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Shekhovtsov SV, Vasiliev GV, Latif R, Poluboyarova TV, Peltek SE, Rapoport IB. The mitochondrial genome of Dendrobaena tellermanica Perel, 1966 (Annelida: Lumbricidae) and its phylogenetic position. Vavilovskii Zhurnal Genet Selektsii 2023; 27:146-152. [PMID: 37063518 PMCID: PMC10090101 DOI: 10.18699/vjgb-23-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/30/2022] [Accepted: 09/30/2022] [Indexed: 04/18/2023] Open
Abstract
Earthworms are an important ecological group that has a significant impact on soil fauna as well as plant communities. Despite their importance, genetic diversity and phylogeny of earthworms are still insufficiently studied. Most studies on earthworm genetic diversity are currently based on a few mitochondrial and nuclear genes. Mitochondrial genomes are becoming a promising target for phylogeny reconstruction in earthworms. However, most studies on earthworm mitochondrial genomes were made on West European and East Asian species, with much less sampling from other regions. In this study, we performed sequencing, assembly, and analysis of the mitochondrial genome of Dendrobaena tellermanica Perel, 1966 from the Northern Caucasus. This species was earlier included into D. schmidti (Michaelsen, 1907), a polytypic species with many subspecies. The genome was assembled as a single contig 15,298 bp long which contained a typical gene set: 13 protein-coding genes (three subunits of cytochrome c oxidase, seven subunits of NADH dehydrogenase, two subunits of ATP synthetase, and cytochrome b), 12S and 16S ribosomal RNA genes, and 22 tRNA genes. All genes were located on one DNA strand. The assembled part of the control region, located between the tRNA-Arg and tRNA-His genes, was 727 bp long. The control region contained multiple hairpins, as well as tandem repeats of the AACGCTT monomer. Phylogenetic analysis based on the complete mitochondrial genomes indicated that the genus Dendrobaena occupied the basal position within Lumbricidae. D. tellermanica was a rather distant relative of the cosmopolitan D. octaedra, suggesting high genetic diversity in this genus. D. schmidti turned out to be paraphyletic with respect to D. tellermanica. Since D. schmidti is known to contain very high genetic diversity, these results may indicate that it may be split into several species.
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Affiliation(s)
- S V Shekhovtsov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Institute of Biological Problems of the North of the Far Eastern Branch of the Russian Academy of Sciences, Magadan, Russia
| | - G V Vasiliev
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - R Latif
- Semnan University, Semnan, Iran
| | - T V Poluboyarova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - S E Peltek
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - I B Rapoport
- Tembotov Institute of Ecology of Mountain Territories of Russian Academy of Sciences, Nalchik, Russia
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Smirnov DN, Shekhovtsov SV, Shipova AA, Gazizova GR, Shagimardanova EI, Bulakhova NA, Meshcheryakova EN, Poluboyarova TV, Khrameeva EE, Peltek SE, Berman DI. De novo assembly and analysis of the transcriptome of the Siberian wood frog Rana amurensis. Vavilovskii Zhurnal Genet Selektsii 2022; 26:109-116. [PMID: 35342853 PMCID: PMC8894097 DOI: 10.18699/vjgb-22-07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/02/2021] [Accepted: 11/02/2021] [Indexed: 11/30/2022] Open
Abstract
The Siberian wood frog Rana amurensis Boulenger, 1886 is the most hypoxia-tolerant amphibian. It can survive for several months in an almost complete absence of oxygen. Little is known about the mechanisms of this remarkable resilience, in part because studies of amphibian genomes are impeded by their large size. To make the Siberian wood frog more amenable for genetic analysis, we performed transcriptome sequencing and de novo assembly for the R. amurensis brain under hypoxia and normoxia, as well as for the normoxic heart. In order to build a de novo transcriptome assembly of R. amurensis, we utilized 125-bp paired-end reads obtained from the brain under normoxia and hypoxia conditions, and from the heart under normoxia. In the transcriptome assembled from about 100,000,000 reads, 81.5 % of transcripts were annotated as complete, 5.3 % as fragmented, and 13.2 % as missing. We detected 59,078 known transcripts that clustered into 22,251 genes; 11,482 of them were assigned to specific GO categories. Among them, we found 6696 genes involved in protein binding, 3531 genes involved in catalytic activity, and 576 genes associated with transporter activity. A search for genes encoding receptors of the most important neurotransmitters, which may participate in the response to hypoxia, resulted in a set of expressed receptors of dopamine, serotonin, GABA, glutamate, acetylcholine, and norepinephrine. Unexpectedly, no transcripts for histamine receptors were found. The data obtained in this study create a valuable resource for studying the mechanisms of hypoxia tolerance in the Siberian wood frog, as well as for amphibian studies in general.
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Affiliation(s)
- D. N. Smirnov
- Center of Life Sciences, Skolkovo Institute of Science and Technology; Ben-Gurion University of the Negev, Department of Life Sciences
| | - S. V. Shekhovtsov
- Institute of the Biological Problems of the North of the Far-Eastern Branch of the Russian Academy of Sciences; Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - A. A. Shipova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - G. R. Gazizova
- Institute of Fundamental Medicine and Biology, Kazan Federal University
| | | | - N. A. Bulakhova
- Institute of the Biological Problems of the North of the Far-Eastern Branch of the Russian Academy of Sciences
| | - E. N. Meshcheryakova
- Institute of the Biological Problems of the North of the Far-Eastern Branch of the Russian Academy of Sciences
| | - T. V. Poluboyarova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - E. E. Khrameeva
- Center of Life Sciences, Skolkovo Institute of Science and Technology
| | - S. E. Peltek
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - D. I. Berman
- Institute of the Biological Problems of the North of the Far-Eastern Branch of the Russian Academy of Sciences
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Rozanov AS, Shekhovtsov SV, Bogacheva NV, Pershina EG, Ryapolova AV, Bytyak DS, S E Peltek. Production of subtilisin proteases in bacteria and yeast. Vavilovskii Zhurnal Genet Selektsii 2021; 25:125-134. [PMID: 34901710 PMCID: PMC8629363 DOI: 10.18699/vj21.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 11/19/2022] Open
Abstract
In this review, we discuss the progress in the study and modification of subtilisin proteases. Despite longstanding applications of microbial proteases and a large number of research papers, the search for new protease genes, the construction of producer strains, and the development of methods for their practical application are still relevant and important, judging by the number of citations of the research articles on proteases and their microbial producers. This enzyme class represents the largest share of the industrial production of proteins worldwide. This situation can explain the high level of interest in these enzymes and points to the high importance of designing domestic technologies for their manufacture. The review covers subtilisin classification, the history of their discovery, and subsequent research on the optimization of their properties. An overview of the classes of subtilisin proteases and related enzymes is provided too. There is a discussion about the problems with the search for (and selection of) subtilases from natural strains of various microorganisms, approaches to (and specifics of) their modification, as well as the relevant genetic engineering techniques. Details are provided on the methods for expression optimization of industrial subtilases of various strains: the details of the most important parameters of cultivation, i.e., composition of the media, culture duration, and the influence of temperature and pH. Also presented are the results of the latest studies on cultivation techniques: submerged and solid-state fermentation. From the literature data reviewed, we can conclude that native enzymes (i.e., those obtained from natural sources) currently hardly have any practical applications because of the decisive advantages of the enzymes modified by genetic engineering and having better properties: e.g., thermal stability, general resistance to detergents and specific resistance to various oxidants, high activity in various temperature ranges, independence from metal ions, and stability in the absence of calcium. The vast majority of subtilisin proteases are expressed in producer strains belonging to different species of the genus Bacillus. Meanwhile, there is an effort to adapt the expression of these enzymes to other microbes, in particular species of the yeast Pichia pastoris.
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Affiliation(s)
- A S Rozanov
- Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Laboratory of Molecular Biotechnologies, Novosibirsk, Russia
| | - S V Shekhovtsov
- Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Laboratory of Molecular Biotechnologies, Novosibirsk, Russia
| | - N V Bogacheva
- Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Laboratory of Molecular Biotechnologies, Novosibirsk, Russia
| | - E G Pershina
- Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Laboratory of Molecular Biotechnologies, Novosibirsk, Russia
| | - A V Ryapolova
- Innovation Centre "Biruch-NT", Malobykovo village, Belgorod region, Russia
| | - D S Bytyak
- Innovation Centre "Biruch-NT", Malobykovo village, Belgorod region, Russia
| | - S E Peltek
- Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Laboratory of Molecular Biotechnologies, Novosibirsk, Russia
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Shekhovtsov SV, Efremov YR, Poluboyarova TV, Peltek SE. Variation in nuclear genome size within the Eisenia nordenskioldi complex (Lumbricidae, Annelida). Vavilovskii Zhurnal Genet Selektsii 2021; 25:647-651. [PMID: 34782884 PMCID: PMC8558923 DOI: 10.18699/vj21.073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 11/19/2022] Open
Abstract
The size of the nuclear genome in eukaryotes is mostly determined by mobile elements and noncoding
sequences and may vary within wide limits. It can differ signif icantly both among higher-order taxa and closely
related species within a genus; genome size is known to be uncorrelated with organism complexity (the so-called
C-paradox). Less is known about intraspecif ic variation of this parameter. Typically, genome size is stable within a
species, and the known exceptions turn out be cryptic taxa. The Eisenia nordenskioldi complex encompasses several
closely related earthworm species. They are widely distributed in the Urals, Siberia, and the Russian Far East, as
well as adjacent regions. This complex is characterized by signif icant morphological, chromosomal, ecological, and
genetic variation. The aim of our study was to estimate the nuclear genome size in several genetic lineages of the
E. nordenskioldi complex using f low cytometry. The genome size in different genetic lineages differed strongly,
which supports the hypothesis that they are separate species. We found two groups of lineages, with small
(250–500 Mbp) and large (2300–3500 Mbp) genomes. Moreover, different populations within one lineage also
demonstrated variation in genome size (15–25 %). We compared the obtained data to phylogenetic trees based
on transcriptome data. Genome size in ancestral population was more likely to be big. It increased or decreased
independently in different lineages, and these processes could be associated with changes in genome size and/or
transition to endogeic lifestyle.
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Affiliation(s)
| | - Ya R Efremov
- Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | | | - S E Peltek
- Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
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Uvarova YE, Bryanskaya AV, Rozanov AS, Shlyakhtun VN, Demidov EA, Starostin KV, Goryachkovskaya TN, Shekhovtsov SV, Slynko NM, Peltek SE. An integrated method for taxonomic identification of microorganisms. Vavilovskii Zhurnal Genet Selektsii 2021; 24:376-382. [PMID: 33659820 PMCID: PMC7716526 DOI: 10.18699/vj20.630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
For accurate species-level identification of microorganisms, researchers today increasingly use a
combination of standard microbiological cultivation and visual observation methods with molecular biological and genetic techniques that help distinguish between species and strains of microorganisms at the level
of DNA or RNA molecules. The aim of this work was to identify microorganisms from the ICG SB RAS Collection
using an integrated approach that involves a combination of various phenotypic and genotypic characteristics. Key molecular-genetic and phenotypic characteristics were determined for 93 microbial strains from the
ICG SB RAS Collection. The strains were characterized by means of morphological, physiological, moleculargenetic, and mass-spectrometric parameters. Specific features of the growth of the strains on different media
were determined, and cell morphology was evaluated. The strains were tested for the ability to utilize various
substrates. The strains studied were found to significantly differ in their biochemical characteristics. Physiological characteristics of the strains from the collection were identified too, e.g., the relationship with oxygen,
type of nutrition, suitable temperature and pH ranges, and NaCl tolerance. In this work, the microorganisms
analyzed were combined into separate groups based on the similarities of their phenotypic characteristics.
This categorization, after further refinement and expansion of the spectrum of taxa and their metabolic maps,
may serve as the basis for the creation of an “artificial” classification that can be used as a key for simplified and
quicker identification and recognition of microorganisms within both the ICG SB RAS Collection and other
collections
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Affiliation(s)
- Yu E Uvarova
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A V Bryanskaya
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A S Rozanov
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - V N Shlyakhtun
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E A Demidov
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - K V Starostin
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - T N Goryachkovskaya
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - S V Shekhovtsov
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - N M Slynko
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - S E Peltek
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Shekhovtsov SV, Rapoport IB, Poluboyarova TV, Geraskina AP, Golovanova EV, Peltek SE. Morphotypes and genetic diversity of Dendrobaena schmidti (Lumbricidae, Annelida). Vavilovskii Zhurnal Genet Selektsii 2020; 24:48-54. [PMID: 33659780 PMCID: PMC7716558 DOI: 10.18699/vj20.594] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Dendrobaena schmidti (Michaelsen, 1907) is a polymorphic earthworm species from the Caucasus and adjacent regions. Adult D. schmidti individuals have highly variable body size (from 1.5 to well over 10 cm) and color (from dark purple to total lack of pigmentation), so a lot of subspecies of D. schmidti have been described; however, the existence of most of them is currently under dispute. We studied the genetic diversity of D. schmidti from seven locations from the Western Caucasus using mitochondrial (a fragment of the cytochrome oxidase I gene) and nuclear (internal ribosomal transcribed spacer 2) DNA. For both genes studied, we found that our sample was split into two groups. The first group included somewhat bigger (3–7.5 cm) individuals that were only slightly pigmented or totally unpigmented (when fixed by ethanol). The second group contained small (1.7–3.5 cm) specimens with dark purple pigmentation. In one of the studied locations these two groups were found in sympatry. However, there were no absolute differences either in general appearance (pigmented/unpigmented, small/big) or among diagnostic characters. Although the two groups differed in size (the majority of individuals from the first group were 5–6 cm long, and of the second one, 2–3 cm), the studied samples overlapped to a certain degree. Pigmentation, despite apparent differences, was also unreliable, since it was heavily affected by fixation of the specimens. Thus, based on the obtained data we can conclude that D. schmidti consists of at least two species that have identical states of diagnostic characters, but differ in general appearance.
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Affiliation(s)
- S V Shekhovtsov
- Institute of Cytology and Genetics of Suberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Institute of Biological Problems of the North of Far Eastern Branch of the Russian Academy of Sciences, Magadan, Russia Novosibirsk State University, Novosibirsk, Russia
| | - I B Rapoport
- Tembotov Institute of Ecology of Mountain Territories of the Russian Academy of Sciences, Nalchik, Russia
| | - T V Poluboyarova
- Institute of Cytology and Genetics of Suberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Institute of Biological Problems of the North of Far Eastern Branch of the Russian Academy of Sciences, Magadan, Russia
| | - A P Geraskina
- Center for Forest Ecology and Productivity of the Russian Academy of Sciences, Moscow, Russia
| | | | - S E Peltek
- Institute of Cytology and Genetics of Suberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Slynko NM, Burmakina NV, Potseluyev OM, Kapustyanchik SY, Galitsin GY, Goryachkovskaya TN, Kuybida LV, Shekhovtsov SV, Peltek SE, Shumny VK. Erratum to: “Gas chromatography-mass spectrometry in the taxonomy of Miscanthus”. Vavilovskii Zhurnal Genet Selektsii 2020; 24:109. [PMID: 33659789 PMCID: PMC7716577 DOI: 10.18699/vj20.603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Vavilovskii Zhurnal Genetiki i Selektsii = Vavilov Journal of Genetics and Breeding. 2019;23(8):1076-1081 (in Russian)
Page 1081, in Acknowledgements instead of
This work was supported by State Budgeted Project АААА-А17-117092070032-4.
should read
This work was supported by State Budgeted Project 0259-2019-0011.
The original article can be found under DOI 10.18699/VJ19.583
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Slynko NM, Burmakina NV, Potseluyev OM, Kapustyanchik SY, Galitsin GY, Goryachkovskaya TN, Kuybida LV, Shekhovtsov SV, Peltek SE, Shumny VK. Gas chromatography-mass spectrometry in the taxonomy of Miscanthus. Vavilovskii Zhurnal Genet Selektsii 2020. [DOI: 10.18699/vj19.583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Chemotaxonomy as a system approach deals with intra- and interspecific polymorphism of a group of taxa in order to clarify their taxonomic positions or to select material for selection or introduction. In this study we performed chemotaxonomic analysis of specimens of Miscanthus sinensis and M. sacchariflorus collected in the Russian Far East and of hybrid plants of both natural and artificial origin. We found 153 substances and identified 143 of them in extracts of eleven Miscanthus plants by gas chromatography-mass spectrometry (GC-MS). These substances can be grouped into alkanes (20 compounds), fatty acids (34), phenols (13), sterols (18) toсopherols (8), norterpenoids (12), and phytols (13), as well as their derivatives. The main components of the extracts of miscanthus samples are fatty acids and their derivatives (total content 19.94–41.02 %), dominated by palmitic and linolenic acids, and sterols (mainly β-sitosterol, stigmasterol, and α-amyrin), which constitute 17.15–31.73 %. The values of the CPI “oddness index” for the alkane components of the extracts were within 1.55–7.18, with extracts from leaves of the Far Eastern samples characterized by the lower half of this range (1.55–2.74), while extracts from leaves of hybrids fell to the upper half (5.78–7.18). Principal component analysis of extraction profiles allowed us to separate three distinct clusters: M. sinensis, M. sachariflorus, and their hybrids, as well as to verify the origin of one of the natural hybrids. The results of chemotaxonomic analysis mostly matched those of DNA sequencing of a fragment of the plastid genome, which, moreover, allowed us to identify the species nature of the maternal plants used to obtain these hybrids. Chemotaxonomic analysis using GC-MS was found to be an efficient additional technique to delimit various morphological forms of M. sinensis, M. sachariflorus, and their hybrids.
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Affiliation(s)
| | | | | | | | | | | | - L. V. Kuybida
- Voevodsky Institute of Chemical Kinetics and Combustion, SB RAS
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Berman DI, Bulakhova NA, Meshcheryakova EN, Shekhovtsov SV. Cold Resistance and the Distribution of Genetic Lineages of the Earthworm Eisenia nordenskioldi (Oligochaeta, Lumbricidae). BIOL BULL+ 2019. [DOI: 10.1134/s1062359019050042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Shekhovtsov SV, Sundukov YN, Blakemore RJ, Gongalsky KB, Peltek SE. Identifying earthworms (Oligochaeta, Megadrili) of the Southern Kuril Islands using DNA barcodes. Anim Biodiv Conserv 2018. [DOI: 10.32800/abc.2018.41.0009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Shekhovtsov SV, Berman DI, Bulakhova NA, Vinokurov NN, Peltek SE. Phylogeography of Eisenia nordenskioldi nordenskioldi (Lumbricidae, Oligochaeta) from the north of Asia. Polar Biol 2017. [DOI: 10.1007/s00300-017-2184-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Shekhovtsov SV, Berman DI, Golovanova EV, Peltek SE. Genetic diversity of the earthworm Eisenia nordenskioldi (Lumbricidae, Annelida). Vavilovskii Zhurnal Genet Selektsii 2017. [DOI: 10.18699/vj17.24-o] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Shekhovtsov SV, Golovanova EV, Bazarova NE, Belova YN, Berman DI, Derzhinsky EA, Shashkov MP, Peltek SE. Genetic diversity of the Aporrectodea caliginosa complex in Russia. Vavilovskii Zhurnal Genet Selektsii 2017. [DOI: 10.18699/vj17.255] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Shekhovtsov SV, Bazarova NE, Berman DI, Bulakhova NA, Golovanova EV, Konyaev SV, Krugova TM, Lyubechanskii II, Peltek SE. DNA barcoding: how many earthworm species are there in the south of West Siberia? Vavilovskii Zhurnal Genet Selektsii 2016. [DOI: 10.18699/vj15.110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Shekhovtsov SV, Golovanova EV, Peltek SE. Different dispersal histories of lineages of the earthworm Aporrectodea caliginosa (Lumbricidae, Annelida) in the Palearctic. Biol Invasions 2015. [DOI: 10.1007/s10530-015-1045-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Tregubchak TV, Shekhovtsov SV, Nepomnyashchikh TS, Peltek SE, Kolchanov NA, Shchelkunov SN. TNF-Binding domain of the variola virus CrmB protein synthesized in Escherichia coli cells effectively interacts with human TNF. DOKL BIOCHEM BIOPHYS 2015; 462:176-80. [PMID: 26163214 DOI: 10.1134/s1607672915030102] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Indexed: 11/23/2022]
Affiliation(s)
- T V Tregubchak
- State Research Center of Virology and Biotechnology Vector, Kol'tsovo, Novosibirsk oblast, 633159, Russia
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Shekhovtsov SV, Berman DI, Peltek SE. Phylogeography of the earthworm Eisenia nordenskioldi nordenskioldi (Lumbricidae, Oligochaeta) in northeastern Eurasia. Dokl Biol Sci 2015; 461:85-8. [PMID: 25937328 DOI: 10.1134/s0012496615020039] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Indexed: 11/22/2022]
Affiliation(s)
- S V Shekhovtsov
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russia,
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Kruchinina MV, Kurilovich SA, Voevoda MI, Gromov AA, Nemtsova EG, Generalov VM, Safatov AS, Generalov KV, Buryak GA, Kruchinin VN, Rykhlitsky SV, Spesivtsev EV, Volodin VA, Mogilnikov KP, Antsygin VD, Peltek SE, Shekhovtsov SV. [MODERN METHODS OF PHYSICAL-CHEMICAL RESEARCH IN GASTROENTEROLOGY PRACTICE: THE EXPERIENCE OF INTERACTION]. Eksp Klin Gastroenterol 2015:74-82. [PMID: 26281181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
UNLABELLED The aim of this work was to assess the potential of some physical and chemical methods for studying erythrocytes and blood serum in gastroenterological practice by the example of colorectal cancer (CC). MATERIALS AND METHODS A total of 26 persons with various stages of colorectal cancer and 16 healthy (control group) were examined. Parameters of erythrocytes and blood serum were investigated by light microscopy, dielectrophoresis in a non-uniform alternating electric field (DEF in NUAEF), terahertz spectroscopy, ellipsometry, Raman-spectroscopy. RESULTS Polymorphism of erythrocytes, rigidity, viscosity, indexes of aggregation and destruction were significantly higher in patients with CC and polarizability, amplitude of erythrocyte deformation in NUAEF being lower than those in the controls. The study of erythrocytes by terahertz spectroscopy revealed the low levels of amplitude transmittance over the whole frequency range in CC patients compared to the controls. The increasing of refractive index, degree of heterogeneity of thin films obtained from the serum in CC patients were observed in considering the ellipsometric parameters. We found a significant increasing of the concentration of antigens to CD24 at the early stage of the disease. The areas of some peaks in Raman spectra were significantly lower in patients with CC compared to the healthy ones, it is possible due to a carotin deficiency. Most of the studied parameters were correlated with the stage of the disease. A set of optical methods for studying blood serum compared with those of histology and radiological methods of diagnosis showed their high sensitivity and specificity, positive and negative predictive value (80 % and above). CONCLUSION The obtained results of the pilot study demonstrate the prospects of using physical and chemical methods of research of erythrocytes and blood serum for early diagnosis, stage of disease and monitoring the effectiveness of treatment of CC.
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Mordvinov VA, Mardanov AV, Ravin NV, Shekhovtsov SV, Demakov SA, Katokhin AV, Kolchanov NA, Skryabin KG. Complete Sequencing of the Mitochondrial Genome of Opisthorchis felineus , Causative Agent of Opisthorchiasis. Acta Naturae 2009. [DOI: 10.32607/20758251-2009-1-1-99-104] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Mordvinov VA, Mardanov CACV, Ravin NV, Shekhovtsov SV, Demakov SА, Katokhin CACV, Kolchanov NА, Skryabin KG. Complete Sequencing of the Mitochondrial Genome of Opisthorchis felineus, Causative Agent of Opisthorchiasis. Acta Naturae 2009; 1:99-104. [PMID: 22649593 PMCID: PMC3347509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Opisthorchis felineus, a hepatic trematode, is the causative agent of opisthorchiasis, a dangerous disease in both human beings and animals. Opisthorchiasis is widespread in Russia, especially Western Siberia. The purpose of the present study was to determine the complete mitochondrial DNA sequence of this flatworm. Two parallel methods were employed: (1) capillary electrophoresis to sequence the mitochondrial genome fragments obtained through specific PCR amplification, and (2) high throughput sequencing of the DNA sample. Both methods made possible the determination of the complete nucleotide sequence of the O. felineus mitochondrial genome. The genome consists of a ring molecule 14,277 nt in length that contains 35 genes coding 2 rRNA, 22 tRNA, and 12 proteins: 3 subunits of cytochrome-C-oxidase, 7 subunits of NADH-dehydrogenase, B apocytochrome, and subunit 6 of ATP-synthetase.Like many other flatworms, O. felineus is characterized by the absence of the ATP-synthetase subunit 8 gene. Nineteen out of the 22 tRNAs have a typical "clover leaf" structure. The tRNA(AGC) and tRNA-Cys genes lack DHU-loops, while the tRNA-Ser(UCA) has 2 alternative structures: one with a DHU-loop, and one without it. Analyzing the results obtained from the high throughput sequencing revealed 45 single-nucleotide polymorphisms within the mitochondrial genome. The results obtained in this study may be used in the development of molecular diagnostic methods for opisthorchiasis. This study shows that high throughput sequencing is a fast and effective method for decoding the mitochondrial genome of animals.
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Affiliation(s)
- V A Mordvinov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Lavrentieva Ave, Novosibirsk, 630090, Russia
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Katokhin AV, Shekhovtsov SV, Konkow S, Yurlova NI, Serbina EA, Vodianitskai SN, Fedorov KP, Loktev VB, Muratov IV, Ohyama F, Makhnev TV, Pel'tek SE, Mordvinov VA. Assessment of the genetic distinctions of Opisthorchis felineus from O. viverrini and Clonorchis sinensis by ITS2 and CO1 sequences. DOKL BIOCHEM BIOPHYS 2008; 421:214-7. [PMID: 18853775 DOI: 10.1134/s1607672908040133] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- A V Katokhin
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, pr. Lavrent'eva 10, Novosibirsk, 630090 Russia
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