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Aksenova T.S., Chirak E.R., Onishchuk O.P., Kurchak O.N., Afonin A.M., Pinaev A.G., Andronov E.E., Provorov N.A. Identification of the ancestral characteristics in the genome of Rhizobium leguminosarum bv. trifolii. Sel'skokhozyaistvennaya Biologiya [Agricultural Biology], 2020, Vol. 55, № 3, p. 489-498.
(how to cite this article)

doi: 10.15389/agrobiology.2020.3.489eng

UDC: 631.461.52:575.22:575.85

Acknowledgements:
Supported financially by Russian Foundation for Basic Research, the project No. 18-34-00839 (collection of nodules and isolation of strains), and Russian Science Foundation, the project No. 19-16-00081 (genome sequencing and bioinformatics data analysis)

IDENTIFICATION OF THE ANCESTRAL CHARACTERISTICS IN THE GENOME OF Rhizobium leguminosarum bv. trifolii

T.S. Aksenova1, E.R. Chirak1, O.P. Onishchuk1, O.N. Kurchak1, A.M. Afonin1, A.G. Pinaev1, E.E. Andronov1, 2, 3, N.A. Provorov1

1All-Russian Research Institute for Agricultural Microbiology, 3, sh. Podbel’skogo, St. Petersburg, 196608 Russia, e-mail tsaksenova@mail.ru, chirak.elizaveta@gmail.com, olony@yandex.ru, okurchak@yahoo.com, aafonin@arriam.ru, agpinaev@gmail.com, eeandr@gmail.com (✉ corresponding author), provorovnik@ya.ru;
2Dokuchaev Soil Science Institute, 7/str. 2, Pyzhyovskii per., Moscow, 119017 Russia;
3Saint-Petersburg State University, 7-9, Universitetskaya nab., St. Petersburg, 199034 Russia

ORCID:
Aksenova T.S. orcid.org/0000-0002-7294-8410
Afonin A.M. orcid.org/0000-0002-8530-0226
Chirak E.R. orcid.org/0000-0002-1610-8935
Pinaev A.G. orcid.org/0000-0001-8272-9679
Onishchuk O.P. orcid.org/0000-0002-5378-7826
Andronov E.E. orcid.org/0000-0002-5204-262X
Kurchak O.N. orcid.org/0000-0003-3555-7426
Provorov N.A. orcid.org/0000-0001-9091-9384

Received March 12, 2020

 

Nodule bacteria of the species Rhizobium leguminosarum are symbiotic N2-fixers that divide into two biotypes: viciae and trifolii (D.C Jordan. et al., 1984). Symbiotic genes, the evolution of which depends on host plants, are responsible for the function of symbiotic nitrogen fixation (J.P.W. Young et al., 1989). Recently it was shown that according to the type of organization of the symbiotic regions of the genomes, rhizobia isolated from the Vavilovia formosa (Stev.) Fed.are close to the protosymbiont of the tribe Fabeae R. leguminosarum bv. viceae (E.R. Chirak et al., 2019). However, in the evolution of R. leguminosarum, there was another earlier divergence between the biotypes viceae and trifolii, the starting point of which was the protosymbiont of the entire species R. leguminosarum, which existed before its separation into biovars. In this work we present the results of genomes sequencing of a group of Rhizobium leguminosarum bv. trifolii and comparisons of the structure of their symbiotic regions with the corresponding regions of the genomes of Rhizobium leguminosarum bv. viciae, related to the ancestral and “advanced” types. In the program CLC Genomics Workbench 7.5.1, we compared the obtained genome-wide sequences of the strains R. leguminosarum bv. trifolii (Oxford Nanopore sequencing technique) with reference strains of R. leguminosarum bv. viceae, related to ancestral and “advanced” types. It was shown that in the genomes of strains of clover symbionts, four of five ancestral characters are found: an increased size of intergenic regions in the symbiotic region, the presence of the nodX gene in the nod-operon, the absence of the nodT gene in the sym-region, and only one copy of the fixNOPQ operon located on the pSym. Based on the results obtained, we suggest that the protosymbiont R. leguminosarum could be close to clover rhizobia.

Keywords: Rhizobium leguminosarum bv. trifolii, symbiosis evolution, symbiotic genes, protosymbiont, genome-wide sequences.

 

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