Karasev, E.S.; Hosid, S.L.; Aksenova, T.S.; Onishchuk, O.P.; Kurchak, O.N.; Dzyubenko, N.I.; Andronov, E.E.; Provorov, N.A. Impacts of Natural Selection on Evolution of Core and Symbiotically Specialized (sym) Genes in the Polytypic Species Neorhizobium galegae. Int. J. Mol. Sci.2023, 24, 16696.
Karasev, E.S.; Hosid, S.L.; Aksenova, T.S.; Onishchuk, O.P.; Kurchak, O.N.; Dzyubenko, N.I.; Andronov, E.E.; Provorov, N.A. Impacts of Natural Selection on Evolution of Core and Symbiotically Specialized (sym) Genes in the Polytypic Species Neorhizobium galegae. Int. J. Mol. Sci. 2023, 24, 16696.
Karasev, E.S.; Hosid, S.L.; Aksenova, T.S.; Onishchuk, O.P.; Kurchak, O.N.; Dzyubenko, N.I.; Andronov, E.E.; Provorov, N.A. Impacts of Natural Selection on Evolution of Core and Symbiotically Specialized (sym) Genes in the Polytypic Species Neorhizobium galegae. Int. J. Mol. Sci.2023, 24, 16696.
Karasev, E.S.; Hosid, S.L.; Aksenova, T.S.; Onishchuk, O.P.; Kurchak, O.N.; Dzyubenko, N.I.; Andronov, E.E.; Provorov, N.A. Impacts of Natural Selection on Evolution of Core and Symbiotically Specialized (sym) Genes in the Polytypic Species Neorhizobium galegae. Int. J. Mol. Sci. 2023, 24, 16696.
Abstract
Nodule bacteria (rhizobia) represent a suitable model to address a range of evolutionary prob-lems including the tradeoff between genetic polymorphism and natural selection. Rhizobia possess the complicated genomes in which symbiotically specialized (sym) genes differ in their natural histories from core genes encoding for housekeeping functions. Diversification of sym genes is responsible for the rhizobia microevolution which depends on the host-induced natural selection. For the rhizobia speciation, diversification of core genes is responsible for which the selective factors are unclear.
In this paper we demonstrate that in the goats’ rue rhizobia (Neorhizobium galegae) populations collected at North Caucasus and composed of two host-specific biovars orientalis and officianalis (N2-fixing symbionts of Galega orientalis and G. officinalis, respectively), evolutionary mechanisms are different for core and sym genes. In both N. galegae biovars, core genes are more polymorphic than sym genes. In bv. orientalis, evolution of core genes occurs under the impacts of driving se-lection (dN/dS > 1), while evolution of sym genes is close to neutral (dN/dS ≈ 1). In bv. officinalis, evolution of core genes is neutral, while for sym genes, it is dependent on purifying selection (dN/dS < 1). A marked phylogenetic congruence of core and sym genes revealed using the ANI analysis may be due to a low intensity of gene transfer within and between N. galegae biovars. Polymorphism of both gene groups and the impacts of driving selection on the core gene evolu-tion are more pronounced in bv. orientalis than in bv. officianalis reflecting the diversities of re-spective host plant species. In bv. orientalis, highly significant (P0 < 0,001) positive correlation was revealed between the p-distance and dN/dS values for core genes, while in bv. officinalis this cor-relation is lowly significant (0,05 < P0 < 0,10). For sym genes, correlation between the p-distance and dN/dS values is negative in bv. officinalis but is not revealed in bv. orientalis. These data along with the functional annotation of core genes implemented using the Gene Ontology tools sug-gests that evolution of bv. officinalis is based mostly on adaptation for in planta niches while in bv. orientalis evolution presumable depends on adaptation for soil niches. New insights into the tradeoff between natural selection and genetic diversity are presented suggesting that the gene polymorphism may be extended by driving selection only in the ecologically versatile organ-isms capable to support a broad spectrum of gene alleles in their genepools.
Keywords
Neorhizobium galegae biovars orientalis and officinalis; polytypic rhizobia species; evolution of symbiosis; core and symbiotically specialized (sym) genes; nucleotide polymorphism of genes; driving and purifying selection; p-distance; dN/dS statistics; goats’ rue (Galega); Illumina
Subject
Biology and Life Sciences, Ecology, Evolution, Behavior and Systematics
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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