Vol 54, No 10 (2018)

In this review, the available data on whole genome duplication in different phylogenetic lineages of animals are summarized, and possible mechanisms of the genome duplication and its role in the evolution of animals are considered. Special attention is paid to the problems of studying the first stages of the genome evolution after its duplication and to the search for species the study of which will make it possible to identify the peculiarities of the genome “diploidization” process after its duplication. A group of species of free-living flatworms from the Macrostomum genus is suggested as a promising model object for such studies. According to our data, the genomes of some Macrostomum members (M. lignano, Macrostomum sp. 8) are a result of recent genome duplication and subsequent chromosome rearrangements. In addition, the peculiarities of morphology, life cycle, small genome size, and simply organized karyotype make Macrostomum almost an ideal model object for studying the early stages of duplicated genome reorganization.

On the basis of the data of phylogeographical analysis, strains of Yersinia pestis are divided into a number of phylogenetic branches, and in accordance with the traditionally used subspecies classification in the CIS countries, they are divided into five subspecies. We conducted a study of the population structure and genetic characteristics of strains belonging to the phylogenetic branch 0.PE4 and its strains of the Altai subspecies—0.PE4a (Russia, Mongolia), the Hissar subspecies—0.PE4h (Tajikistan), the Talas population—0.PE4t (Kyrgyzstan), and the microtus population—0.PE4m (China). The uniformity of phenotypic and genetic characteristics of strains of the 0.PE4 branch has been established and the necessity of their association into one subspecies, the Central Asian (Y. pestis subsp. central asiatica), has been substantiated. The dendrogram demonstrates the presence of four separate subclusters corresponding to four populations: 0.PE4a (Altai strains), 0.PE4h (Hissar strains), 0.PE4t (Talas strains), and 0.PE4m (microtus strains) in the composition of the 0.PE4 cluster, which we propose to allocate to four biovars of the Central Asian subspecies: Altai, Hissar, Talas, and Microtus. A number of mutations specific only to 0.PE4 strains were detected. A DNA target was found and a method for differentiating the Central Asian subspecies (strains avirulent for humans) from other strains of Y. pestis by Real-Time PCR was developed.

Earlier, we discovered a gene family encoding hevein-like antimicrobial peptides (WAMP) in the highly resistant wheat species Triticum kiharae Dorof. et Migusch. and related species of the Triticum and Aegilops genera. These peptides suppress growth and development of fungi and bacteria by inhibition of secreted metalloproteinases of the pathogens. In this study, we analyzed wamp homologs in the wild cereal Elytrigia repens Desv. ex Nevski, which is an invasive weed. The wamp homologs were isolated by PCR with E. repens genomic DNA or cDNA and primers specific to the wheat wamp genes. The nucleotide sequences of three novel E. repenswamp genes encoding the precursors of the antimicrobial peptides named ERAMP-1, ERAMP-2 and ERAMP-3 were determined. The mature peptide regions of the precursors differed in single amino acid substitutions. It was shown that ERAMP-2 and ERAMP-3 have valine at position 34 affecting the degree of fungal proteinase inhibition, which has not been found in other WAMP homologs. To elucidate the role of the valine residue in the E. repens peptide antifungal activity, the recombinant peptide was expressed in E. coli and its antifungal activity was assayed against a range of phytopathogenic fungi belonging to ascomycetes. The peptide was more active than the wheat WAMP-1 peptide against three of four tested fungi infecting cereals and other plant species. The results obtained contribute to our knowledge of the biodiversity of wamp genes in Poaceae. In addition, they expand our understanding of the repertoire of defensive genes in E. repens responsible for its enhanced pathogen resistance.

The objective of this study was to identify genetic variations of glutenins, granule-bound starch synthase I (GBSS I), puroindolines, and polyphenol oxidase (PPO) among 33 Mongolian wheat lines for Mongolian wheat breeding program. Mongolian wheat lines mainly carried Glu-A1b (54.5%), Glu-B1c (87.9%), and Glu-D1d (72.2%) among high molecular weight-glutenin subunits and Glu-A3b (42.4%) and Glu-B3g (60.6%) among low molecular weight-glutenin subunits. Based on allelic compositions of puroindolines, soft wheat accounted for 51.5% (17 wheat lines) while hard wheat accounted for 48.5% (16 wheat lines) among these Mongolian wheat lines. Most Mongolian wheats were wild-type (87.9%) in GBSS I allele composition while four cultivars (Darkhan-196, Darkhan-201, Darkhan-203, and Tsogt) carried Wx-B1b allele. Ppo-A1a, Ppo-B1b, and Ppo-D1a were predominantly found at PPO loci. Their frequencies were 66.7, 100 and 57.6%, respectively.

Genetic polymorphism and the population genetic structure of ranch (maintained at the fur farms) and feral American minks inhabiting the geographical region of the Caspian–Baltic watershed of the European part of Russia were investigated using eight microsatellite loci. A relatively high level of genetic variability of these forms with a tendency of higher polymorphism in the feral population was revealed. Between ranch and feral minks, not considerable, but highly statistically significant genetic differences were established. The gene pool of free-ranging minks does not bear traces of recent hybridization with ranch forms. The feral population is characterized by a distinct genetic structure and a pronounced pattern of genetic isolation by distance. Statistically significant differences in the genetic structure of local groups of animals inhabiting different regions of the studied territory are determined by the recent history of naturalization of the invasive species, including deliberate introduction in the northeast of the studied region and colonization of other parts of the Caspian–Baltic watershed by the descendants of the fur farm escapees.

Variability of the Onne-DAB gene, which encodes the β-chain of class II major histocompatibility complex molecule (MHCII), is studied using One_MHC2_109, One_MHC2_190v2, and One_MHC2_251v2 single nucleotide polymorphisms (SNP) in the two largest Asian-Pacific coast populations of sockeye salmon that reproduce in the Ozernaya River and Kamchatka River basins. Differences in the nature of inheritance and degree of polymorphism of One_MHC2_190v2 and One_MHC2_251v2 are observed in samples from both lake-river systems, whereas One_MHC2_109 was uninformative. Samples collected from the lake and river spawning grounds of Lake Kurilskoe are characterized by high estimates of intrapopulation genetic diversity, whereas no intersample differences are revealed in the frequencies of haplotypes and phenotypes of the joint MHC2 locus. This can be interpreted as the result of balancing selection in sequences encoding the MHCII peptide-binding region in this sockeye salmon population. This hypothesis is also confirmed by Ewens–Watterson neutrality tests. On the contrary, low genetic diversity estimates and significant heterogeneity of haplotype and phenotypic frequencies at the MHC2 locus are observed in the samples of early (spring) sockeye salmon from the Kamchatka River basin, apparently owing to the action of directional pathogen-induced selection in the Onne-DAB gene in some localities of the lake-river system.

Population structuring of a species provide basic information for biological conservation. We investigated the genetic structure of seven populations of Rana pseudodalmatina, an endemic species of the Ranidae inhabiting the Hyrcanian forests in northern Iran, based on the genetic variation of two partial mitochondrial DNA sequences (16S rRNA and cytochrome b genes). Molecular genetic analyses revealed remarkable variation among populations of R. pseudodalmatina. The phylogenetic trees clearly indicated two distinct haplogroups, which largely corresponded to their geographic locations. A strong population structure was found (Φ_CT = 0.559, P = 0.027) with high haplotype diversity (Hd = 0.88) and low nucleotide diversity (π = 0.0041). Analysis of molecular variance (AMOVA) indicated that most of the observed genetic variation (55.92%) occurred between the two haplogroups. Also, Mantel tests revealed a significant correlation between geographic and genetic distances (R² = 0.33, P = 0.005). Finally, the star-like topology of haplotype network and also neutrality tests provide strong evidence for population expansion in two haplogroups. All the findings of the present study, suggest a strong evidence for past expansion of isolated populations of R. pseudodalmatina, which their isolation could be largely attributed to rising level of the Caspian Sea during last glacial periods in the Pleistocene.

The purpose of this study was to investigate the angiotensin-converting enzyme (ACE) gene associations with the clinical picture of the most frequent complications of acute myocardial infarction (MI). The study included 190 patients who underwent one or more MI included in the WHO Register of Acute Myocardial Infarction. All the patients underwent genetic research for the identification of allelic variants of the ACE gene (polymorphism I/D). It was found that the DD genotype of the ACE gene is associated with a more frequent occurrence of acute left ventricular aneurysm (ALVA) (OR = 2.46, 95% CI 1.08–5.63, p = 0.037, χ² = 4.73). In the group of patients with acute left ventricular failure (ALVF), the picture looked different: the genotype II of the ACE gene was more frequent (OR = 2.86, 95% CI 1.35–6.08, p = 0.007, χ² = 7.81). Patients in the group without ALVF were carriers of the allele D more often (77.1%) (p = 0.007, χ² = 7.81). Discovered genetic associations favor the consideration of the ACE gene as a genetic predictor of the development of ALVA in the acute period of MI. Further study of this gene in combination with other genetic markers of MI, as well as analysis of distribution of the genotypes of the ACE gene among deceased patients who underwent MI, will allow us to understand the genetic mechanisms of the development of other complications of MI, in particular, ALVF. All this will ensure the development of new highly effective personalized approaches to the prevention and treatment of complications of acute MI and the improvement of immediate and remote prognosis of patients.

The demographic parameters and Y-chromosomal variation in the Ulchi population, an indigenous ethnic group of Khabarovsk krai, were studied. The demographic portrait was compiled using the data from the books of rural household accounting (7521 records, including 1562 on Ulchi). The structure of the gene pool was characterized for 45 SNP markers of the Y chromosome: 52 DNA samples were analyzed. The total number of Ulchi in the period between the censuses of 1926–2002 showed stable growth (723–2913 individuals) and slightly decreased by 2010 (2765 individuals). The study revealed an imbalance in the sex ratio (SR = 1 : 1.7) and the age structure close to the stationary type and providing a simple type of reproduction of the Ulchi. Analysis of the marital structure demonstrated a high rate of assimilation of the Ulchi by the Russian-speaking population dominant in all places of their compact settlement. Analysis for the SNP markers of the Y chromosomes (23 haplogroups were found) revealed a strong similarity of the Ulchi to the populations of the Amur River region and Okhotsk coast and a relative proximity to the Central Asian populations as given by haplogroup C. Genotyping of five new SNP markers within haplogroup C and 17 STR markers provided a correct phylogenetic analysis of haplogroup C in the Ulchi and neighboring peoples. It did not confirm the powerful gene drift in the Ulchi, which one might expect owing to their low effective size, likely because the Ulchi population was subdivided and thus managed to retain its diversity. However, this analysis revealed traces of intense interaction of the Ulchi with the peoples of the Far East and Central Asia over the past one to three thousand years. Therefore, the results of a recent study of the similarity of the ancient genomes of Primorye with the Ulchi indicate not the uniqueness of the Ulchi but the fact that this ancient gene pool was preserved in a vast milieu of populations of the Far East interlaced with gene flows both with each other and with populations of Central Asia.

Previously, in the strain Streptomyces rimosus ATCC10970 (producer of oxytetracycline), the aminoglycoside phosphotransferase AphVIII, determining kanamycin, neomycin, and paromomycin resistance, was identified and characterized. Recently, the authors obtained the 3D structure of AphVIII. The 14 aph genes, including gene aphVIII, were annotated when the genome of S. rimosus ATCC10970 was sequenced. In the present study, a new aph(3'')-Id (aphSR3) gene encoding streptomycin phosphotansferase was first identified in the strain of S. rimosus ATCC10970 using bioinformatic and comparative phylogenetic analysis of the aphSR1-aphSR14 genes with the previously known aph genes from clinical isolates and producer strains of aminoglycoside antibiotics belonging to seven subfamilies. When cloning, it was found that the gene aphSR3 (aph(3'')-Id) in Escherichia coli causes resistance to streptomycin at a concentration of 150 μg/mL. The obtained data can be used in practical terms to study the distribution and features of the functions of genes that determine the natural resistance to aminoglycoside antibiotics in actinobacteria of the genus Streptomyces.