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

/ O. V. Goryachkina [et al.] // Plant Syst. Evol. - 2013. - Vol. 299, Is. 2. - P471-479, DOI 10.1007/s00606-012-0737-y. - Cited References: 36. - The authors thank Aleksander P. Isaev Ph.D. (Institute for Biological Problems of Cryolithozone SB RAS, Yakutsk), Alexey P. Barchenkov Ph.D. (V.N. Sukachev Institute of Forest SB RAS, Krasnoyarsk), and Candagdorj Jamiyansuren Ph.D. (Institute of Botany, Mongolian Academy of Sciences, Ulaanbaatar) for supplying the seed samples. This work was supported by grant no. 76 from the Integration Program of the Siberian Branch of the Russian Academy of Sciences and the Russian Foundation for Basic Research (Projects No. 11-04-00063 and 10-04-90780). . - 9. - ISSN 0378-2697РУБ Plant Sciences + Evolutionary Biology

Аннотация: Karyotypes of three Larix species (L. sibirica, L. gmelinii, and L. cajanderi) were analyzed using fluorescence in situ hybridization (FISH) with 45S and 5S ribosomal RNA gene probes and 4',6-diamidino-2-phenylindole (DAPI) staining. Two major 45S ribosomal DNA (rDNA) loci (per haploid genome) have been observed in the intercalary regions of two metacentric chromosomes, III and IV, of L. sibirica; in addition to them, minor nucleolus organizing regions (NORs) were mapped in pericentromeric regions of chromosomes I, II, VI, and XII. Two closely related species, L. gmelinii and L. cajanderi, showed similar hybridization patterns; both species possessed an additional major locus of 45S rDNA in the distal region of the long arm of submetacentric chromosome VII that is absent in L. sibirica. Only one locus of the 5S rDNA was found in all larch species we studied; it was located in the distal region of the chromosome III short arm, which also carried the major NOR in the opposite arm. This chromosome containing major loci of the two ribosomal RNA gene families can serve as a marker of the genus Larix. The intra- and interspecific karyotype diversity in the genus Larix is discussed.

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Держатели документа:
[Goryachkina, Olga V.
Muratova, Elena N.] Russian Acad Sci, VN Sukachev Inst Forest, Siberian Branch, Krasnoyarsk 660036, Russia
[Badaeva, Ekaterina D.
Zelenin, Alexandr V.] Russian Acad Sci, VA Engelhardt Mol Biol Inst, Moscow 119991, Russia

Доп.точки доступа:
Goryachkina, O.V.; Badaeva, E.D.; Muratova, E.N.; Zelenin, A.V.

[Text] / A. Y. Larionova, N. V. Yakhneva, A. P. Abaimov // Russ. J. Genet. - 2004. - Vol. 40, Is. 10. - P1127-1133, DOI 10.1023/B:RUGE.0000044756.55722.d8. - Cited References: 32 . - 7. - ISSN 1022-7954РУБ Genetics & Heredity

Аннотация: Within- and among-population diversity of Gmelin larch Larix gmelinii (Rupr.) Rupr. from Evenkia was inferred from data on 17 genes determining allozyme diversity of ten enzymes. More than 50% of the genes proved to be polymorphic. On average, each tree was heterozygous at 9.2% genes. Heterozygosity expected from the Hardy-Weinberg proportions was higher, 12.5%. A deficit of heterozygous genotypes was observed in all populations under study and attributed to inbreeding. With Wright's F statistics, average individual inbreeding was estimated at 26.6% relative to the population (F-IS) and at 27.8% relative to the species (F-IT). The greatest deficit of heterozygosity was observed for the youngest population II. Within- population variation accounted for more than 98% of the total variation, while the contribution of among-population variation was 1.66%. Genetic distance between populations varied from 0.0025 to 0.0042, averaging 0.0035.

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Russian Acad Sci, Sukachev Inst Forestry, Krasnoyarsk 660036, Russia

Доп.точки доступа:
Larionova, A.Y.; Yakhneva, N.V.; Abaimov, A.P.

[Text] / A. Y. Larionova // Russ. J. Genet. - 2002. - Vol. 38, Is. 12. - P1391-1396, DOI 10.1023/A:1021639806123. - Cited References: 34 . - 6. - ISSN 1022-7954РУБ Genetics & Heredity

Аннотация: The main parameters of genetic variability have been determined in an isolated natural Scotch pine population from Chita oblast (Tsasuchei Forest) by analysis of 19 genes coding for nine enzymes: GDH, IDH, LAP, PGM, AAT, ADH, MDH, 6-PGD, and DIA. Polymorphic genes constituted 63.2% of all structural genes studied in the population at the 99% polymorphism criterion. The mean number of alleles per locus was 1.63. The observed and expected heterozygosities were 0.237 and 0.251, respectively. These estimates are close to the corresponding mean values for Scotch pine according to the data on 18 or more structural genes.

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Russian Acad Sci, Sukachev Inst Forestry, Krasnoyarsk 660036, Russia

Доп.точки доступа:
Larionova, A.Y.

[Текст] / D. L. Grodnitsky // Zhurnal Obshchei Biol. - 2000. - Vol. 61, Is. 4. - С. 371-380. - Cited References: 74 . - 10. - ISSN 0044-4596РУБ Biology

Аннотация: Neo-Darwinism is a result of synthesis of Darwinian concept of natural selection with Weismannian concept of germ plasm. The concept of germ plasm is based on a hypothesis that phenotypic traits are completely determined by genes. Hence, neo-Darwinism describes evolution as a process of alternation of ene frequencies under the effect of natural selection. This is an inadequate approach to the study of evolution. In the course of evolution, genes change their functions, whereas phenotypic characters change their corresponding genes. As a result, every step of evolutionary transformation changes the structure of phenotype-to-genotype correspondence. Therefore, phenotypic evolution cannot be described in genetic terms, the same as to human languages cannot be translated one into another whenever the meaning of words is constantly changing. Consequently, Weismannian germ-plasm concept adequately desribes the relation of characters to genes only during stasis, but is inapplicable to evolution.

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Держатели документа:
Russian Acad Sci, Siberian Branch, Sukachev Inst Forest Res, Krasnoyarsk 660036, Russia

Доп.точки доступа:
Grodnitsky, D.L.

/ D. L. Grodnitskii // Zhurnal obshchei biologii. - 2000. - Vol. 61, Is. 4. - С. 371-380 . - ISSN 0044-4596
Аннотация: Neo-Darwinism is a result of synthesis of Darwinian concept of natural selection with Weismannian concept of germ plasma. The concept of germ plasma is based on a hypothesis that phenotypic traits are completely determined by genes. Hence, neo-Darwinism describes evolution as a process of alternation of gene frequencies under the effect of natural selection. This is an inadequate approach to the study of evolution. In the course of evolution, genes change their functions, whereas phenotypic characters change their corresponding genes. As a result, every step of evolutionary transformation changes the structure of phenotype-to-genotype correspondence. Therefore, phenotypic evolution cannot be described in genetic terms, the same as to human languages cannot be translated one into another whenever the meaning of words is constantly changing. Consequently, Weismannian germ-plasma concept adequately describes the relation of characters to genes only during stasis, but is inapplicable to evolution.

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Держатели документа:
Sukachev Institute of Forest Research, Siberian Branch, Russian Academy of Sciences, Krasnoyarsk, Russia.

Доп.точки доступа:
Grodnitskii, D.L.

/ A. Gittel [et al.] // ISME J. - 2013, DOI 10.1038/ismej.2013.219 . - ISSN 1751-7362
Аннотация: Cryoturbation, the burial of topsoil material into deeper soil horizons by repeated freeze-thaw events, is an important storage mechanism for soil organic matter (SOM) in permafrost-affected soils. Besides abiotic conditions, microbial community structure and the accessibility of SOM to the decomposer community are hypothesized to control SOM decomposition and thus have a crucial role in SOM accumulation in buried soils. We surveyed the microbial community structure in cryoturbated soils from nine soil profiles in the northeastern Siberian tundra using high-throughput sequencing and quantification of bacterial, archaeal and fungal marker genes. We found that bacterial abundances in buried topsoils were as high as in unburied topsoils. In contrast, fungal abundances decreased with depth and were significantly lower in buried than in unburied topsoils resulting in remarkably low fungal to bacterial ratios in buried topsoils. Fungal community profiling revealed an associated decrease in presumably ectomycorrhizal (ECM) fungi. The abiotic conditions (low to subzero temperatures, anoxia) and the reduced abundance of fungi likely provide a niche for bacterial, facultative anaerobic decomposers of SOM such as members of the Actinobacteria, which were found in significantly higher relative abundances in buried than in unburied topsoils. Our study expands the knowledge on the microbial community structure in soils of Northern latitude permafrost regions, and attributes the delayed decomposition of SOM in buried soils to specific microbial taxa, and particularly to a decrease in abundance and activity of ECM fungi, and to the extent to which bacterial decomposers are able to act as their functional substitutes.The ISME Journal advance online publication, 12 December 2013; doi:10.1038/ismej.2013.219.

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Держатели документа:
1] Department of Biology, Centre for Geobiology, University of Bergen, Bergen, Norway
Austrian Polar Research Institute, Vienna, Austria
Department of Ecosystems Biology, University of South Bohemia, Ceske Budejovice, Czech Republic
Institut fur Bodenkunde, Leibniz Universitat Hannover, Hannover, Germany
1] Institute of Genomics and Systems Biology, Argonne National Laboratory, Argonne, IL, USA
Computation Institute, University of Chicago, Chicago, IL, USA
Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
1] Austrian Polar Research Institute, Vienna, Austria
Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
Department of Earth Science, Centre for Geobiology, University of Bergen, Bergen, Norway
Division of Ecosystem Modelling, Institute of Coastal Research, Helmholtz Zentrum Geesthacht, Geesthacht, Germany
Central Siberian Botanical Garden, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
1] Institut fur Bodenkunde, Leibniz Universitat Hannover, Hannover, Germany
VN Sukachev Institute of Forest, Siberian Branch of Russian Academy of Sciences, Akademgorodok, Russia
Department of Biology, Centre for Geobiology, University of Bergen, Bergen, Norway
Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria

Доп.точки доступа:
Gittel, A.; Barta, J.; Kohoutova, I.; Mikutta, R.; Owens, S.; Gilbert, J.; Schnecker, J.; Wild, B.; Hannisdal, B.; Maerz, J.; Lashchinskiy, N.; Capek, P.; Santruckova, H.; Gentsch, N.; Shibistova, O.; Guggenberger, G.; Richter, A.; Torsvik, V.L.; Schleper, C.; Urich, T.

[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]

[Text] / N. Kirichenko [et al.] // ZooKeys. - 2016. - Is. 579. - P99-156, DOI 10.3897/zookeys.579.7166. - Cited References:68. - We are grateful to the team at the Biodiversity Institute of Ontario, University of Guelph, Ontario, Canada for their great assistance in the production of DNA barcodes. Funding for DNA barcoding and sequence analysis was partly provided by the Government of Canada through Genome Canada and the Ontario Genomics Institute in support of the International Barcode of Life project, and by NSERC. Genetic analyses were also partly funded by INRA, UR0633 Zoologie Forestiere's core funding. Our work was also aided by the BOLD informatics platform whose development is funded by the Ontario Ministry of Economic Development and Innovation. NK was supported by a fellowship of LE STUDIUM (R), France and the Russian foundation for basic research (grant No 15-29-02645). . - ISSN 1313-2989. - ISSN 1313-2970РУБ Zoology

Аннотация: During a DNA barcoding campaign of leaf-mining insects from Siberia, a genetically divergent lineage of a gracillariid belonging to the genus Micrurapteryx was discovered, whose larvae developed on Caragana Fabr. and Medicago L. (Fabaceae). Specimens from Siberia showed similar external morphology to the Palearctic Micrurapteryx gradatella and the Nearctic Parectopa occulta but differed in male genitalia, DNA barcodes, and nuclear genes histone H3 and 28S. Members of this lineage are re-described here as Micrurapteryx caraganella (Hering, 1957), comb. n., an available name published with only a brief description of its larva and leaf mine. Micrurapteryx caraganella is widely distributed throughout Siberia, from Tyumen oblast in the West to Transbaikalia in the East. Occasionally it may severely affect its main host, Caragana arborescens Lam. This species has been confused in the past with Micrurapreryx gradatella in Siberia, but field observations confirm that M. gradatella exists in Siberia and is sympatric with M. caraganella, at least in the Krasnoyarsk region, where it feeds on different host plants (Vicia amoena Fisch. and Vicia sp.). In addition, based on both morphological and molecular evidence as well as examination of type specimens, the North American Parectopa occulta Braun, 1922 and Parectopa albicostella Braun, 1925 are transferred to Micrurapteryx as M. occulta (Braun, 1922), comb. n. with albicostella as its junior synonym (syn. n.). Characters used to distinguish Micrurapteryx from Parectopa are presented and illustrated. These findings provide another example of the potential of DNA barcoding to reveal overlooked species and illuminate nomenclatural problems.

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Держатели документа:
Sukachev Inst Forest SB RAS, Akademgorodok 50-28, Krasnoyarsk 660036, Russia.
Siberian Fed Univ, 79 Svobodny Pr, Krasnoyarsk 660041, Russia.
INRA, Zool Forestiere UR0633, F-45075 Orleans, France.
Museo Civ Storia Nat, Lungadige Porta Vittoria 9, I-37129 Verona, Italy.
Univ Oulu, Dept Genet & Physiol, POB 3000, FI-90014 Oulu, Finland.
Agr & Agri Food Canada, Ottawa Res & Dev Ctr, Cent Expt Farm, Ottawa, ON K1A 0C6, Canada.
Univ Tours, Inst Rech Biol Insecte, CNRS UMR 7261, UFR Sci & Tech, F-37200 Tours, France.

Доп.точки доступа:
Kirichenko, Natalia; Triberti, Paolo; Mutanen, Marko; Magnoux, Emmanuelle; Landry, Jean-Francois; Lopez-Vaamonde, Carlos; Government of Canada through Genome Canada; Ontario Genomics Institute; NSERC; INRA [UR0633]; Ontario Ministry of Economic Development and Innovation; LE STUDIUM(R), France; Russian foundation for basic research [15-29-02645]

/ 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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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

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

/ N. Kirichenko [et al.] // PLoS ONE. - 2017. - Vol. 12, Is. 2, DOI 10.1371/journal.pone.0171104 . - ISSN 1932-6203
Аннотация: Knowing the phylogeographic structure of invasive species is important for understanding the underlying processes of invasion. The micromoth Phyllonorycter issikii, whose larvae damage leaves of lime trees Tilia spp., was only known from East Asia. In the last three decades, it has been recorded in most of Europe, Western Russia and Siberia. We used the mitochondrial cytochrome c oxidase subunit I (COI) gene region to compare the genetic variability of P. issikii populations between these different regions. Additionally, we sequenced two nuclear genes (28S rRNA and Histone 3) and run morphometric analysis of male genitalia to probe for the existence of cryptic species. The analysis of COI data of 377 insect specimens collected in 16 countries across the Palearctic revealed the presence of two different lineages: P. issikii and a putative new cryptic Phyllonorycter species distributed in the Russian Far East and Japan. In P. issikii, we identified 31 haplotypes among which 23 were detected in the invaded area (Europe) and 10 were found in its putative native range in East Asia (Russian Far East, Japan, South Korea and China), with only two common haplotypes. The high number of haplotypes found in the invaded area suggest a possible scenario of multiple introductions. One haplotype H1 was dominant (119 individuals, 67.2%), not only throughout its expanding range in Europe and Siberia but, intriguingly, also in 96% of individuals originating from Japan. We detected eight unique haplotypes of P. issikii in East Asia. Five of them were exclusively found in the Russian Far East representing 95% of individuals from that area. The putative new cryptic Phyllonorycter species showed differences from P. issikii for the three studied genes. However, both species are morphologically undistinguishable. They occur in sympatry on the same host plants in Japan (Sendai) and the Russian Far East (Primorsky krai) without evidence of admixture. © 2017 Kirichenko et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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Sukachev Institute of Forest SB RAS, Federal Research Center Krasnoyarsk Science Center SB RAS, Krasnoyarsk, Russian Federation
Siberian Federal University, Krasnoyarsk, Russian Federation
INRA, UR0633 Zoologie Forestiere, Orleans, France
Museo Civico di Storia Naturale, Verona, Italy
Department of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
UMR CBGP (INRA, CIRAD, IRD, SupAgro), Montpellier, France
Department of Biological Science and Biotechnology, Hannam University, Daejeon, South Korea
College of Life Sciences, Nankai University, Tianjin, China
Institut de Recherche sur la Biologie de l'Insecte, CNRS UMR 7261, Universite Francois-Rabelais de Tours, UFR Sciences et Techniques, Tours, France

Доп.точки доступа:
Kirichenko, N.; Triberti, P.; Ohshima, I.; Haran, J.; Byun, B. -K.; Li, H.; Augustin, S.; Roques, A.; Lopez-Vaamonde, C.

/ H. Santruckova [et al.] // Soil Biol. Biochem. - 2018. - Vol. 119. - P11-21, DOI 10.1016/j.soilbio.2017.12.021 . - ISSN 0038-0717
Аннотация: The occurrence of dark fixation of CO2 by heterotrophic microorganisms in soil is generally accepted, but its importance for microbial metabolism and soil organic carbon (C) sequestration is unknown, especially under C-limiting conditions. To fill this knowledge gap, we measured dark 13CO2 incorporation into soil organic matter and conducted a 13C-labelling experiment to follow the 13C incorporation into phospholipid fatty acids as microbial biomass markers across soil profiles of four tundra ecosystems in the northern circumpolar region, where net primary productivity and thus soil C inputs are low. We further determined the abundance of various carboxylase genes and identified their microbial origin with metagenomics. The microbial capacity for heterotrophic CO2 fixation was determined by measuring the abundance of carboxylase genes and the incorporation of 13C into soil C following the augmentation of bioavailable C sources. We demonstrate that dark CO2 fixation occurred ubiquitously in arctic tundra soils, with increasing importance in deeper soil horizons, presumably due to increasing C limitation with soil depth. Dark CO2 fixation accounted on average for 0.4, 1.0, 1.1, and 16% of net respiration in the organic, cryoturbated organic, mineral and permafrost horizons, respectively. Genes encoding anaplerotic enzymes of heterotrophic microorganisms comprised the majority of identified carboxylase genes. The genetic potential for dark CO2 fixation was spread over a broad taxonomic range. The results suggest important regulatory function of CO2 fixation in C limited conditions. The measurements were corroborated by modeling the long-term impact of dark CO2 fixation on soil organic matter. Our results suggest that increasing relative CO2 fixation rates in deeper soil horizons play an important role for soil internal C cycling and can, at least in part, explain the isotopic enrichment with soil depth. © 2018 Elsevier Ltd

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University of South Bohemia, Department of Ecosystems Biology, Ceske Budejovice, Czech Republic
Institute of Microbiology, Ernst-Moritz-Arndt University Greifswald, Greifswald, Germany
Department of Physical Geography, Stockholm University, Sweden
Austrian Polar Research Institute, Vienna, Austria
Department of Environmental Science, University of Eastern Finland, PO Box 1627, Kuopio, Finland
Leibniz Universitat Hannover, Institut fur Bodenkunde, Hannover, Germany
University of Bergen, Centre for Geobiology, Department of Biology, Bergen, Norway
Siberian Branch of Russian Academy of Sciences, Central Siberian Botanical Garden, Novosibirsk, Russian Federation
Soil Science and Soil Protection, Martin Luther University Halle-Wittenberg, Germany
University of Vienna, Department of Ecogenomics and Systems Biology, Division of Archaea Biology and Ecogenomics, Vienna, Austria
University of Vienna, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Vienna, Austria
Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, United States
Laboratory of Food Biotechnology, ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, Zurich, Switzerland
Siberian Branch of Russian Academy of Sciences, VN Sukachev Institute of Forest, Krasnoyarsk, Russian Federation
Department of Environmental Science and Analytical Chemistry, Stockholm University, Stockholm, Sweden
Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden

Доп.точки доступа:
Santruckova, H.; Kotas, P.; Barta, J.; Urich, T.; Capek, P.; Palmtag, J.; Eloy Alves, R. J.; Biasi, C.; Diakova, K.; Gentsch, N.; Gittel, A.; Guggenberger, G.; Hugelius, G.; Lashchinsky, N.; Martikainen, P. J.; Mikutta, R.; Schleper, C.; Schnecker, J.; Schwab, C.; Shibistova, O.; Wild, B.; Richter, A.

/ N. Kirichenko [et al.] // ZooKeys. - 2018. - Is. 736. - P79-118, DOI 10.3897/zookeys.736.20739. - Cited References:57. - We thank E.J. van Nieukerken (The Netherlands), H. Kuroko, A. Kawakita, N. Hirano, K. Niimi, M. Murase, S. Yagi, C. Tsuji (Japan), G. Deschka (Austria), M. Jones (USA), A. Lastuvka, Z. Lastuvka (Czech Republic), A. Cama, J. Nel (France) and P. van Wielink (The Netherlands) for providing specimens and / or DNA barcodes of Phyllocnistis spp., J.C. Koster (The Netherlands) for preparing the genitalia slide of P. cornella, C. van den Berg (The Netherlands) for helping with collection of P. cornella in Japan, S.V. Baryshnikova and M.G. Ponomarenko (Russia) for checking the collections of their institutes for Cornus-feeding Phyllocnistis and for their useful remarks. Special thanks to R. Brito and G.R.P Moreira (Brazil) for their careful reading of the latest version of our manuscript, to D. Lees (UK) for checking the English, to the reviewers R. Rougerie (France) and D. Wagner (USA) and to the editor E.J. van Nieukerken for their insightful comments and suggestions. N. Kirichenko was supported by a fellowship of LE STUDIUM (R), Institute for advanced studies - Loire Valley, France (grant No. INRA-URZF-007); French Embassy in Russia, Bourse Metchnikov (grant No. 908981L, Campus France) and by the Russian Foundation for Basic Research (grant No. 15-29-02645). T. Hirowatari. and I. Ohshima were supported by JSPS KAKENHI (grant No. JP16H05766). . - ISSN 1313-2989. - ISSN 1313-2970РУБ Zoology

Аннотация: During an ongoing DNA-barcoding campaign of the leaf-mining moths that feed on woody plants in Northeast Asia, four lineages of the genus Phyllocnistis (Gracillariidae, Phyllocnistinae) were discovered on dogwood (Cornus spp): P. cornella Ermolaev, 1987 on C. controversa Hemsl. (Japan: Hokkaido) and three new species - one feeding on C. controversa, C. florida L. and C. macrophylla Wall. in Japan (Honshu, Shikoku, Kyushu), a second species on C. macrophylla in China (Yunnan) and a third on Siberian dogwood Cornus alba L. in Russia (Siberia). All these species showed differences in morphology, in the barcode region of the cytochrome c oxidase I gene and in two nuclear genes (histone H3 and 28S ribosomal RNA). No correlation was found between the deep mitochondrial splits observed and the Wolbachia infection pattern. Based on both morphological and molecular evidence, the three recently discovered lineages are described here as new species: P. indistincta Kobayashi & Triberti, sp. n. (Japan), P. saepta Kirichenko, Ohshima & Huang, sp. n. (China) and P. verae Kirichenko, Triberti & Lopez-Vaamonde, sp. n. (Russia). In addition, the authors re-describe the adult morphology of P. cornella, provide the first record of this species from Japan and highlight the diagnostic characters that allow these Cornus-feeding Phyllocnistis species to be distinguished.

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RAS, Sukachev Inst Forest, SB, Akademgorodok 50-28, Krasnoyarsk 660036, Russia.
Siberian Fed Univ, 79 Svobodny Pr, Krasnoyarsk 660041, Russia.
INRA, UR0633, Zool Forestiere, F-45075 Orleans, France.
Museo Civ Storia Nat, Lungadige Porta Vittoria 9, I-37129 Verona, Italy.
Osaka Prefecture Univ, Grad Sch Life & Environm Sci, Entomol Lab, Sakai, Osaka 5998531, Japan.
Kyushu Univ, Fac Agr, Entomol Lab, 6-10-1 Hakozaki, Fukuoka 8128581, Japan.
Univ Hawaii, Dept Plant & Environm Protect Sci, 3050 Maile Way, Honolulu, HI 96822 USA.
Nat Biodivers Ctr, POB 9557, NL-2300 RA Leiden, Netherlands.
Kyoto Prefectural Univ, Dept Life & Environm Sci, Kyoto 6068522, Japan.
Hunan Agr Univ, Hunan Prov Key Lab Biol & Control Plant Dis & Ins, Changsha 410128, Hunan, Peoples R China.
South China Agr Univ, Dept Entomol, Guangzhou 510642, Guangdong, Peoples R China.
Univ Francois Rabelais Tours, CNRS, Inst Rech Biol Insecte, UMR 7261,UFR Sci & Tech, F-37200 Tours, France.

Доп.точки доступа:
Kirichenko, Natalia; Triberti, Paolo; Kobayashi, Shigeki; Hirowatari, Toshiya; Doorenweerd, Camiel; Ohshima, Issei; Huang, Guo-Hua; Wang, Min; Magnoux, Emmanuelle; Lopez-Vaamonde, Carlos; LE STUDIUM(R), Institute for advanced studies - Loire Valley, France [INRA-URZF-007]; French Embassy in Russia, Bourse Metchnikov (Campus France) [908981L]; Russian Foundation for Basic Research [15-29-02645]; JSPS KAKENHI [JP16H05766]

/ I. V. Kornienko [et al.] // Mitochondrial DNA Part B Resour. - 2018. - Vol. 3, Is. 2. - P596-598, DOI 10.1080/23802359.2018.1473721 . - ISSN 2380-2359
Аннотация: We present a complete sequence and an annotation of the mitochondrial genome of the woolly mammoth (Mammuthus primigenius) found in 2012 on Maly Lyakhovsky Island (North-Eastern Siberia, Russia). The genome was 16,851 bp long and contained 13 protein-coding, 22 tRNA, and 2 rRNA genes. It was AT reach (61.3%) with A = 32.9%, T = 28.4%, C = 25.3%, and G = 13.4%. © 2018 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.

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Department of Strategic Research, Southern Scientific Centre, Russian Academy of Sciences, Rostov-on-Don, Russian Federation
Laboratory of Biological Objects Identification, Southern Federal University, Rostov-on-Don, Russian Federation
Department of Forensic Medicine, Mechnikov North-Western State Medical University, Russian Federation
Laboratory of Forest Genetics and Selection, V. N. Sukachev Institute of Forest, Siberian Branch of Russian Academy of Sciences, Krasnoyarsk, Russian Federation
Laboratory of Forest Genomics, Genome Research and Education Center, Siberian Federal University, Krasnoyarsk, Russian Federation
Institute of Applied Ecology of the North, North-Eastern Federal University, Yakutsk, Russian Federation
Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Gottingen, Gottingen, Germany
Laboratory of Population Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russian Federation
Department of Ecosystem Science and Management, Texas A&M University, College Station, TX, United States

Доп.точки доступа:
Kornienko, I. V.; Faleeva, T. G.; Oreshkova, N. V.; Grigoriev, S. E.; Grigoreva, L. V.; Simonov, E. P.; Kolesnikova, A. I.; Putintseva, Y. A.; Krutovsky, K. V.

/ 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

/ A. I. Kolesnikova [et al.] // BMC Genomics. - 2019. - Vol. 20. - Ст. 351, DOI 10.1186/s12864-019-5732-z. - Cited References:80. - This study was funded by the Research Grant No. 14.Y26.31.0004 from the Government of the Russian Federation. The funding body did not contribute in the design of the study, collection, analysis, interpretation of data, or writing the manuscript. . - ISSN 1471-2164РУБ Biotechnology & Applied Microbiology + Genetics & Heredity

Аннотация: BackgroundSpecies in the genus Armillaria (fungi, basidiomycota) are well-known as saprophytes and pathogens on plants. Many of them cause white-rot root disease in diverse woody plants worldwide. Mitochondrial genomes (mitogenomes) are widely used in evolutionary and population studies, but despite the importance and wide distribution of Armillaria, the complete mitogenomes have not previously been reported for this genus. Meanwhile, the well-supported phylogeny of Armillaria species provides an excellent framework in which to study variation in mitogenomes and how they have evolved over time.ResultsHere we completely sequenced, assembled, and annotated the circular mitogenomes of four species: A. borealis, A. gallica, A. sinapina, and A. solidipes (116,443, 98,896, 103,563, and 122,167bp, respectively). The variation in mitogenome size can be explained by variable numbers of mobile genetic elements, introns, and plasmid-related sequences. Most Armillaria introns contained open reading frames (ORFs) that are related to homing endonucleases of the LAGLIDADG and GIY-YIG families. Insertions of mobile elements were also evident as fragments of plasmid-related sequences in Armillaria mitogenomes. We also found several truncated gene duplications in all four mitogenomes.ConclusionsOur study showed that fungal mitogenomes have a high degree of variation in size, gene content, and genomic organization even among closely related species of Armillara. We suggest that mobile genetic elements invading introns and intergenic sequences in the Armillaria mitogenomes have played a significant role in shaping their genome structure. The mitogenome changes we describe here are consistent with widely accepted phylogenetic relationships among the four species.

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Держатели документа:
Siberian Fed Univ, Inst Fundamental Biol & Biotechnol, Genome Res & Educ Ctr, Lab Forest Genom, Krasnoyarsk 660036, Russia.
Russian Acad Sci, Fed Res Ctr, Lab Genom Res & Biotechnol, Siberian Branch,Krasnoyarsk Sci Ctr, Krasnoyarsk 660036, Russia.
Russian Acad Sci, Inst Anim Systemat & Ecol, Siberian Branch, Novosibirsk 630091, Russia.
Russian Acad Sci, VN Sukachev Inst Forest, Lab Forest Genet & Select, Siberian Branch, Krasnoyarsk 660036, Russia.
Russian Acad Sci, VN Sukachev Inst Forest, Lab Reforestat Mycol & Plant Pathol, Siberian Branch, Krasnoyarsk 660036, Russia.
Siberian Fed Univ, Inst Space & Informat Technol, Dept High Performance Comp, Krasnoyarsk 660074, Russia.
Univ Toronto, Dept Biol, Mississauga, ON 15L 1C6, Canada.
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:
Kolesnikova, Anna, I; Putintseva, Yuliya A.; Simonov, Evgeniy P.; Biriukov, Vladislav V.; Oreshkova, Natalya, V; Pavlov, Igor N.; Sharov, Vadim V.; Kuzmin, Dmitry A.; Anderson, James B.; Krutovsky, Konstantin, V; Krutovsky, Konstantin; Government of the Russian Federation [14, Y26.31.0004]

/ I. V. Kornienko [et al.] // Mol. Biol. - 2019. - Vol. 53, Is. 4. - P560-570, DOI 10.1134/S002689331904006X . - ISSN 0026-8933
Аннотация: Abstract: The woolly mammoth mitochondrial genome (including the Malolyakhovsky mammoth) has been previously sequenced, followed by the annotation of all its genes (MF770243). In this study, based on the Malolyakhovsky mammoth, we describe for the first time the sites of functional significance in the control region of the woolly mammoth mitogenome. © 2019, Pleiades Publishing, Inc.

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Southern Scientific Centre, Russian Academy of Sciences, Rostov-on-Don, 344006, Russian Federation
Ivanovsky Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, 344090, Russian Federation
Branch No. 2 of the 111th Main State Center of Medical Forensic and Criminalistic Examinations,Ministry of Defense of the Russian Federation, Rostov-on-Don, 344000, Russian Federation
Sukachev Institute of Forest, Siberian Branch, Russian Academy of Sciences, Krasnoyarsk, 660036, Russian Federation
Genome Research and Education Center, Siberian Federal University, Krasnoyarsk, 660036, Russian Federation
Laboratory of Genomic Research and Biotechnology, Federal Research Center Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences, Krasnoyarsk, 660036, Russian Federation
Lazarev Mammoth Museum, Institute of Applied Ecology of the North,North-Eastern Federal University, Yakutsk, 677980, Russian Federation
International Common Use Center Molecular Paleontology, North-Eastern Federal University, Yakutsk, 677980, Russian Federation
Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Gottingen, Gottingen, 37077, Germany
Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russian Federation
Department of Ecosystem Science and Management, Texas A&M University, College Station, TX 77843-2138, United States

Доп.точки доступа:
Kornienko, I. V.; Faleeva, T. G.; Oreshkova, N. V.; Grigoriev, S. E.; Grigorieva, L. V.; Putintseva, Y. A.; Krutovsky, K. V.

/ V. S. Akulova, V. V. Sharov, A. I. Aksyonova [et al.] // BMC Genomics. - 2020. - Vol. 21. - Ст. 534, DOI 10.1186/s12864-020-06964-6. - Cited References:48. - This work including the study and collection, analysis and interpretation of data, and writing the manuscript was supported by research grant. 14.Y26.31.0004 from the Government of the Russian Federation with partial funding from the Federal Research Center "Krasnoyarsk Scientific Center", Siberian Branch, Russian Academy of Sciences (grants No 0287-2019-0002, No 0356-2016-0704, and No 0356-2019-0024). The funding agencies played no role in the design of the study and collection material, analysis and interpretation of data, and in writing the manuscript. Publication cost have been funded by the Open Access Publication Funds of the University of Gottingen. . - ISSN 1471-2164РУБ Biotechnology & Applied Microbiology + Genetics & Heredity

Аннотация: Background: Massive forest decline has been observed almost everywhere as a result of negative anthropogenic and climatic effects, which can interact with pests, fungi and other phytopathogens and aggravate their effects. Climatic changes can weaken trees and make fungi, such as Armillaria more destructive. Armillaria borealis (Marxm. & Korhonen) is a fungus from the Physalacriaceae family (Basidiomycota) widely distributed in Eurasia, including Siberia and the Far East. Species from this genus cause the root white rot disease that weakens and often kills woody plants. However, little is known about ecological behavior and genetics of A. borealis. According to field research data, A. borealis is less pathogenic than A. ostoyae, and its aggressive behavior is quite rare. Mainly A. borealis behaves as a secondary pathogen killing trees already weakened by other factors. However, changing environment might cause unpredictable effects in fungus behavior. ResultsThe de novo genome assembly and annotation were performed for the A. borealis species for the first time and presented in this study. The A. borealis genome assembly contained similar to 68 Mbp and was comparable with similar to 60 and similar to 79.5 Mbp for the A. ostoyae and A. mellea genomes, respectively. The N50 for contigs equaled 50,544bp. Functional annotation analysis revealed 21,969 protein coding genes and provided data for further comparative analysis. Repetitive sequences were also identified. The main focus for further study and comparative analysis will be on the enzymes and regulatory factors associated with pathogenicity. ConclusionsPathogenic fungi such as Armillaria are currently one of the main problems in forest conservation. A comprehensive study of these species and their pathogenicity is of great importance and needs good genomic resources. The assembled genome of A. borealis presented in this study is of sufficiently good quality for further detailed comparative study on the composition of enzymes in other Armillaria species. There is also a fundamental problem with the identification and classification of species of the Armillaria genus, where the study of repetitive sequences in the genomes of basidiomycetes and their comparative analysis will help us identify more accurately taxonomy of these species and reveal their evolutionary relationships.

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Держатели документа:
Siberian Fed Univ, Inst Fundamental Biol & Biotechnol, Lab Forest Genom, Genome Res & Educ Ctr, Krasnoyarsk 660036, Russia.
Russian Acad Sci, Krasnoyarsk Sci Ctr, Siberian Branch, Lab Genom Res & Biotechnol,Fed Res Ctr, Krasnoyarsk 660036, Russia.
Siberian Fed Univ, Inst Space & Informat Technol, Dept High Performance Comp, Krasnoyarsk 660074, Russia.
Russian Acad Sci, Siberian Branch, VN Sukachev Inst Forest, Lab Forest Genet & Select, Krasnoyarsk 660036, Russia.
Natl Res Tech Univ, Dept Informat, Irkutsk 664074, Russia.
Russian Acad Sci, Siberian Branch, Limnol Inst, Irkutsk 664033, Russia.
Russian Acad Sci, Siberian Branch, VN Sukachev Inst Forest, Lab Reforestat Mycol & Plant Pathol, Krasnoyarsk 660036, Russia.
Reshetnev Siberian State Univ Sci & Technol, Dept Chem Technol Wood & Biotechnol, Krasnoyarsk 660049, Russia.
Georg 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:
Akulova, Vasilina S.; Sharov, Vadim V.; Aksyonova, Anastasiya I.; Putintseva, Yuliya A.; Oreshkova, Natalya V.; Feranchuk, Sergey I.; Kuzmin, Dmitry A.; Pavlov, Igor N.; Litovka, Yulia A.; Krutovsky, Konstantin V.; Krutovsky, Konstantin; Government of the Russian Federation [14.Y26.31.0004]; Federal Research Center "Krasnoyarsk Scientific Center", Siberian Branch, Russian Academy of Sciences [0287-2019-0002, 0356-2016-0704, 0356-2019-0024]; University of Gottingen

/ 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