Труды сотрудников ИЛ им. В.Н. Сукачева СО РАН

[Text] / V. L. Semerikov [et al.] // Russ. J. Genet. - 2015. - Vol. 51, Is. 12. - P1199-1203, DOI 10.1134/S1022795415120108. - Cited References:20. - We thank Y.Y. Hhrunyk, A. I. Vidjakin, V.V. Tarakanov, E.V. Hantemirova, and I.V. Tikhonova for assistance with the pine material collection. The study was supported by Russian Foundation for Basic Research (grant 13-04-01028) and by Russian Federation Government (grant 14.Y26.31.0004). . - ISSN 1022-7954. - ISSN 1608-3369РУБ Genetics & Heredity

Аннотация: Fragments of genomic DNA of Scots pine (Pinus sylvestris L.) homologous to the mitochondrial DNA (mtDNA) contigs of Norway spruce (Picea abies (L.) Karst.) and loblolly pine (Pinus taeda L.) were resequenced in a sample of the Scots pine trees of European, Siberian, Mongolian, and Caucasian origin in order to develop mtDNA markers. Flanking non-coding regions of some mitochondrial genes were also investigated and resequenced. Five single nucleotide polymorphisms (SNPs) and a single minisatellite locus were identified. Caucasian samples differed from the rest by three SNPs. Two SNPs have been linked to an early described marker in the first intron of the nad7 gene, and all together revealed three haplotypes in European populations. No variable SNPs were found in the Siberian and Mongolian populations. The minisatellite locus contained 41 alleles across European, Siberian, and Mongolian populations, but, this locus demonstrated a weak population differentiation (F (ST) = 5.8), probably due to its high mutation rate.

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Держатели документа:
Russian Acad Sci, Ural Branch, Inst Plant & Anim Ecol, Ekaterinburg 620144, Russia.
Siberian Fed Univ, Genome Res & Educ Ctr, Krasnoyarsk 660036, Russia.
Russian Acad Sci, Siberian Branch, Sukachev Inst Forest, Krasnoyarsk 660036, Russia.
Univ Gottingen, D-37077 Gottingen, Germany.
Russian Acad Sci, Vavilov Inst Gen Genet, Moscow 119991, Russia.
Texas A&M Univ, College Stn, TX 77843 USA.

Доп.точки доступа:
Semerikov, V. L.; Putintseva, Yu. A.; Oreshkova, N. V.; Semerikova, S. A.; Krutovsky, K. V.; Russian Foundation for Basic Research [13-04-01028]; Russian Federation Government [14.Y26.31.0004]

/ A. Kononov [et al.] // BMC Genet. - 2016. - Vol. 17, DOI 10.1186/s12863-016-0463-5 . - ISSN 1471-2156
Аннотация: Background: Moths of genus Dendrolimus (Lepidoptera: Lasiocampidae) are among the major pests of coniferous forests worldwide. Taxonomy and nomenclature of this genus are not entirely established, and there are many species with a controversial taxonomic position. We present a comparative evolutionary analysis of the most economically important Dendrolimus species in Eurasia. Results: Our analysis was based on the nucleotide sequences of COI and COII mitochondrial genes and ITS2 spacer of nuclear ribosomal genes. All known sequences were extracted from GenBank. Additional 112 new sequences were identified for 28 specimens of D. sibiricus, D. pini, and D. superans from five regions of Siberia and the Russian Far East to be able to compare the disparate data from all previous studies. In total, 528 sequences were used in phylogenetic analysis. Two clusters of closely related species in Dendrolimus were found. The first cluster includes D. pini, D. sibiricus, and D. superans; and the second, D. spectabilis, D. punctatus, and D. tabulaeformis. Species D. houi and D. kikuchii appear to be the most basal in the genus. Conclusion: Genetic difference among the second cluster species is very low in contrast to the first cluster species. Phylogenetic position D. tabulaeformis as a subspecies was supported. It was found that D. sibiricus recently separated from D. superans. Integration of D. sibiricus mitochondrial DNA sequences and the spread of this species to the west of Eurasia have been established as the cause of the unjustified allocation of a new species: D. kilmez. Our study further clarifies taxonomic problems in the genus and gives more complete information on the genetic structure of D. pini, D. sibiricus, and D. superans. © 2016 The Author(s).

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Держатели документа:
Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Science, 10 Prospekt Lavrentyeva, Novosibirsk, Russian Federation
USDA-APHIS-PPQ CPHST, Otis Laboratory, Building 1398, Otis Air National Guard Base, Buzzards Bay, MA, United States
Marshall University, Department of Biological Sciences, 1601 5th Avenue, Huntington, WV, United States
V.N. Sukachev Institute of Forest, the Siberian Branch of the Russian Academy of Science, 50/28 Akademgorodok, Krasnoyarsk, Russian Federation

Доп.точки доступа:
Kononov, A.; Ustyantsev, K.; Wang, B.; Mastro, V. C.; Fet, V.; Blinov, A.; Baranchikov, Y.

/ E. I. Bondar [et al.] // BMC Bioinformatics. - 2019. - Vol. 20: 11th International Multiconference on Bioinformatics of Genome (AUG 20-25, 2018, Novosibirsk, RUSSIA). - Ст. 38, DOI 10.1186/s12859-018-2571-x. - Cited References:25. - The presented study was a part of the project "Genomic studies of major boreal coniferous forest tree species and their most dangerous pathogens in the Russian Federation" funded by the Government of the Russian Federation (grant No 14.Y26.31.0004). Publication costs are funded by the BioMed Central Membership of the University of Gottingen. . - ISSN 1471-2105РУБ Biochemical Research Methods + Biotechnology & Applied Microbiology

Аннотация: BackgroundThe main objectives of this study were sequencing, assembling, and annotation of chloroplast genome of one of the main Siberian boreal forest tree conifer species Siberian larch (Larix sibirica Ledeb.) and detection of polymorphic genetic markers - microsatellite loci or simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs).ResultsWe used thedata of the whole genome sequencing of three Siberian larch trees from different regions - theUrals, Krasnoyarsk, and Khakassia, respectively. Sequence reads were obtained using the Illumina HiSeq2000 in the Laboratory of Forest Genomics at the Genome Research and Education Center ofthe Siberian Federal University. The assembling was done using the Bowtie2 mapping program and the SPAdes genomic assembler. The genome annotation was performed using the RAST service. We used the GMATo program for the SSRs search, and the Bowtie2 and UGENE programs for the SNPs detection. Length of the assembled chloroplast genome was 122,561bp, which is similar to 122,474bp in the closely related European larch (Larix decidua Mill.). As a result of annotation and comparison of the data with theexisting data available only for three larch species - L. decidua, L. potaninii var. chinensis (complete genome 122,492bp), and L. occidentalis (partial genome of 119,680bp), we identified 110 genes, 34 of which represented tRNA, 4 rRNA, and 72 protein-coding genes. In total, 13 SNPs were detected; two of them were in the tRNA-Arg and Cell division protein FtsH genes, respectively. In addition, 23 SSR loci were identified.ConclusionsThe complete chloroplast genome sequence was obtained for Siberian larch for the first time. The reference complete chloroplast genomes, such as one described here, would greatly help in the chloroplast resequencing and search for additional genetic markers using population samples. The results of this research will be useful for further phylogenetic and gene flow studies in conifers.

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Siberian Fed Univ, Genome Res & Educ Ctr, Lab Forest Genom, Krasnoyarsk 660036, Russia.
Russian Acad Sci, VN Sukachev Inst Forest, Lab Forest Genet & Select, Siberian Branch, Krasnoyarsk 660036, Russia.
Georg August Univ Gottingen, Dept Forest Genet & Forest Tree Breeding, Busgenweg 2, D-37077 Gottingen, Germany.
Russian Acad Sci, Vavilov Inst Gen Genet, Lab Populat Genet, Moscow 119333, Russia.
Texas A&M Univ, Dept Ecosyst Sci & Management, College Stn, TX 77843 USA.

Доп.точки доступа:
Bondar, Eugeniya I.; Putintseva, Yuliya A.; Oreshkova, Nataliya V.; Krutovsky, Konstantin V.; Krutovsky, Konstantin; Government of the Russian Federation [14.Y26.31.0004]; University of Gottingen

/ D. A. Kuzmin [et al.] // BMC Bioinformatics. - 2019. - Vol. 20: 11th International Multiconference on Bioinformatics of Genome (AUG 20-25, 2018, Novosibirsk, RUSSIA). - Ст. 37, DOI 10.1186/s12859-018-2570-y. - Cited References:32. - This study was funded by a research grant No. 14.Y26.31.0004 from the Government of the Russian Federation. No funding agency played any role in the design or conclusion of this study. Publication costs are funded by the BioMed Central Membership of the University of Gottingen. . - ISSN 1471-2105РУБ Biochemical Research Methods + Biotechnology & Applied Microbiology

Аннотация: BackgroundDe novo assembling of large genomes, such as in conifers (similar to 12-30 Gbp), which also consist of similar to 80% of repetitive DNA, is a very complex and computationally intense endeavor. One of the main problems in assembling such genomes lays in computing limitations of nucleotide sequence assembly programs (DNA assemblers). As a rule, modern assemblers are usually designed to assemble genomes with a length not exceeding the length of the human genome (3.24 Gbp). Most assemblers cannot handle the amount of input sequence data required to provide sufficient coverage needed for a high-quality assembly.ResultsAn original stepwise method of de novo assembly by parts (sets), which allows to bypass the limitations of modern assemblers associated with a huge amount of data being processed, is presented in this paper. The results of numerical assembling experiments conducted using the model plant Arabidopsis thaliana, Prunus persica (peach) and four most popular assemblers, ABySS, SOAPdenovo, SPAdes, and CLC Assembly Cell, showed the validity and effectiveness of the proposed stepwise assembling method.ConclusionUsing the new stepwise de novo assembling method presented in the paper, the genome of Siberian larch, Larix sibirica Ledeb. (12.34 Gbp) was completely assembled de novo by the CLC Assembly Cell assembler. It is the first genome assembly for larch species in addition to only five other conifer genomes sequenced and assembled for Picea abies, Picea glauca, Pinus taeda, Pinus lambertiana, and Pseudotsuga menziesii var. menziesii.

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Siberian Fed Univ, Genome Res & Educ Ctr, Lab Forest Genom, Krasnoyarsk 660036, Russia.
Siberian Fed Univ, Inst Space & Informat Technol, Dept High Performance Comp, Krasnoyarsk 660074, Russia.
Natl Res Tech Univ, Dept Informat, Irkutsk 664074, Russia.
Russian Acad Sci, Limnol Inst, Siberian Branch, Irkutsk 664033, Russia.
Russian Acad Sci, VN Sukachev Inst Forest, Lab Forest Genet & Select, Siberian Branch, Krasnoyarsk 660036, Russia.
Georg August Univ Gottingen, Dept Forest Genet & Forest Tree Breeding, D-37077 Gottingen, Germany.
Russian Acad Sci, NI Vavilov Inst Gen Genet, Lab Populat Genet, Moscow 119333, Russia.
Texas A&M Univ, Dept Ecosyst Sci & Management, College Stn, TX 77843 USA.

Доп.точки доступа:
Kuzmin, Dmitry A.; Feranchuk, Sergey I.; Sharov, Vadim V.; Cybin, Alexander N.; Makolov, Stepan V.; Putintseva, Yuliya A.; Oreshkova, Natalya V.; Krutovsky, Konstantin V.; Krutovsky, Konstantin; Government of the Russian Federation - BioMed Central Membership of the University of Gottingen [14, Y26.31.0004]

[Текст] : статья / Н. В. Орешкова [и др.] // Генетика. - 2019. - Т. 55, № 4. - С. 418-425, DOI 10.1134/S001667581904009X . - ISSN 0016-6758
   Перевод заглавия: Development of Nuclear Microsatellite Markers with Long (Tri-, Tetra-, Penta-and Hexanucleotide) Motifs for Three Larch Species Based on the de novoWhole Genome Sequencing of Siberian Larch (Larix sibirica Ledeb.)

УДК

575.113

582.475.4

Аннотация: Лиственница сибирская Larix sibirica Ledeb. является одной из преобладающих бореальных пород в Евразии и имеет высокую экономическую и экологическую ценность. Однако, несмотря на это, разработка и использование микросателлитных маркеров для ее исследования остаются недостаточными. Микросателлитные маркеры уже долгое время являются признанным инструментом для оценки популяционной изменчивости и структуры видов. В настоящей работе был проведен поиск простых три-, тетра-, пента- и гексануклеотидных тандемных повторов в геномной референсной de novo сборке лиственницы сибирской, локусы которой легко генотипируются даже путем простого гель-электрофореза. Всего было найдено более тысячи предположительных микросателлитных локусов. На основе этих данных были разработаны и проверены 60 пар олигонуклеотидных ПЦР праймеров. По итогам тестирования праймеров на образцах ДНК из трех видов лиственницы (L. sibirica Ledeb., L. gmelinii (Rupr.) Rupr. и L. cajanderi Mayr.) были отобраны 14 наиболее перспективных полиморфных локусов, которые могут успешно применяться для изучения и идентификации не только лиственницы сибирской, но также лиственниц Гмелина и Каяндера.
Siberian larch Larix sibirica Ledeb. is one of the major boreal tree species in Eurasia and has a considerable economic and ecological value. Despite that importance, the development and use of microsatellite markers in this species remain limited. Microsatellite markers are considered to be a valuable tool for estimation of population diversity and structure. Availability of draft reference assembly of the Siberian larch genome allowed us to identify 1015 microsatellite loci or simple sequence repeats (SSRs) with tri-, tetra-, penta- and hexa-nucleotide motifs. For 60 of them PCR primers were designed and tested for amplification in L. sibirica and for their cross-genus transferability to L. gmelinii (Rupr.) Rupr. and L. cajanderi Mayr. Here we present a set of 14 reliable and polymorphic nuclear SSR markers that can be used for further population genetic studies, breeding programs and timber origin identification.

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Держатели документа:
Геттингенский университет им. Георга-Августа
Институт леса им. В.Н. Сукачева Сибирского отделения Российской академии наук : 660036, Красноярск, Академгородок, 50, стр. 28
Институт общей генетики им. Н.И. Вавилова Российской академии наук
Научно-образовательный центр геномных исследований Сибирского федерального университета
Техасский АМ университет, Колледж Стейшн

Доп.точки доступа:
Орешкова, Наталья Викторовна; Бондар, Е.И.; Bondar E.I.; Путинцева, Ю.А.; Putintseva Yu. A.; Шаров, В.В.; Sharov V.V.; Кузьмин, Д.А.; Kuzmin D.A.; Крутовский, К.В.; Krutovsky K.V.

/ A. K. Ekart, V. L. Semerikov, A. Y. Larionova, A. N. Kravchenko // Russ. J. Gen. - 2020. - Vol. 56, Is. 7. - P869-873, DOI 10.1134/S1022795420070030 . - ISSN 1022-7954
Аннотация: Abstract: The variability of the mitochondrial locus mh44 was studied in 24 natural populations of Siberian spruce (Picea obovata Ledeb.). Thirteen allelic variants differing in the number of repeats of the 32-nucleotide minisatellite motif were identified. The parameters of intra- and interpopulation diversity and the level of differentiation of the spruce populations included in the study were determined. © 2020, Pleiades Publishing, Inc.

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Держатели документа:
Sukachev Institute of Forest, Siberian Branch, Russian Academy of Sciences, Krasnoyarsk, 660036, Russian Federation
Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Yekaterinburg, 620144, Russian Federation

Доп.точки доступа:
Ekart, A. K.; Semerikov, V. L.; Larionova, A. Y.; Kravchenko, A. N.

/ A. K. Ekart, V. L. Semerikov, A. Y. Larionova, A. N. Kravchenko // Russ. J. Genet. - 2020. - Vol. 56, Is. 7. - P869-873, DOI 10.1134/S1022795420070030. - Cited References:18. - This study was carried out under basic research project no. 0356-2019-0024 with partial support from the Russian Foundation for Basic Research (project no. 13-04-00777a). . - ISSN 1022-7954. - ISSN 1608-3369РУБ Genetics & Heredity

Аннотация: The variability of the mitochondrial locusmh44was studied in 24 natural populations of Siberian spruce (Picea obovataLedeb.). Thirteen allelic variants differing in the number of repeats of the 32-nucleotide minisatellite motif were identified. The parameters of intra- and interpopulation diversity and the level of differentiation of the spruce populations included in the study were determined.

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Держатели документа:
Russian Acad Sci, Sukachev Inst Forest, Siberian Branch, Krasnoyarsk 660036, Russia.
Russian Acad Sci, Inst Plant & Anim Ecol, Ural Branch, Ekaterinburg 620144, Russia.

Доп.точки доступа:
Ekart, A. K.; Semerikov, V. L.; Larionova, A. Ya; Kravchenko, A. N.; Russian Foundation for Basic ResearchRussian Foundation for Basic Research (RFBR) [0356-2019-0024]; [13-04-00777a]

[Текст] : статья / А. К. Экарт, В. Л. Семериков, А. Я. Ларионова // Генетика. - 2020. - Т. 56, № 7. - С. 842-847 : табл., DOI 10.31857/S0016675820070036 . - ISSN 0016-6758
   Перевод заглавия: VARIABILITY OF THE MH44 LOCUS OF MITOCHONDRIAL DNAIN SIBERIAN SPRUCE POPULATIONS

УДК	575.174.015.3:582.475.2

Аннотация: Изучена изменчивость локуса mh44 мтДНК в 24 природных популяциях ели сибирской (Picea obovata Ledeb.). Идентифицировано 13 аллельных вариантов, различающихся по числу повторов 32-нуклеотидного минисателлитного мотива. Определены параметры внутри- и межпопуляционного разнообразия, уровень дифференциации включенных в исследование популяций ели
The variability of the mitochondrial locus mh44 was studied in 24 natural populations of Siberian spruce (Picea obovata Ledeb.). Thirteen allelic variants differing in the number of repeats of the 32-nucleotide minisatellite motif were identified. The parameters of intra- and interpopulation diversity and the level of differentiation of the spruce populations included in the study were determined

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Держатели документа:
Институт леса им. В.Н. Сукачева СО РАН : 660036, Красноярск, Академгородок, 50, стр. 28

Доп.точки доступа:
Экарт, Александр Карлович; Ekart, Alexandr Karlovich; Семериков, В.Л.; Semerikov V.L.; Ларионова, Альбина Яковлевна; Larionova, Al''bina Yakovlevna; Кравченко, Анна Николаевна; Kravchenko, Anna Nikolayevna

/ S. V. Prudnikova, S. Y. Evgrafova, T. G. Volova // Chemosphere. - 2021. - Vol. 263. - Ст. 128180, DOI 10.1016/j.chemosphere.2020.128180 . - ISSN 0045-6535
Аннотация: The present study investigates, for the first time, the structure of the microbial community of cryogenic soils in the subarctic region of Siberia and the ability of the soil microbial community to metabolize degradable microbial bioplastic – poly-3-hydroxybutyrate [P(3HB)]. When the soil thawed, with the soil temperature between 5-7 and 9–11 °C, the total biomass of microorganisms at a 10-20-cm depth was 226–234 mg g?1 soil and CO2 production was 20–46 mg g?1 day?1. The total abundance of microscopic fungi varied between (7.4 ± 2.3) ? 103 and (18.3 ± 2.2) ? 103 CFU/g soil depending on temperature; the abundance of bacteria was several orders of magnitude greater: (1.6 ± 0.1) ? 106 CFU g?1 soil. The microbial community in the biofilm formed on the surface of P(3HB) films differed from the background soil in concentrations and composition of microorganisms. The activity of microorganisms caused changes in the surface microstructure of polymer films, a decrease in molecular weight, and an increase in the degree of crystallinity of P(3HB), indicating polymer biodegradation due to metabolic activity of microorganisms. The clear-zone technique – plating of isolates on the mineral agar with polymer as sole carbon source – was used to identify P(3HB)-degrading microorganisms inhabiting cryogenic soil in Evenkia. Analysis of nucleotide sequences of rRNA genes was performed to identify the following P(3HB)-degrading species: Bacillus pumilus, Paraburkholderia sp., Pseudomonas sp., Rhodococcus sp., Stenotrophomonas rhizophila, Streptomyces prunicolor, and Variovorax paradoxus bacteria and the Penicillium thomii, P. arenicola, P. lanosum, Aspergillus fumigatus, and A. niger fungi. © 2020 Elsevier Ltd

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Держатели документа:
Siberian Federal University, 79 Svobodny Pr, Krasnoyarsk, 660041, Russian Federation
V.N. Sukachev Institute of Forest, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 50/28 Akademgorodok, Krasnoyarsk, 660036, Russian Federation
Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 50/50 Akademgorodok, Krasnoyarsk, 660036, Russian Federation
Melnikov Permafrost Institute, SB RAS, 36 Merzlotnaya St., Yakutsk, 677010, Russian Federation

Доп.точки доступа:
Prudnikova, S. V.; Evgrafova, S. Y.; Volova, T. G.

/ Y. A. Putintseva, E. I. Bondar, E. P. Simonov [et al.] // BMC Genomics. - 2020. - Vol. 21, Is. 1. - P654, DOI 10.1186/s12864-020-07061-4 . - ISSN 1471-2164
Аннотация: BACKGROUND: Plant mitochondrial genomes (mitogenomes) can be structurally complex while their size can vary from ~?222 Kbp in Brassica napus to 11.3 Mbp in Silene conica. To date, in comparison with the number of plant species, only a few plant mitogenomes have been sequenced and released, particularly for conifers (the Pinaceae family). Conifers cover an ancient group of land plants that includes about 600 species, and which are of great ecological and economical value. Among them, Siberian larch (Larix sibirica Ledeb.) represents one of the keystone species in Siberian boreal forests. Yet, despite its importance for evolutionary and population studies, the mitogenome of Siberian larch has not yet been assembled and studied. RESULTS: Two sources of DNA sequences were used to search for mitochondrial DNA (mtDNA) sequences: mtDNA enriched samples and nucleotide reads generated in the de novo whole genome sequencing project, respectively. The assembly of the Siberian larch mitogenome contained nine contigs, with the shortest and the largest contigs being 24,767?bp and 4,008,762?bp, respectively. The total size of the genome was estimated at 11.7 Mbp. In total, 40 protein-coding, 34 tRNA, and 3 rRNA genes and numerous repetitive elements (REs) were annotated in this mitogenome. In total, 864 C-to-U RNA editing sites were found for 38 out of 40 protein-coding genes. The immense size of this genome, currently the largest reported, can be partly explained by variable numbers of mobile genetic elements, and introns, but unlikely by plasmid-related sequences. We found few plasmid-like insertions representing only 0.11% of the entire Siberian larch mitogenome. CONCLUSIONS: Our study showed that the size of the Siberian larch mitogenome is much larger than in other so far studied Gymnosperms, and in the same range as for the annual flowering plant Silene conica (11.3 Mbp). Similar to other species, the Siberian larch mitogenome contains relatively few genes, and despite its huge size, the repeated and low complexity regions cover only 14.46% of the mitogenome sequence.

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Держатели документа:
Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russian Federation
Laboratory of Genomic Research and Biotechnology, Federal Research Center "Krasnoyarsk Science Center", Russian Academy of Sciences, Siberian Branch, Krasnoyarsk, 660036, Russian Federation
Institute of Environmental and Agricultural Biology (X-BIO), University of Tyumen, Tyumen, 625003, Russian Federation
Department of High Performance Computing, Institute of Space and Information Technologies, Siberian Federal University, Krasnoyarsk, 660074, Russian Federation
Laboratory of Forest Genetics and Selection, V. N. Sukachev Institute of Forest, Russian Academy of Sciences, Siberian Branch, Krasnoyarsk, 660036, Russian Federation
Laboratory of Plant Genetic Engineering, Siberian Institute of Plant Physiology and Biochemistry, Russian Academy of Sciences, Siberian Branch, Irkutsk, 664033, Russian Federation
Institute of Computational Modeling, Russian Academy of Sciences, Siberian Branch, Krasnoyarsk, 660036, Russian Federation
Department of Plant Physiology, UPSC, Umea University, Umea, S-90187, Sweden
Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Gottingen, Gottingen37077, Germany
Center for Integrated Breeding Research, George-August University of Gottingen, Gottingen37075, Germany
Laboratory of Population Genetics, N.I. Vavilov Institute of General Genetics, Russian Academy of SciencesMoscow 119333, Russian Federation
Department of Ecosystem Science and Management, Texas A&M University, TX, College Station, United States

Доп.точки доступа:
Putintseva, Y. A.; Bondar, E. I.; Simonov, E. P.; Sharov, V. V.; Oreshkova, N. V.; Kuzmin, D. A.; Konstantinov, Y. M.; Shmakov, V. N.; Belkov, V. I.; Sadovsky, M. G.; Keech, O.; Krutovsky, K. V.

/ Y. A. Putintseva, E. I. Bondar, E. P. Simonov [et al.] // BMC Genomics. - 2020. - Vol. 21, Is. 1. - Ст. 654, DOI 10.1186/s12864-020-07061-4. - Cited References:70. - This study was supported by research grants No 14.Y26.31.0004 from the Russian Federation Government for the "Genomics of the key boreal forest conifer species and their major phytopathogens in the Russian Federation" project and. 16-04-01400 from the Russian Foundation for Basic Research. OK was supported by TC4F and the KEMPE Foundations. Open Access funding enabled and organized by Projekt DEAL. . - ISSN 1471-2164РУБ Biotechnology & Applied Microbiology + Genetics & Heredity

Аннотация: Background: Plant mitochondrial genomes (mitogenomes) can be structurally complex while their size can vary from similar to 222 Kbp inBrassica napusto 11.3 Mbp inSilene conica. To date, in comparison with the number of plant species, only a few plant mitogenomes have been sequenced and released, particularly for conifers (the Pinaceae family). Conifers cover an ancient group of land plants that includes about 600 species, and which are of great ecological and economical value. Among them, Siberian larch (Larix sibiricaLedeb.) represents one of the keystone species in Siberian boreal forests. Yet, despite its importance for evolutionary and population studies, the mitogenome of Siberian larch has not yet been assembled and studied. Results: Two sources of DNA sequences were used to search for mitochondrial DNA (mtDNA) sequences: mtDNA enriched samples and nucleotide reads generated in the de novo whole genome sequencing project, respectively. The assembly of the Siberian larch mitogenome contained nine contigs, with the shortest and the largest contigs being 24,767 bp and 4,008,762 bp, respectively. The total size of the genome was estimated at 11.7 Mbp. In total, 40 protein-coding, 34 tRNA, and 3 rRNA genes and numerous repetitive elements (REs) were annotated in this mitogenome. In total, 864 C-to-U RNA editing sites were found for 38 out of 40 protein-coding genes. The immense size of this genome, currently the largest reported, can be partly explained by variable numbers of mobile genetic elements, and introns, but unlikely by plasmid-related sequences. We found few plasmid-like insertions representing only 0.11% of the entire Siberian larch mitogenome. Conclusions: Our study showed that the size of the Siberian larch mitogenome is much larger than in other so far studied Gymnosperms, and in the same range as for the annual flowering plantSilene conica(11.3 Mbp). Similar to other species, the Siberian larch mitogenome contains relatively few genes, and despite its huge size, the repeated and low complexity regions cover only 14.46% of the mitogenome sequence.

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Держатели документа:
Siberian Fed Univ, Lab Forest Genom, Genome Res & Educ Ctr, Inst Fundamental Biol & Biotechnol, Krasnoyarsk 660036, Russia.
Russian Acad Sci, Lab Genom Res & Biotechnol, Fed Res Ctr, Siberian Branch,Krasnoyarsk Sci Ctr, Krasnoyarsk 660036, Russia.
Univ Tyumen, Inst Environm & Agr Biol XBIO, Tyumen 625003, Russia.
Siberian Fed Univ, Inst Space & Informat Technol, Dept High Performance Comp, Krasnoyarsk 660074, Russia.
Russian Acad Sci, VN Sukachev Inst Forest, Lab Forest Genet & Select, Siberian Branch, Krasnoyarsk 660036, Russia.
Russian Acad Sci, Siberian Inst Plant Physiol & Biochem, Lab Plant Genet Engn, Siberian Branch, Irkutsk 664033, Russia.
Russian Acad Sci, Inst Computat Modeling, Siberian Branch, Krasnoyarsk 660036, Russia.
Umea Univ, Dept Plant Physiol, UPSC, S-90187 Umea, Sweden.
August Univ Gottingen, Dept Forest Genet & Forest Tree Breeding, D-37077 Gottingen, Germany.
George August Univ Gottingen, Ctr Integrated Breeding Res, D-37075 Gottingen, Germany.
Russian Acad Sci, NI Vavilov Inst Gen Genet, Lab Populat Genet, Moscow 119333, Russia.
Texas A&M Univ, Dept Ecosyst Sci & Management, College Stn, TX 77843 USA.

Доп.точки доступа:
Putintseva, Yuliya A.; Bondar, Eugeniya I.; Simonov, Evgeniy P.; Sharov, Vadim V.; Oreshkova, Natalya V.; Kuzmin, Dmitry A.; Konstantinov, Yuri M.; Shmakov, Vladimir N.; Belkov, Vadim I.; Sadovsky, Michael G.; Keech, Olivier; Krutovsky, Konstantin V.; Krutovsky, Konstantin; Russian Federation Government [14.Y26.31.0004]; Russian Foundation for Basic ResearchRussian Foundation for Basic Research (RFBR) [16-04-01400]; TC4F Foundation; KEMPE Foundation; Projekt DEAL

/ S. V. Prudnikova, S. Y. Evgrafova, T. G. Volova // Chemosphere. - 2021. - Vol. 263. - Ст. 128180, DOI 10.1016/j.chemosphere.2020.128180. - Cited References:101. - This study (polymer synthesis and investigation) was financially supported by Project "Agropreparations of the new generation: a strategy of construction and realization" (Agreement No 074-02-2018-328) in accordance with Resolution No 220 of the Government of the Russian Federation of April 9, 2010, "On measures designed to attract leading scientists to the Russian institutions of higher learning", and by the State assignment of the Ministry of Science and Higher Education of the Russian Federation No. FSRZ-2020-0006 (investigation of polymer degradation in soils of Evenkia). . - ISSN 0045-6535. - ISSN 1879-1298РУБ Environmental Sciences

Аннотация: The present study investigates, for the first time, the structure of the microbial community of cryogenic soils in the subarctic region of Siberia and the ability of the soil microbial community to metabolize degradable microbial bioplastic - poly-3-hydroxybutyrate [P(3HB)]. When the soil thawed, with the soil temperature between 5-7 and 9-11 degrees C, the total biomass of microorganisms at a 10-20-cm depth was 226-234 mg g(-1) soil and CO2 production was 20-46 mg g(-1)W day(-1). The total abundance of microscopic fungi varied between (7.4 +/- 2.3) x 10(3) and (18.3 +/- 2.2) x 10(3) CFU/g soil depending on temperature; the abundance of bacteria was several orders of magnitude greater: (1.6 +/- 0.1) x 10(6) CFU g(-1) soil. The microbial community in the biofilm formed on the surface of P(3HB) films differed from the background soil in concentrations and composition of microorganisms. The activity of microorganisms caused changes in the surface microstructure of polymer films, a decrease in molecular weight, and an increase in the degree of crystallinity of P(3HB), indicating polymer biodegradation due to metabolic activity of microorganisms. The clear-zone technique e plating of isolates on the mineral agar with polymer as sole carbon source e was used to identify P(3HB)-degrading microorganisms inhabiting cryogenic soil in Evenkia. Analysis of nucleotide sequences of rRNA genes was performed to identify the following P(3HB)degrading species: Bacillus pumilus, Paraburkholderia sp., Pseudomonas sp., Rhodococcus sp., Stenotrophomonas rhizophila, Streptomyces prunicolor, and Variovorax paradoxus bacteria and the Penicillium thomii, P. arenicola, P. lanosum, Aspergillus fumigatus, and A. niger fungi. (C) 2020 Elsevier Ltd. All rights reserved.

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Держатели документа:
Siberian Fed Univ, 79 Svobodny Pr, Krasnoyarsk 660041, Russia.
Krasnoyarsk Sci Ctr SB RAS, Fed Res Ctr, VN Sukachev Inst Forest, 50-28 Akademgorodok, Krasnoyarsk 660036, Russia.
Krasnoyarsk Sci Ctr SB RAS, Fed Res Ctr, Inst Biophys SB RAS, 50-50 Akademgorodok, Krasnoyarsk 660036, Russia.
SB RAS, Melnikov Permafrost Inst, 36 Merzlotnaya St, Yakutsk 677010, Russia.

Доп.точки доступа:
Prudnikova, Svetlana, V; Evgrafova, Svetlana Yu; Volova, Tatiana G.; Project "Agropreparations of the new generation: a strategy of construction and realization" [074-02-2018-328]; Government of the Russian Federation [220]; Ministry of Science and Higher Education of the Russian Federation [FSRZ-2020-0006]

/ V. L. Semerikov, S. A. Semerikova, Y. A. Putintseva // Russ. J. Gen. - 2021. - Vol. 57, Is. 11. - P1258-1262, DOI 10.1134/S1022795421100112 . - ISSN 1022-7954
Аннотация: Abstract: The results of phylogenetic analysis of 15 species, representing all the main evolutionary lineages of the genus Abies, and Keteleeria davidiana, used as an outgroup, are presented. The data include the nucleotide sequences of mitochondrial DNA about 28 kb in length obtained by partial resequencing of the assembly of the mitochondrial genome of the Siberian fir A. sibirica. The basal position of the mtDNA haplotypes of some American firs has been established, which confirms the American origin of modern Abies. The mitotypes of most Eurasian species form a daughter clade with respect to American firs, indicating its origin as a result of one migration from America to Eurasia. At the same time, previously obtained data on nuclear and chloroplast DNA indicate repeated migrations of firs from America to Eurasia. This conflict between mitochondrial and nuclear data can be explained by a hybrid capture of mitochondrial DNA of native Eurasian species by migrant species. © 2021, Pleiades Publishing, Inc.

Scopus

Держатели документа:
Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Yekaterinburg, 620144, Russian Federation
Sukachev Institute of Forest, Siberian Branch, Russian Academy of Sciences, Krasnoyarsk, 660036, Russian Federation

Доп.точки доступа:
Semerikov, V. L.; Semerikova, S. A.; Putintseva, Y. A.

/ V. L. Semerikov, S. A. Semerikova, Y. A. Putintseva // Russ. J. Genet. - 2021. - Vol. 57, Is. 11. - P1258-1262, DOI 10.1134/S1022795421100112. - Cited References:17. - This work was carried out within the framework of the state assignment of the Institute of Plant and Animal Ecology of the Ural Branch of the Russian Academy of Sciences and with the financial support of the Russian Foundation for Basic Research, project no. 19-04-00795. . - ISSN 1022-7954. - ISSN 1608-3369РУБ Genetics & Heredity

Аннотация: The results of phylogenetic analysis of 15 species, representing all the main evolutionary lineages of the genus Abies, and Keteleeria davidiana, used as an outgroup, are presented. The data include the nucleotide sequences of mitochondrial DNA about 28 kb in length obtained by partial resequencing of the assembly of the mitochondrial genome of the Siberian fir A. sibirica. The basal position of the mtDNA haplotypes of some American firs has been established, which confirms the American origin of modern Abies. The mitotypes of most Eurasian species form a daughter clade with respect to American firs, indicating its origin as a result of one migration from America to Eurasia. At the same time, previously obtained data on nuclear and chloroplast DNA indicate repeated migrations of firs from America to Eurasia. This conflict between mitochondrial and nuclear data can be explained by a hybrid capture of mitochondrial DNA of native Eurasian species by migrant species.

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Держатели документа:
Russian Acad Sci, Inst Plant & Anim Ecol, Ural Branch, Ekaterinburg 620144, Russia.
Russian Acad Sci, Sukachev Inst Forest, Siberian Branch, Krasnoyarsk 660036, Russia.

Доп.точки доступа:
Semerikov, V. L.; Semerikova, S. A.; Putintseva, Yu A.; Russian Foundation for Basic ResearchRussian Foundation for Basic Research (RFBR) [19-04-00795]

[Текст] : научное издание / С. В. Новикова, Н. В. Орешкова, В. В. Шаров, В. Л. Семериков, К. В. Крутовский // Сибирский экологический журнал. - 2023. - Т. 30, № 5. - С. 675-691, DOI 10.15372/SEJ20230509 . - ISSN 0869-8619
   Перевод заглавия: GENETIC STRUCTURE AND GEOGRAPHICAL DIFFERENTIATION OF SIBERIAN LARCH (LARIX SIBIRICA LEDEB.) POPULATIONS BASED ON GENOME GENOTYPING BY SEQUENCING

ГРНТИ

68.47.03

Аннотация: Приведены результаты исследования генетической дифференциации популяций лиственницы сибирской (Larix sibirica Ledeb.) в широтном градиенте климатических условий, полученные на основе генотипирования генома с помощью высокопроизводительного секвенирования геномных районов ДНК, ассоциированных с сайтами рестрикции (ddRADseq). Изучена также корреляция пяти основных климатических переменных с изменчивостью 47 929 генетических маркеров - однонуклеотидных полиморфизмов или “снипов” (от английского SNPs - single nucleotide polymorphisms). Всего изучено 125 деревьев: 61 дерево в четырех популяциях вдоль западной географической трансекты и 64 дерева в четырех популяциях вдоль восточной географической трансекты. Выявлен 21 SNPs с признаками отбора, включая 9 SNPs аутлайеров, чья изменчивость не может быть объяснена селективно-нейтральными процессами, и 12 SNPs, чья изменчивость коррелировала с изменчивостью некоторых климатических факторов. Семь SNPs расположены в интронах митохондриальных генов, три расположены вблизи митохондриальных генов, кодирующих NAD2 и рибосомальные белки S7 и S11, один на отдалении от ядерного гена, кодирующего белок, гомологичный связанному с микротрубочками futsch-подобному белку Arabidopsis thaliana, два в белковых генах неизвестной природы и три в контигах, не содержащих гены, и для которых не найдены гомологичные последовательности в NCBI GenBank.
The genetic differentiation of Siberian larch (Larix sibirica Ledeb.) populations in the latitudinal gradient of climatic conditions was studied based on high-throughput double digest restriction-site associated DNA sequencing (ddRADseq) data. We studied the correlation of five main climatic variables with the variability of 47,929 single nucleotide polymorphisms (SNPs). A total of 125 trees were studied: 61 trees in four populations along the western geographic transect and 64 trees in four populations along the eastern geographic transect. 21 SNPs with signatures of selection were identified, including 9 outlier SNPs whose variability cannot be explained by selectively neutral processes, and 12 SNPs whose variability correlated with the environmental factors. Seven SNPs are located in the introns of mitochondrial genes, three are located relatively close to the mitochondrial genes encoding NAD2 and ribosomal proteins S7 and S11, one is located at a distance from the nuclear gene encoding a protein homologous to the microtubule-associated futsch-like protein of Arabidopsis thaliana, two in the protein genes of an unknown nature and three in contigs containing no genes, and for which no homologous sequences were found in the NCBI GenBank.

РИНЦ

Держатели документа:
ИЛ СО РАН : 660036, Красноярск, Академгородок, 50, стр. 28

Доп.точки доступа:
Орешкова, Наталья Викторовна; Шаров, В.В.; Семериков, В.Л.; Semerikov V.L.; Крутовский, Константин Валерьевич; Krutovsky, Konstantin V.