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] / O. V. Kvitko, E. N. Muratova, E. V. Bazhina // Contemp. Probl. Ecol. - 2011. - Vol. 4, Is. 6. - P641-646, DOI 10.1134/S1995425511060129. - Cited References: 25. - The study has been carried out under support of the Russian Foundation of Basic Research (grants no. 08-04-90001Bel_a, 09-04-98000). . - 6. - ISSN 1995-4255РУБ Ecology

Аннотация: The cytogenetic study of Abies sibirica seed progenies in declining fir stands of West Sayan High Mountains has been carried out. The increased amount of chromosome and genome mutations, pathologies of mitotic cycle and cells with micronuclei were found at studying. The revealed irregularities may be the result of a long-term exposure to extreme environmental factors and probably reflect the high degree of disturbance of the ecosystem in this region.

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Держатели документа:
[Kvitko, O. V.
Muratova, E. N.
Bazhina, E. V.] Russian Acad Sci, Siberian Branch, VN Sukachev Inst Forest, Krasnoyarsk 660036, Russia

Доп.точки доступа:
Kvitko, O.V.; Muratova, E.N.; Bazhina, E.V.

[Text] / T. S. Sedelnikova, E. N. Muratova // Russ. J. Ecol. - 2002. - Vol. 33, Is. 5. - P303-308, DOI 10.1023/A:1020232524851. - Cited References: 31 . - 6. - ISSN 1067-4136РУБ Ecology

Аннотация: The results of a karyological study on Siberian stone pines growing in the bog demonstrated differences from the populations of this species studied earlier with respect to sizes of chromosomes and location of secondary constrictions. The number of nucleolar organizer regions in the chromosomes of Siberian stone pine trees growing in the bog was larger than in other populations. A wide spectrum of chromosome aberrations was revealed, which had not been observed in this species before. These were genome and chromosome aberrations of various types, as well as structural aberrations accompanied by changes in the number of chromosomes. It is assumed that the aberrations in the karyotype of Siberian stone pine resulted from stressful conditions.

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Держатели документа:
Russian Acad Sci, Siberian Div, Sukachev Isnt Forestry, Krasnoyarsk 660036, Russia

Доп.точки доступа:
Sedelnikova, T.S.; Muratova, E.N.

[Текст] / D. L. Grodnitsky // Zhurnal Obshchei Biol. - 1999. - Vol. 60, Is. 5. - С. 488-509. - Cited References: 158 . - 22. - ISSN 0044-4596РУБ Biology

Аннотация: Consequences derived from the synthetic theory of evolution are in contradiction with facts. The theory affirms that the evolution rate depends on gene variability, intensity of recombination and press of natural selection. It means that fecund organisms with short life cycle have to evolve very quickly. In reality the quickest evolution is observed in mammals, for example in elephants. The theory predicts that evolution can not base only on mutation in the absence of recombination. But parthenogenetic and asexual species evolve very quick, and their variability is not less than that of sexual forms. Contrarily to the neo-Darwinism ideology, evolution takes place not only in constant environment and is often absent even in changing ecosystems. Reproductive isolation and fluctuations in population number are not sufficient conditions for the beginning of evolutionary changes. Numerous data show that the space of opportunities where evolving organisms can travel is constrained by morpho-functional and morpho-genetic factors more than it was considered by the synthetic theory of evolution. It means that evolution should be explained not only in terms of genome, but also using onthogenetic development of an organism and its interactions with environment. Application of organism-focused terminology is possible in the frame of the theory also based on the idea of natural selection, but providing different prognoses, sometimes opposite to the neo-Darwinistic ones.

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

Доп.точки доступа:
Grodnitsky, D.L.

[Текст] / E. N. MURATOVA // IZVESTIYA AKADEMII NAUK SSSR SERIYA BIOLOGICHESKAYA. - 1991. - Is. 5. - С. 689-699. - Cited References: 33 . - 11. - ISSN 0002-3329РУБ Biology

Аннотация: Cytogenetic peculiarities of Pinus sylvestris L. within a population from Southern Zabaikalje were studied. This population was similar to that of Pinus sylvestris from other populations but genome mutations and chromosomal rearrangements (ring and polycentric chromosomes) were found in this population.


Доп.точки доступа:
MURATOVA, E.N.

[Text] / N. V. Oreshkova [et al.] // Russ. J. Genet. - 2014. - Vol. 50, Is. 9. - P934-941, DOI 10.1134/S1022795414090105. - Cited References: 36. - The authors gratefully acknowledge the scientific director of the Center for Genomic Research of the Siberian State University (Krasnoyarsk), Senior Investigator at the Vavilov Institute of General Genetics, Russian Academy of Sciences (Moscow), Professor of Texas Agromechanical University (USA), and the University of Goettingen (Germany), Konstantin V. Krutovsky for assistance in interpreting the data and advice in writing this article. This work was supported by the Program of the Presidium of Russian Academy of Sciences no. 30 "Wildlife: Current Status and Problems of Development." . - ISSN 1022-7954. - ISSN 1608-3369РУБ Genetics & Heredity

Аннотация: We evaluated the population structure of the bog and dry land populations of the Siberian pine Pinus sibirica (P. sibrica) in Western Siberia using nuclear genome markers. Six pairs of nuclear microsatellite loci were used for this analysis. We detected 30 allelic variants in 120 individuals of four populations of P. sibirica. We established that the studied populations differ by genetic structure. The most essential differences were identified between the Siberian pine population from oligotrophic bog and the group of populations from dry land within eutrophic bogs and near settlements P. sibirica forest (F (ST) = 0.019; D (N) = 0.053). We estimated that diversification of the West Siberian populations of P. sibirica exceeded 2.4% (F (ST) = 0.024), based on an analysis of SSR markers.

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Держатели документа:
[Oreshkova, N. V.
Sedel'nikova, T. S.
Pimenov, A. V.
Efremov, S. P.] Russian Acad Sci, Sukachev Inst Forestry, Siberian Branch, Krasnoyarsk 660036, Russia
ИЛ СО РАН

Доп.точки доступа:
Oreshkova, N.V.; Sedel'nikova, T.S.; Pimenov, A.V.; Efremov, S.P.; Presidium of Russian Academy of Sciences [30]

[Text] / K. V. Krutovsky [et al.] // In Vitro Cell. Dev. Biol.-Plant. - 2014. - Vol. 50, Is. 5. - P655-664, DOI 10.1007/s11627-014-9619-z. - Cited References: 77. - This study was supported by Research Grant No. 14.Y26.31.0004 from the Government of the Russian Federation. . - ISSN 1054-5476. - ISSN 1475-2689РУБ Plant Sciences + Cell Biology + Developmental Biology

Аннотация: The objective of this study was to obtain a genetically stable haploid in vitro-derived line from Siberian larch (Larix sibirica Ledeb.) using megagametophyte explants, which then could be used for different molecular genetic studies, including whole genome de novo sequencing. However, cytogenetic analysis and genotyping of 11 microsatellite loci showed high levels of genomic instability and a high frequency of mutation in the obtained megagametophyte-derived callus cultures. All cultures contained new mutations in one or more microsatellite loci.

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Держатели документа:
[Krutovsky, Konstantin V.] Univ Gottingen, Dept Forest Genet & Forest Tree Breeding, Busgen Inst, D-37077 Gottingen, Germany
[Krutovsky, Konstantin V.] Texas A&M Univ, Dept Ecosyst Sci & Management, College Stn, TX 77843 USA
[Krutovsky, Konstantin V.] Russian Acad Sci, NI Vavilov Inst Gen Genet, Moscow 119333, Russia
[Krutovsky, Konstantin V.
Tretyakova, Iraida N.
Oreshkova, Nataliay V.
Vaganov, Eugene A.] Siberian Fed Univ, Genome Res & Educ Ctr, Krasnoyarsk 660036, Russia
[Tretyakova, Iraida N.
Oreshkova, Nataliay V.
Pak, Maria E.
Kvitko, Olga V.] Russian Acad Sci, Lab Forest Genet & Select, VN Sukachev Inst Forest, Siberian Branch, Krasnoyarsk 660036, Russia
[Vaganov, Eugene A.] Siberian Fed Univ, Dept Ecol & Environm Studies, Inst Econ Management & Environm Studies, Krasnoyarsk 660041, Russia
ИЛ СО РАН

Доп.точки доступа:
Krutovsky, K.V.; Tretyakova, I.N.; Oreshkova, N.V.; Pak, M.E.; Kvitko, O.V.; Vaganov, E.A.; Government of the Russian Federation [14.Y26.31.0004]

[Text] / N. Kirichenko [et al.] // ZooKeys. - 2015. - Is. 473. - P157-176, DOI 10.3897/zookeys.473.8543. - Cited References:44. - We acknowledge the team at the Biodiversity Institute of Ontario,University of Guelph, Ontario, Canada for their assistance in theproduction of DNA barcodes. Funding for DNA barcoding was partlyprovided by the government of Canada through Genome Canada and theOntario Genomics Institute in support of the International Barcode ofLife project, and by NSERC. Sequence analysis was enabled by a grantfrom the government of Canada through Genome Canada and the OntarioGenomics Institute in support of the International Barcode of LifeProject. Our work was also aided by the BOLD informatics platform whosedevelopment is funded by the Ontario Ministry of Economic Developmentand Innovation. Peter Huemer gratefully acknowledges funding frominatura Erlebnis Naturschau (Dornbirn, Austria) and the Promotion ofEducational Policies, University and Research Department of theAutonomous Province of Bolzano - South Tyrol for support of the project"Genetic biodiversity archive - DNA barcoding of Lepidoptera of thecentral Alpine region (South, East and North Tyrol)". Natalia Kirichenkowas supported by a fellowship of LE STUDIUM (R), France. . - ISSN 1313-2989. - ISSN 1313-2970РУБ Zoology

Аннотация: Europe has one of the best-known Lepidopteran faunas in the world, yet many species are still being discovered, especially in groups of small moths. Here we describe a new gracillariid species from the southeastern Alps, Callisto basistrigella Huemer, Deutsch & Triberti, sp. n. It shows differences from its sister species C. coffeella in morphology, the barcode region of the cytochrome c oxidase I gene and the nuclear gene histone H3. Both C. basistrigella and C. coffeella can co-occur in sympatry without evidence of admixture. Two C. basistrigella specimens show evidence of introgression. We highlight the importance of an integrative approach to delimit species, combining morphological and ecological data with mitochondrial and nuclear sequence data. Furthermore, in connection with this study, Ornix blandella Muller - Rutz, 1920, syn. n. is synonymized with C. coffeella (Zetterstedt, 1839).

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Держатели документа:
INRA, Zool Forestiere UR0633, F-45075 Orleans, France.
SB RAS, Sukachev Inst Forest, Krasnoyarsk 660036, Russia.
Siberian Fed Univ, Krasnoyarsk 660041, Russia.
Tiroler Landesmuseen Betriebsgesellsch MbH, Nat Wissensch Abt, A-6020 Innsbruck, Austria.
Museo Civ Storia Nat, I-I37129 Verona, Italy.
Museum Natl Hist Nat, ISYEB, UMR7205, F-75005 Paris, France.
ИЛ СО РАН

Доп.точки доступа:
Kirichenko, Natalia; Huemer, Peter; Deutsch, Helmut; Triberti, Paolo; Rougerie, Rodolphe; Lopez-Vaamonde, Carlos; government of Canada through Genome Canada; Ontario Genomics Institutein support of the International Barcode of Life project; NSERC; Ontario Ministry of Economic Development and Innovation; inatura Erlebnis Naturschau (Dornbirn, Austria); Promotion of Educational Policies,University and Research Department of the Autonomous Province of Bolzano- South Tyrolfellowship of LE STUDIUM(R), France

[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]

/ M. M. Belokon [et al.] // Russ. J. Gen. - 2016. - Vol. 52, Is. 12. - P1263-1271, DOI 10.1134/S1022795416120036 . - ISSN 1022-7954
Аннотация: Siberian stone pine, Pinus sibirica Du Tour is one of the most economically and environmentally important forest-forming species of conifers in Russia. To study these forests a large number of highly polymorphic molecular genetic markers, such as microsatellite loci, are required. Prior to the new high-throughput next generation sequencing (NGS) methods, discovery of microsatellite loci and development of micro-satellite markers were very time consuming and laborious. The recently developed draft assembly of the Siberian stone pine genome, sequenced using the NGS methods, allowed us to identify a large number of microsatellite loci in the Siberian stone pine genome and to develop species-specific PCR primers for amplification and genotyping of 70 microsatellite loci. The primers were designed using contigs containing short simple sequence tandem repeats from the Siberian stone pine whole genome draft assembly. Based on the testing of primers for 70 microsatellite loci with tri-, tetra- or pentanucleotide repeats, 18 most promising, reliable and polymorphic loci were selected that can be used further as molecular genetic markers in population genetic studies of Siberian stone pine. © 2016, Pleiades Publishing, Inc.

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Держатели документа:
Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russian Federation
Russian Center of Forest Health, Federal Forestry Agency, Pushkino, Russian Federation
Sukachev Institute of Forest, Siberian Branch of the Russian Academy of Sciences, Krasnoyarsk, Russian Federation
Genome Research and Education Center, Siberian Federal University, Krasnoyarsk, Russian Federation
Georg-August University of Gottingen, Gottingen, Germany
Texas A&M University, College Station, TX, United States

Доп.точки доступа:
Belokon, M. M.; Politov, D. V.; Mudrik, E. A.; Polyakova, T. A.; Shatokhina, A. V.; Belokon, Y. S.; Oreshkova, N. V.; Putintseva, Y. A.; Sharov, V. V.; Kuzmin, D. A.; Krutovsky, K. V.

/ N. V. Oreshkova [et al.] // Russ. J. Genet. - 2017. - Vol. 53, Is. 11. - P1194-1199, DOI 10.1134/S1022795417110096. - Cited References:12. - The study was done as a part of the project "Genomics of the Key Boreal Forest Conifer Species and Then Major Phytopathogens in the Russian Federation" funded by the Government of the Russian Federation (grant no. 14.Y26.31.0004). . - ISSN 1022-7954. - ISSN 1608-3369РУБ Genetics & Heredity

Аннотация: This special issue of the journal is devoted to the outstanding population geneticist Yuri Petrovich Altukhov, who paid much attention in his research to the development of molecular genetic markers for population studies. Over the past time markers and methods of their development have undergone significant change. Thanks to modem methods of whole genome sequencing, it has become possible to develop markers of very different types-selectively neutral, as well as functional. Among them, microsatellite markers remain the most informative, convenient, reproducible, relatively inexpensive, and polymorphic. Whole genome sequencing greatly facilitates their discovery and development. This paper is devoted to the development of new microsatellite markers for a very important species of boreal forest-Siberian larch (Larix sibirica Ledeb.). Using a draft assembly of the larch genome, several thousand contigs containing microsatellite loci with di-, tri, tetra-, and pentanucleotide motifs were selected. A total of 59 pairs of PCR primers were tested for loci with dinucleotide motifs as the most variable. From them, 11 pairs were finally selected for 11 loci with dinucleotide repeats, which showed a high level of polymorphism and can be used in various population genetic studies and to identify the origin of wood and plant material.

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Держатели документа:
Siberian Fed Univ, Genome Res & Educ Ctr, Krasnoyarsk 660036, Russia.
Russian Acad Sci, Siberian Branch, Sukachev Inst Forest, Krasnoyarsk 660036, Russia.
Georg August Univ Gottingen, D-37077 Gottingen, Germany.
Russian Acad Sci, Vavilov Inst Gen Genet, Moscow 119333, Russia.
Texas A&M Univ, College Stn, TX 77843 USA.

Доп.точки доступа:
Oreshkova, N. V.; Putintseva, Yu. A.; Sharov, V. V.; Kuzmin, D. A.; Krutovsky, K. V.; Krutovsky, Konstantin; Government of the Russian Federation [14.Y26.31.0004]

/ V. L. Semerikov [et al.] // Tree Genet. Genomes. - 2018. - Vol. 14, Is. 1. - Ст. 8, DOI 10.1007/s11295-017-1222-0. - Cited References:27. - This study was funded by the research grants No. 16-04-00607 from the Russian Basic Research Foundation and No. 14.Y26.31.0004 from the Government of the Russian Federation. . - ISSN 1614-2942. - ISSN 1614-2950РУБ Forestry + Genetics & Heredity + Horticulture

Аннотация: During Quaternary glaciations, the ranges of Northern Eurasia forest species periodically experienced contraction followed by subsequent re-colonizations in the interglacial intervals. However, unlike the broadleaf trees of temperate forests, taiga species seem not to have retreated fully to southern regions in unfavorable periods and possibly survived at mid-latitudes in multiple refugia. Here, we report a study of genetic variation of three mitochondrial DNA markers in 90 populations of Scots pine (Pinus sylvestris) located from Eastern Europe to Eastern Siberia. The geographic distribution of seven mitotypes demonstrated the split between western and eastern populations approximately along the 38th meridian. Genetic diversity in the western part was significantly higher than in the eastern one. Five mitotypes were western-and one eastern-specific. One mitotype was common in both regions, but in the eastern part it occurred only in the South Urals and adjacent areas. The geographic structure in the mitotype distribution supports a hypothesis of post-glacial re-colonization of the studied territory from the European and Ural refugia.

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Держатели документа:
Russian Acad Sci, Inst Plant & Anim Ecol, Ural Branch, Ekaterinburg 620144, Russia.
Siberian Fed Univ, Genome Res & Educ Ctr, Lab Forest Genom, Krasnoyarsk 660036, Russia.
Russian Acad Sci, Krasnoyarsk Sci Ctr, VN Sukachev Inst Forest, West Siberian Branch,Fed Res Ctr,Siberian Branch, Novosibirsk 630082, Russia.
Russian Acad Sci, VN Sukachev Inst Forest, Lab Forest Genet & Select, Fed Res Ctr,Krasnoyarsk Sci Ctr,Siberian Branch, Krasnoyarsk 660036, Russia.
Russian Acad Sci, Komi Sci Ctr, Inst Biol, Ural Branch, Kirov 610035, Russia.
Georg August Univ Gottingen, Dept Forest Genet & Forest Tree Breeding, Buesgenweg 2, D-37077 Gottingen, Germany.
Russian Acad Sci, NI Vavilov Inst Gen Genet, Lab Populat Genet, Moscow 119991, Russia.
Texas A&M Univ, Dept Ecosyst Sci & Management, 2138 TAMU, College Stn, TX 77843 USA.

Доп.точки доступа:
Semerikov, Vladimir L.; Semerikova, Svetlana A.; Putintseva, Yuliya A.; Tarakanov, Vyacheslav V.; Tikhonova, Irina V.; Vidyakin, Anatoliy I.; Oreshkova, Natalia V.; Krutovsky, Konstantin V.; Russian Basic Research Foundation [16-04-00607]; Government of the Russian Federation [14.Y26.31.0004]

/ 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

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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.

/ O. V. Goryachkina [et al.] // Cytologia. - 2018. - Vol. 83, Is. 3. - P322-328, DOI 10.1508/cytologia.83.323. - Cited References:34. - Authors express sincerely thanks to Dr. Oreshkova N.V., V. N. Sukachev Institute of Forest SB RAS, for supplying of L. sibirica genomic DNA, and Dr. Shcherban A.B., The Federal Research Center Institute of Cytology and Genetics SB RAS for preparation of 5S rDNA probe. The study was funded by Russian Foundation for Basic Research and Government of Krasnoyarsk Territory, Krasnoyarsk Region Science and Technology Support (project No 16-44-243068), Russian Foundation for Basic Research and Belarus (project 18-54-00010), Investment Foundation FASIE (project 0040522). . - ISSN 0011-4545РУБ Cell Biology + Genetics & Heredity

Аннотация: We present the results of cytogenetic analysis of seven young and long-term cultured embryogenic cell lines (CLs) of Larix sibirica obtained by somatic embryogenesis. All CLs were found to be mixoploid. Three CLs (1, 2 and 6 years of cultivation) were the most stable cytogenetically with 91-96% cells having diploid chromosome number 2n=24, typical for the species. These CLs can be successfully used for the development of planting material and in clonal plantation forestry. At the same time, some embryogenic CLs were shown to possess various chromosome and genome mutations. We found two aneuploidy proliferating CLs (2n=25 and 28) capable of somatic embryo formation. One of the CLs analyzed in a current study was found to be cytogenetically unstable with chromosome numbers ranging from 24 to 35 and containing one-two micronuclei in the interphase cells. Fluorescent in situ hybridization (FISH) and morphometric analyses of karyotypes of these embryogenic CLs allow an assumption that the trisomy for one or several chromosomes is the most widespread type of genomic disturbances in embryogenic CLs of L. sibirica.

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Russian Acad Sci, Sukachev Inst Forest, Krasnoyarsk Sci Ctr, Siberian Branch,Fed Res Ctr, Akademgorodok 50-28, Krasnoyarsk 660036, Russia.
Russian Acad Sci, Vavilov Inst Gen Genet, Gubkin Str 3, Moscow 119333, Russia.

Доп.точки доступа:
Goryachkina, Olga V.; Park, Maria E.; Tretyakova, Iraida N.; Badaeva, Ekaterina D.; Muratova, Elena N.; Russian Foundation for Basic Research; Government of Krasnoyarsk Territory, Krasnoyarsk Region Science and Technology Support [16-44-243068]; Investment Foundation FASIE [0040522]; [18-54-00010]

/ D. Semizer-Cuming [et al.] // Nat. Ecol. Evol. - 2018, DOI 10.1038/s41559-018-0761-6 . - Article in Press. - ISSN 2397-334X
Аннотация: Ash forests in North America and Eurasia are rapidly being lost to two invasive alien species: the emerald ash borer and Chalara ash dieback fungus. We argue that better regulatory policy and science-based intervention can help slow losses, and recommend an international consortium to coordinate science-based intervention. © 2018, Springer Nature Limited.

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Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Gottingen, Gottingen, Germany
Forest, Nature and Biomass, Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen, Denmark
Laboratory of Population Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russian Federation
Laboratory of Forest Genomics, Genome Research and Education Center, Siberian Federal University, Krasnoyarsk, Russian Federation
Department of Ecosystem Science and Management, Texas A&M University, College Station, TX, United States
Sukachev Institute of Forest FRC KSC of the Siberian Branch of the Russian Academy of Sciences, Krasnoyarsk, Russian Federation
Department of Environmental Sciences, American University, Washington, DC, United States

Доп.точки доступа:
Semizer-Cuming, D.; Krutovsky, K. V.; Baranchikov, Y. N.; Kj?r, E. D.; Williams, C. G.

/ N. I. Kirichenko [et al.] // Contemp. Probl. Ecol. - 2018. - Vol. 11, Is. 6. - P576-593, DOI 10.1134/S1995425518060033. - Cited References:82. - Sampling in Siberia was funded by the Russian Foundation for Basic Research, project no. 15-29-02645ofi_m). DNA barcoding was supported by the Embassy of France in Moscow (Vernadsky Program, project no 908981L, Campus France); the Le Studium (Institute of Loire Valley, Orleans, France); and the Government of Canada via Canada Genome and the Ontario Institute of Genomics within the program International Barcode of Life project, NSERC. The study was partly supported by the EU program COST Action FP1401 "Global Warning: A Global Network of Nurseries as Early Warning System against Alien Tree Pests." For publication, we used materials from the biological resource scientific collection of the Central Siberian Botanical Garden (SB RAS) "Collections of Live Plants in Open and Closed Ground," USU 440534 (collection of arboreal plants). . - ISSN 1995-4255. - ISSN 1995-4263РУБ Ecology

Аннотация: This paper provides an overview of the leaf-mining insect community feeding on willows (Salix spp.) and poplars (Populus spp.) in Siberia. According to published data and our own observations, 50 leaf-mining insect species (i.e., 24 species of Lepidoptera, 15 Coleoptera, 6 Diptera, and 5 Hymenoptera) feed on those two plant genera in Siberia. Using an integrative approach combining field work, morphological and DNA barcoding analyses, we identified 32 leaf-mining insect species from 14 regions across Siberia (i.e. 64% of all leaf-mining species known on Salicaceae in this part of Russia). Among them, 26 species most often found in parks and botanical gardens, represented new faunistic records for several poorly explored regions of Siberia. We have more than doubled the list of Salicaceae-feeding leaf-mining insects in Tomsk oblast, Altai krai, and the Republic of Tuva, and for the first time provided data on leaf-miners for the Khanty-Mansi Autonomous Okrug. The micromoth Phyllocnistis gracilistylella (Gracillariidae), recently described from Japan, was found on a new host plant (Salix caprea) in the south of Krasnoyarsk krai, is new for Russia. Eight leafmining insect species (i.e., five gracillariids: Phyllocnistis labyrinthella, Ph. unipunctella, Phyllonorycter apparella, Ph. sagitella, and Ph. populifoliella; two beetles: Zeugophora scutellaris and Isochnus sequensi; and one sawfly: Heterarthrus ochropoda) can outbreak on poplars, most often in urban plantations, botanical gardens, and plant nurseries in Siberia, and can also affect natural stands. Forty-five species of 50 leaf-mining insects known to feed on willow and poplar in Siberia also occur in Central and Eastern Europe. The remaining five species (Phyllocnistis gracilistylella, Phyllonorycter sibirica, Heterarthrus fasciatus, Tachyerges dauricus, and Isochnus arcticus) are recorded in Asia only. Species richness of the family Gracillariidae, the most diverse on Salicaceae in Siberia, displays 80% similarity to that in the European part of Russia and 71% to the Russian Far East. We discuss the faunal similarity of these regions and highlight the importance of applying an integrative approach combining ecological, morphological analyses, and DNA barcoding to explore and characterize the insect fauna of poorly studied regions of Asian part of Russia.

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Russian Acad Sci, Sukachev Inst Forest, Krasnoyarsk Sci Ctr, Siberian Branch, Krasnoyarsk 660036, Russia.
Siberian Fed Univ, Krasnoyarsk 660041, Russia.
INRA, UR633, Zool Forestiere, F-45075 Orleans, France.
Russian Acad Sci, Fed Sci Ctr East Asia Terr Biodivers, Far Eastern Branch, Vladivostok 690022, Russia.
Far Eastern Fed Univ, Vladivostok 690922, Russia.
Univ Tours, UFR Sci & Tech, CNRS, Inst Rech Biol Insecte,UMR 7261, Ave Monge,Parc Grandmont, F-37200 Tours, France.

Доп.точки доступа:
Kirichenko, N. I.; Skvortsova, M. V.; Petko, V. M.; Ponomarenko, M. G.; Lopez-Vaamonde, C.; Russian Foundation for Basic Research [15-29-02645ofi_m]; Embassy of France in Moscow (Vernadsky Program, Campus France) [908981L]; Le Studium (Institute of Loire Valley, Orleans, France); Government of Canada via Canada Genome; Government of Canada via Ontario Institute of Genomics within the program International Barcode of Life project, NSERC; EU program COST Action "Global Warning: A Global Network of Nurseries as Early Warning System against Alien Tree Pests" [FP1401]

/ E. Simonov [et al.] // Acta Herpetologica. - 2018. - Vol. 13, Is. 2. - P185-189, DOI 10.13128/Acta_Herpetol-23394 . - ISSN 1827-9635
Аннотация: The steppes ratsnake, Elaphe dione (Pallas, 1773), is widely distributed across Eurasia, but the systematics and phylogeography of this species remain poorly studied. Sequencing of the full mitochondrial genome of this species provides a reference for its further study. Here, we report the full mitochondrial genome of an E. dione specimen from Krasnoyarsk Krai (East Siberia, Russia). We found that it is highly similar to the previously reported mitochondrial genome of the sister species, E. bimaculata. Both species misidentification by the authors of E. bimaculata mitogenome and the introgressive hybridization between these taxa can possibly explain this observation. © Firenze University Press.

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Laboratory of Forest Genomics, Genome Research and Education Center, Siberian Federal University, Krasnoyarsk, 660036, Russian Federation
Laboratory of Biodiversity Monitoring, Tomsk State University, Tomsk, 634050, Russian Federation
Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, 630090, Russian Federation
Laboratory of Forest Genetics and Selection, V.N. Sukachev Institute of Forest, Siberian Branch of Russian Academy of Sciences, Krasnoyarsk, 660036, Russian Federation
Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Gottingen, Busgenweg 2, Gottingen, 37077, Germany
Laboratory of Population Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russian Federation
Department of Ecosystem Science and Management, Texas A&M University, College StationTX 77843-2138, United States

Доп.точки доступа:
Simonov, E.; Lisachov, A.; Oreshkova, N.; 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

/ 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]