common for the macro-evolutionary and micro-evolutionary processes. The revealed genomic features are in concordance with a relict status of the vavilovia strains, indicating that V. formosa coexists with ancestral microsymbionts, which are presumably close to the LCA of R. leguminosarum bv. viciae.

Rhizobia Isolated from the Relict Legume Vavilovia formosa Represent a Genetically Specific Group within Rhizobium leguminosarum biovar viciae

“…In this report, with the help of group separation statistics, we demonstrated that intergroup divergence pertains to both gene categories ( Figure 5), although in hkg genes it is not pronounced enough to result in the emergence of new species. The last statement is also supported by the ANI statistics for Vaf genomes compared to Rlv, as reported by Chirak [46].…”

“…Together with the proposed ancestral status of V. formosa, these data suggested that its strains might also preserve ancestral features, which were most clearly expressed at the level of concatenates of hkg and sym genes. Data indicating pronounced ancestral features for the sym gene arrangement within the bacterial genomes have been presented by Chirak et al [46].…”

Defining the Rhizobium leguminosarum Species Complex

“…Recently, several published [ 21 , 50 , 52 ] and unpublished [ 53 ] studies have augmented the public databases with a large number of new genome sequences assigned to, or related to, R. leguminosarum . In addition, there have been numerous contributions of individual genomes [ 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 ]. Here, we examine this wealth of genomic information in order to establish whether R. leguminosarum , in the broad sense, is a distinct entity, and whether it can be subdivided into clearly defined groups that might, in future, be named as separate species within the overall R. leguminosarum species complex (Rlc).…”

Evolutionary Genetics of Microbial Symbiosis

“…In this Special Issue, we present a collection of new reviews and original research papers that target the genetic machinery behind the evolution of microbial symbioses, using both classical and novel experimental model systems. These include microbial symbioses with arthropod hosts [3][4][5], leguminous plants [6,7], social amoebae [8], and the largely understudied symbiosis of fungi in insects [9]. These papers provide key examples of current research on the microbial genetic repertoire (genes, genomic features, and their molecular evolution) and metabolic interactions (including biochemical and cellular mechanisms) involved in symbiotic interplay.…”