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

1
All-Russia Research Institute of Agricultural Microbiology, St. Petersburg 196608, Russia
2
Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russia
3
Saint-Petersburg State University, St. Petersburg 199034, Russia
4
V.V. Dokuchaev Soil Science Institute of Russian Academy of Science, Moscow 119017, Russia
*
Author to whom correspondence should be addressed.
Genes 2019, 10(12), 990; https://doi.org/10.3390/genes10120990
Received: 23 October 2019 / Revised: 22 November 2019 / Accepted: 27 November 2019 / Published: 1 December 2019
(This article belongs to the Special Issue Evolutionary Genetics of Microbial Symbiosis)
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.
Keywords: Rhizobium leguminosarum biovar viciae; genomic rearrangements; symbiotic and housekeeping genes; evolution of symbiosis; last common ancestor (LCA); Vavilovia formosa; horizontal gene transfer Rhizobium leguminosarum biovar viciae; genomic rearrangements; symbiotic and housekeeping genes; evolution of symbiosis; last common ancestor (LCA); Vavilovia formosa; horizontal gene transfer
MDPI and ACS Style

Chirak, E.R.; Kimeklis, A.K.; Karasev, E.S.; Kopat, V.V.; Safronova, V.I.; Belimov, A.A.; Aksenova, T.S.; Kabilov, M.R.; Provorov, N.A.; Andronov, E.E. Search for Ancestral Features in Genomes of Rhizobium leguminosarum bv. viciae Strains Isolated from the Relict Legume Vavilovia formosa. Genes 2019, 10, 990.

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