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Search for Ancestral Features in Genomes of Rhizobium leguminosarum bv. viciae Strains Isolated from the Relict Legume Vavilovia formosa
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Rhizobia Isolated from the Relict Legume Vavilovia formosa Represent a Genetically Specific Group within Rhizobium leguminosarum biovar viciae

1
All-Russian Research Institute of Agricultural Microbiology, Saint Petersburg 196608, Russia
2
Saint-Petersburg State University, Saint Petersburg 199034, Russia
3
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), 991; https://doi.org/10.3390/genes10120991
Received: 23 October 2019 / Revised: 20 November 2019 / Accepted: 27 November 2019 / Published: 1 December 2019
(This article belongs to the Special Issue Evolutionary Genetics of Microbial Symbiosis)
Twenty-two rhizobia strains isolated from three distinct populations (North Ossetia, Dagestan, and Armenia) of a relict legume Vavilovia formosa were analysed to determine their position within Rhizobium leguminosarum biovar viciae (Rlv). These bacteria are described as symbionts of four plant genera Pisum, Vicia, Lathyrus, and Lens from the Fabeae tribe, of which Vavilovia is considered to be closest to its last common ancestor (LCA). In contrast to biovar viciae, bacteria from Rhizobium leguminosarum biovar trifolii (Rlt) inoculate plants from the Trifolieae tribe. Comparison of house-keeping (hkg: 16S rRNA, glnII, gltA, and dnaK) and symbiotic (sym: nodA, nodC, nodD, and nifH) genes of the symbionts of V. formosa with those of other Rlv and Rlt strains reveals a significant group separation, which was most pronounced for sym genes. A remarkable feature of the strains isolated from V. formosa was the presence of the nodX gene, which was commonly found in Rlv strains isolated from Afghanistan pea genotypes. Tube testing of different strains on nine plant species, including all genera from the Fabeae tribe, demonstrated that the strains from V. formosa nodulated the same cross inoculation group as the other Rlv strains. Comparison of nucleotide similarity in sym genes suggested that their diversification within sym-biotypes of Rlv was elicited by host plants. Contrariwise, that of hkg genes could be caused by either local adaptation to soil niches or by genetic drift. Long-term ecological isolation, genetic separation, and the ancestral position of V. formosa suggested that symbionts of V. formosa could be responsible for preserving ancestral genotypes of the Rlv biovar.
Keywords: Rhizobium leguminosarum bv. viciae; Vavilovia formosa (Stev.) Fed.; tribe Fabeae; evolution of symbiosis; housekeeping genes (hkg); symbiotic (sym) genes; group separation Rhizobium leguminosarum bv. viciae; Vavilovia formosa (Stev.) Fed.; tribe Fabeae; evolution of symbiosis; housekeeping genes (hkg); symbiotic (sym) genes; group separation
MDPI and ACS Style

Kimeklis, A.K.; Chirak, E.R.; Kuznetsova, I.G.; Sazanova, A.L.; Safronova, V.I.; Belimov, A.A.; Onishchuk, O.P.; Kurchak, O.N.; Aksenova, Т.S.; Pinaev, A.G.; Andronov, E.E.; Provorov, N.A. Rhizobia Isolated from the Relict Legume Vavilovia formosa Represent a Genetically Specific Group within Rhizobium leguminosarum biovar viciae. Genes 2019, 10, 991.

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