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

: материалы временных коллективов / O.V Trefilova, P. A. Oskorbin // Boreal forests in a changing world: challenges and needs for action: Proceedings of the International conference August 15-21 2011, Krasnoyarsk, Russia. - Krasnoyarsk : V.N. Sukachev Institute of forest SB RAS, 2011. - С. 65-69. - Библиогр. в конце ст.
Аннотация: The major parameters of the carbon cycle were studied in the pine stands of green moss and lichen proups of forest type using biometric method. The study was carried out for stands age sequence (15-260 years old) in the Zotinskii experimental polygon of Yenisei Transect. Heterotrophic respiration changes a little with age of the pine stands, therefore, net ecosystem production of these stands, in generally, mainly determines by age changes in the net primary production intensity.

Держатели документа:
Институт леса им. В.Н. Сукачева Сибирского отделения Российской академии наук : 660036, Красноярск, Академгородок 50/28

Доп.точки доступа:
Oskorbin, Pavel Anatol'yevich; Оскорбин, Павел Анатольевич; Трефилова, Ольга Владимировна

: материалы временных коллективов / D. I. Nazimova [и др.] // Boreal forests in a changing world: challenges and needs for action: Proceedings of the International conference August 15-21 2011, Krasnoyarsk, Russia. - Krasnoyarsk : V.N. Sukachev Institute of forest SB RAS, 2011. - С. 248. - Библиогр. в конце ст.
Аннотация: A model is proposed where succession is considered to be a sequence of ecological phase transitions. Field data for various stages of succession processes are used to verify the model.

Держатели документа:
Институт леса им. В.Н. Сукачева Сибирского отделения Российской академии наук : 660036, Красноярск, Академгородок 50/28

Доп.точки доступа:
Soukhovolsky, Vladislav Grigor'yevich; Суховольский, Владислав Григорьевич; Овчинникова, Тамара Михайловна

[Текст] = Clarification of taxonomic status of Rhododendron Ledebourii Pojark. Using the aflp wethod DNA sequence analysis : материалы временных коллективов / Н. А. Тихонова // Исследование компонентов лесных экосистем Сибири: Материалы конференции молодых ученых, 5-6 апреля 2012 г. , Красноярск. - Красноярск : Институт леса им. В.Н. Сукачева СО РАН , 2012. - Вып. 13. - С. 64-67. - Библиогр. в конце ст.
Аннотация: AFLP genetic analysis of DNA sequences of seven populations of rhododendrons of section Rhodorastra, growing in the mountains of southern Siberia was carried out. The data obtained confirmed species' status of Rhododendron ledebourii. The limits of areas of Rhododendrons ledebourii and Rh. dauricum were specified.

Держатели документа:
Институт леса им. В.Н. Сукачева Сибирского отделения Российской академии наук : 660036, Красноярск, Академгородок, 50/28

Доп.точки доступа:
Tikhonova Natal'ya Alexandrovna

[Text] / T. T. Efremova, T. M. Ovchinnikova, V. G. Sukhovol'skii // Eurasian Soil Sci. - 2006. - Vol. 39, Is. 6. - P588-596, DOI 10.1134/S1064229306060020. - Cited References: 26 . - 9. - ISSN 1064-2293РУБ Soil Science

Аннотация: The application of multiparametric statistical methods has confirmed that peat soils are different in the degree of their drainage and properties because of their modification during a 20 - 25 year period of artificial drainage operation. The following sequence represents the relative significance of the contribution to the soil changes of the parameters studied: groundwater table air capacity pH T-0 Eh water-soluble: C Fe3+ and the activity of soil oxidoreductases in the following sequence: peroxidase catalase dehydrogenase. The necessity to supplement the substantive - genetic principle of the classification of drained peat soils with characterization of their water regime is substantiated.

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

Доп.точки доступа:
Efremova, T.T.; Ovchinnikova, T.M.; Sukhovol'skii, V.G.

/ T. C. Harrington [et al.] // Plant Disease. - 2002. - Vol. 86, Is. 4. - P418-422 . - ISSN 0191-2917
Аннотация: Ceratocystis laricicola and C. polonica are fungal symbionts of bark beetle species of the genus lps that attack species of Larix and Picea, respectively, across Eurasia. Earlier studies found that these fungal species were morphologically identical, had similar isozymes patterns, and had identical internal transcribed spacer (ITS) sequences of the rDNA operon. We analyzed 27 isolates from Europe, southwestern Siberia (Russia) and Japan, representing the known geographic ranges of the two species. Phylogenetic analysis of the DNA sequences of a portion of the MAT-2 idiomorph showed these species to be distinct, with the Japanese isolates of C. laricicola having a sequence slightly different (5 bp) from those of the Russian and European isolates of C. laricicola. Sexual compatibility tests showed full interfertility among isolates of C. polonica from Europe, Russia and Japan, but isolates of C. polonica were not fully interfertile with isolates of C. laricicola. A Russian and a European isolate of C. laricicola mated with each other but not with the Japanese isolates of C. laricicola. Mature L. sibirica and P. obovata were inoculated with isolates of C. laricicola and C. polonica from Europe, Russia, and Japan, and measurement of lesions in the inner bark/cambium region demonstrated strong host specialization. The data suggest that the two fungal species are very closely related and are distinguished primarily by their physiological specialization to the hosts of their bark beetle vectors.

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Держатели документа:
Department of Plant Pathology, Iowa State University, Ames, IO 50011, United States
Laboratory of Microbiology, Sukachev Institute of Forestry, Krasnoyarsk, Russian Federation
Department of Plant Pathology, Iowa State University, United States

Доп.точки доступа:
Harrington, T.C.; Pashenova, N.V.; McNew, D.L.; Steimel, J.; Konstantinov, M.Yu.

/ E. F. Vedrova // Eurasian Soil Science. - 1997. - Vol. 30, Is. 2. - P181-188 . - ISSN 1064-2293
Аннотация: Forest-litter decomposition in 25-year-old cedar, pine, larch, spruce, aspen, and birch plantations is under consideration. The specific rate of decomposition in this sequence of forest litters changes as follows: 0.81, 1.00, 1.04, 1.36, 1.70, and 1.88 mg C/g C per day. The C-CO2 evolution into the atmosphere totals 77-92% of C losses during the decomposition. Humus formation is the most intensive beneath cedar and aspen litters (23.1 and 21.2% of C losses, respectively). The specific rate of humification of aspen and birch litters (0.36 and 0.22 mg C/g C per day) is 1.5-2.0 times higher than that for cedar (0.19) and pine (0.16) litters and 2-3 times higher than that for larch (0.11) and spruce (0.10) ones. The rate of C-CO2 evolution from the sandy-loamy substrate (C content is 0.39%) and from the A horizon of dark gray forest soil (C content is 5.35%) is 178 and 334 g C/m2 per year, respectively.

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Держатели документа:
Sukachev Institute of Forestry, Siberian Division, Russian Academy of Sciences, Krasnoyarsk, Russian Federation

Доп.точки доступа:
Vedrova, E.F.

[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

/ C. -H. Cheng [et al.] // Geoderma. - 2016. - Vol. 265. - P187-195, DOI 10.1016/j.geoderma.2015.11.028 . - ISSN 0016-7061
Аннотация: Steep mountain terrain, fractured geological environments, and intense precipitation events are primary factors that contribute to frequent landslides in mountainous regions. Landslides exert an immense impact on forest ecosystems and substantially change soil properties; understanding these changes is crucial to facilitating subsequent forest revegetation and management. In this study, the effects of landslide on soil physicochemical properties were investigated in a moist montane forest ecosystem in Xitou, Central Taiwan. We established a dataset comprised historical soil survey data obtained in 1976 and data from soil samples taken in 2012 at the same locations to compare differences in soil properties after landslide deposition, and also conducted soil sampling along a landslide/nonlandslide affected sequence to determine how the degree of landslide deposition affected soil physicochemical properties. The results indicated that rock fragment content, soil pH value, bulk density, inorganic carbon, and base saturation increased following landslide deposition and that severe landslide deposition caused more substantial increases. By contrast, the thicknesses of the O and A horizons, soil organic carbon, total nitrogen, and cation-exchange capacity significantly decreased following landslides; these decreases were more substantial with increasing degree of landslide deposition. Exchangeable potassium, calcium, magnesium, and available phosphorus content, however, were unaffected by landslide deposition. The results demonstrated that soil physicochemical properties were significantly altered after landslide deposition; these resultant changes, particularly in regard to high soil pH value, poor structure, and low soil organic carbon and total nitrogen, are expected to influence functions in forest ecosystems. © 2015 Elsevier B.V.

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Держатели документа:
School of Forestry and Resource Conservation, National Taiwan University, Taipei, Taiwan
NTU Experimental Forest, National Taiwan University, Nantou, Taiwan
Institute of Forest SR RAS, Krasnoyarsk, Russian Federation

Доп.точки доступа:
Cheng, C.-H.; Hsiao, S.-C.; Huang, Y.-S.; Hung, C.-Y.; Pai, C.-W.; Chen, C.-P.; Menyailo, O. V.
Свободных экз. нет

[Text] / N. N. Selochnik [et al.] // Silva. Fenn. - 2015. - Vol. 49, Is. 5. - Ст. 1328. - Cited References:65. - We thank Dr. Wilhelm de Beer from the Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, for his advice regarding the phylogenetic component of this study. The study was financially supported by the University of Helsinki and the Emil Aaltonen Foundation, Finland; the members of the Tree Protection Co-operative Programme (TPCP), the THRIP initiative of the Department of Trade and Industry, and the University of Pretoria, South Africa. . - ISSN 0037-5330. - ISSN 2242-4075РУБ Forestry

Аннотация: Several eastern European countries have reported outbreaks of oak die-back during the 1980's. Species of Ophiostoma Syd. were isolated from diseased trees and have been suggested to be the possible causal agents of the die-back, but this view have generally not been accepted. In order to monitor the post-outbreak region of oak die-back and to consider the possible role of Ophiostoma spp. in the syndrome, research has been conducted in the Tellerman forest, Voronezh region, Russia between 2005 and 2011. Our study resulted in the isolation of ophiostomatoid fungi from Quercus robur L. trees displaying external signs of desiccation. Fungi were identified based on morphological characteristics and DNA sequence comparisons. Three species of Ophiostoma were identified including O. grandicarpum (Kowalski & Butin) Rulamort, a species closely related to O. abietinum Marm. & Butin, O. fusiforme Aghayeva & M.J. Wingf. and O. lunatum Aghayeva & M.J. Wingf. representing a poorly understood species complex, and most commonly O. quercus (Georgev.) Nannf. Pathogenicity of these fungi was tested using artificial inoculations on Q. robur trees. The fungi were shown to be non-pathogenic and unlikely to play any role in oak die-back. These fungi are most likely only components in a complex of abiotic, biotic and anthropogenic factors that have contributed to a die-back of Quercus spp. in Russia.

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Держатели документа:
Forest Sci Inst RAS, Uspenskoye 143030, Moscow Region, Russia.
VN Sukachev Inst Forest SB RAS, Krasnoyarsk 660036, Russia.
St Petersburg State Forest Tech Univ, Dept Forest Protect & Game Management, St Petersburg 194021, Russia.
Univ Pretoria, FABI, ZA-0002 Pretoria, South Africa.
Univ Helsinki, Dept Forest Sci, FI-00014 Helsinki, Finland.

Доп.точки доступа:
Selochnik, Nelly N.; Pashenova, Nataliya V.; Sidorov, Evgeny; Wingfield, Michael J.; Linnakoski, Riikka; University of Helsinki; Emil Aaltonen Foundation, Finland

[Text] / N. N. Selochnik [et al.] // Silva. Fenn. - 2015. - Vol. 49, Is. 5. - Ст. 1328, DOI 10.14214/sf.1328. - Cited References:65. - We thank Dr. Wilhelm de Beer from the Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, for his advice regarding the phylogenetic component of this study. The study was financially supported by the University of Helsinki and the Emil Aaltonen Foundation, Finland; the members of the Tree Protection Co-operative Programme (TPCP), the THRIP initiative of the Department of Trade and Industry, and the University of Pretoria, South Africa. . - ISSN 0037-5330. - ISSN 2242-4075РУБ Forestry

Аннотация: Several eastern European countries have reported outbreaks of oak die-back during the 1980's. Species of Ophiostoma Syd. were isolated from diseased trees and have been suggested to be the possible causal agents of the die-back, but this view have generally not been accepted. In order to monitor the post-outbreak region of oak die-back and to consider the possible role of Ophiostoma spp. in the syndrome, research has been conducted in the Tellerman forest, Voronezh region, Russia between 2005 and 2011. Our study resulted in the isolation of ophiostomatoid fungi from Quercus robur L. trees displaying external signs of desiccation. Fungi were identified based on morphological characteristics and DNA sequence comparisons. Three species of Ophiostoma were identified including O. grandicarpum (Kowalski & Butin) Rulamort, a species closely related to O. abietinum Marm. & Butin, O. fusiforme Aghayeva & M.J. Wingf. and O. lunatum Aghayeva & M.J. Wingf. representing a poorly understood species complex, and most commonly O. quercus (Georgev.) Nannf. Pathogenicity of these fungi was tested using artificial inoculations on Q. robur trees. The fungi were shown to be non-pathogenic and unlikely to play any role in oak die-back. These fungi are most likely only components in a complex of abiotic, biotic and anthropogenic factors that have contributed to a die-back of Quercus spp. in Russia.

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Держатели документа:
Forest Sci Inst RAS, Uspenskoye 143030, Moscow Region, Russia.
VN Sukachev Inst Forest SB RAS, Krasnoyarsk 660036, Russia.
St Petersburg State Forest Tech Univ, Dept Forest Protect & Game Management, St Petersburg 194021, Russia.
Univ Pretoria, FABI, ZA-0002 Pretoria, South Africa.
Univ Helsinki, Dept Forest Sci, FI-00014 Helsinki, Finland.

Доп.точки доступа:
Selochnik, Nelly N.; Pashenova, Nataliya V.; Sidorov, Evgeny; Wingfield, Michael J.; Linnakoski, Riikka; University of Helsinki; Emil Aaltonen Foundation, Finland

/ 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.

/ 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

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

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

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

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

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

УДК

575.113

582.475.4

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

РИНЦ

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

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

/ N. V. Oreshkova [et al.] // Russ. J. Genet. - 2019. - Vol. 55, Is. 4. - P444-450, DOI 10.1134/S1022795419040094. - Cited References:22. - The study was done as a part of the project "Genomics of the Key Boreal Forest Conifer Species and Their 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: Siberian larch (Larix sibirica Ledeb.) is one of the major boreal tree species in Eurasia and has a considerable economic and ecological value. Despite that importance, the development and use of microsatellite markers in this species remain limited. Microsatellite markers are considered to be a valuable tool for estimation of population diversity and structure. Availability of a draft reference assembly of the Siberian larch genome allowed us to identify 1015 microsatellite loci or simple sequence repeats (SSRs) with tri-, tetra-, penta-, and hexanucleotide motifs. For 60 of them PCR primers were designed and tested for amplification in L. sibirica and for their within-genus transferability to L. gmelinii (Rupr.) Rupr. and L. cajanderi Mayr. Here, we present a set of 14 reliable and polymorphic new nuclear SSR markers that can be used for further population genetic studies, breeding programs, and timber origin identification.

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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 119991, Russia.
Texas A&M Univ, College Stn, TX 77843 USA.

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

/ M. I. Makarov, T. I. Malysheva, O. V. Menyailo // Eurasian Soil Sci. - 2019. - Vol. 52, Is. 9. - P1028-1037, DOI 10.1134/S1064229319090059. - Cited References:48. - This study was supported by the Russian Science Foundation, project no. 16-14-10208. . - ISSN 1064-2293. - ISSN 1556-195XРУБ Soil Science

Аннотация: Isotopic composition of nitrogen in soils can be an informative indicator of N transformation processes and sources of N nutrition of plants, but data on d15N of labile N compounds are scarce. It is shown that N transformation in meadow-alpine soils (Leptic Umbrisols) of the northwestern Caucasus (Teberda Reserve, Karachay-Cherkess Republic) leads to well-expressed differences in isotopic signatures of different N compounds: d15N of extractable organic matter > d15Ntotal > d15N-> d15N-The range of d15N in this sequence reaches 25%. Differences in d15N within the same pool of N in soils of different alpine ecosystems, as well as seasonal dynamics of d15N-are much less pronounced (the range of d15N is 2-4%). The values of d15Ntotal and d15N-positively correlate with N mineralization and nitrification and demonstrate the accumulation of heavy N isotope in soils of the alpine ecosystems with more active N transformation processes. Obviously, nitrification is the key process controlling the isotopic signature of NThe role of N mineralization in the fractionation of N isotopes is less obvious, and 15N accumulation in the extractable organic matter can be related to the significant content of "heavy" microbial N in extractable organic N pool.

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Держатели документа:
Lomonosov Moscow State Univ, Moscow 119991, Russia.
Russian Acad Sci, Siberian Branch, Sukachev Inst Forest, Krasnoyarsk 660036, Russia.

Доп.точки доступа:
Makarov, M., I; Malysheva, T., I; Menyailo, O., V; Russian Science FoundationRussian Science Foundation (RSF) [16-14-10208]

/ J. H. Park, I. N. Pavlov, M. J. Kim [et al.] // Sustainability. - 2020. - Vol. 12, Is. 6. - Ст. 2535, DOI 10.3390/su12062535. - Cited References:60. - This research was funded by the project on Korea Basidiomycota Resources Center of the National Research Foundation (NRF) funded by the Korean government, grant number NRF2015M3A9B8029237. . - ISSN 2071-1050РУБ Green & Sustainable Science & Technology + Environmental Sciences

Аннотация: Wood-decay fungi (WDF) play a significant role in recycling nutrients, using enzymatic and mechanical processes to degrade wood. Designated as a biodiversity hot spot, Central Siberia is a geographically important region for understanding the spatial distribution and the evolutionary processes shaping biodiversity. There have been several studies of WDF diversity in Central Siberia, but identification of species was based on morphological characteristics, lacking detailed descriptions and molecular data. Thus, the aim of this study was to identify WDF in Central Siberia, regarding the degradation of host trees based on both morphological and molecular analyses. We collected 106 WDF samples from Krasnoyarsk and the Republic of Khakassia in 2014 and 2017, and identified a total of 52 fungal species from six main host tree genera. In order to assess the host preference of the WDF, we examined previous literature, and data from this study. We confirmed a division in host preference of WDF between gymnosperms and angiosperms. DNA-based identification and host preference assessment of the WDF provide preliminary data on WDF diversity and their role in nutrient cycles in the ecosystem of Central Siberia. To fully understand WDF diversity in Central Siberia, continuous long-term surveys, including DNA sequence data, are needed.

WOS

Держатели документа:
Seoul Natl Univ, Sch Biol Sci, Seoul 08826, South Korea.
Seoul Natl Univ, Inst Microbiol, Seoul 08826, South Korea.
Russian Acad Sci, VN Sukachev Inst Forest, Siberian Branch, Lab Reforestat Mycol & Plant Pathol, Krasnoyarsk 660036, Russia.
Reshetnev Siberian State Univ Sci & Technol, Dept Chem Technol Wood & Biotechnol, Krasnoyarsk 660049, Russia.
Natl Inst Forest Sci, Forest Prod Dept, Wood Utilizat Div, Seoul 02455, South Korea.
Changwon Natl Univ, Dept Biol & Chem, Chang Won 51140, South Korea.
Lingnan Univ, Sci Unit, Tuen Mun, Peoples R China.

Доп.точки доступа:
Park, Ji-Hyun; Pavlov, Igor N.; Kim, Min-Ji; Park, Myung Soo; Oh, Seung-Yoon; Park, Ki Hyeong; Fong, Jonathan J.; Lim, Young Woon; Pavlov, Igor; project on Korea Basidiomycota Resources Center of the National Research Foundation (NRF) - Korean government [NRF2015M3A9B8029237]

/ J.-H. Park, I. N. Pavlov, M.-J. Kim [et al.] // Sustainability. - 2020. - Vol. 12, Is. 6. - Ст. 2535, DOI 10.3390/su12062535 . - ISSN 2071-1050
Аннотация: Wood-decay fungi (WDF) play a significant role in recycling nutrients, using enzymatic and mechanical processes to degrade wood. Designated as a biodiversity hot spot, Central Siberia is a geographically important region for understanding the spatial distribution and the evolutionary processes shaping biodiversity. There have been several studies of WDF diversity in Central Siberia, but identification of species was based on morphological characteristics, lacking detailed descriptions and molecular data. Thus, the aim of this study was to identify WDF in Central Siberia, regarding the degradation of host trees based on both morphological and molecular analyses. We collected 106 WDF samples from Krasnoyarsk and the Republic of Khakassia in 2014 and 2017, and identified a total of 52 fungal species from six main host tree genera. In order to assess the host preference of the WDF, we examined previous literature, and data from this study. We confirmed a division in host preference of WDF between gymnosperms and angiosperms. DNA-based identification and host preference assessment of the WDF provide preliminary data on WDF diversity and their role in nutrient cycles in the ecosystem of Central Siberia. To fully understand WDF diversity in Central Siberia, continuous long-term surveys, including DNA sequence data, are needed. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.

Scopus

Держатели документа:
School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, South Korea
Laboratory of Reforestation, Mycology and Plant Pathology, V. N. Sukachev Institute of Forest, Siberian Branch of Russian Academy of Sciences, Krasnoyarsk, 660036, Russian Federation
Department of Chemical Technology ofWood and Biotechnology, Reshetnev Siberian State University of Science and Technology, Krasnoyarsk, 660049, Russian Federation
Wood Utilization Division, Forest Products Department, National Institute of Forest Science, Seoul, 02455, South Korea
Department of Biology and Chemistry, Changwon National University, Changwon, 51140, South Korea
Science Unit, Lingnan University, Tuen Mun, Hong Kong

Доп.точки доступа:
Park, J. -H.; Pavlov, I. N.; Kim, M. -J.; Park, M. S.; Oh, S. -Y.; Park, K. H.; Fong, J. J.; Lim, Y. W.

/ 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

Scopus

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.