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

/ 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] / 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] / 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]

/ 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]

/ 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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Держатели документа:
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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Держатели документа:
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

[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]

[Текст] : материалы временных коллективов / Е. Н. Муратова // Сибирский лесной журнал. - 2019. - № : 4. - С. 49-62. - Библиогр. в конце ст. . - ISSN 2311-1410
Аннотация: Сделан обзор основных плодовых древесных и древовидных растений тропической зоны. Дана их характеристика, рассмотрены биологические особенности, приведены данные о местах их происхождения, о регионах, где они культивируются. Представлена информация о результатах кариологических исследований этих видов, использовании методов молекулярной цитогенетики, сравнительной геномики и транскриптомики для некоторых из них. В тропических странах выращиваются такие культуры, как манго индийское - один из самых вкусных и популярных фруктов, хлебное дерево, индийское хлебное дерево (джекфрут), дынное дерево (папайя), сырное дерево (моринда цитрусолистная), томатное дерево (тамарилло), огуречное дерево (билимби), широко употребляемые в пищу. Приведена информация по таким интересным плодовым растениям, как дуриан, мангостин, питахайя, лонган, личи, рамбутан, пулазан, канистель, аки и др. Проведен обзор видов плодовых растений родов Annona , Psidium, Syzygium, Averrhoa, Ziziphus, Passiflora. Огромное значение в плодоводстве тропиков и субтропиков имеют разные виды цитрусовых и сорта бананов. Установлено, что среди тропических плодовых древесных и древовидных растений имеются ди-, три- и тетраплоиды, в кариотипах некоторых видов встречаются В-хромосомы. Многие тропические плодовые являются полиплоидными (манго, хлебное дерево, джекфрут, виды родов Psidium, Syzygium и Ziziphus ). Некоторые виды, возможно, древние полиплоиды, об этом свидетельствуют результаты секвенирования их геномов. У ряда тропических плодовых древесных растений наблюдаются явления каули- и рамифлории (джекфрут, чемпедак, папайя, дуриан), когда цветы и затем плоды образуются на стволе и крупных ветвях. Некоторые виды размножаются вегетативным путем. У рассматриваемых плодовых, как и у многих других растений, широко распространена гибридизация (мангостин, виды родов Citrus, Annona, Hylocereus, Musa ), встречается полиэмбриония

https://elibrary.ru/item.asp?id=40881972
: 660036, Красноярск, Академгородок, 50, стр. 28

Доп.точки доступа:
Муратова, Елена Николаевна; Muratova, Elena Nikolayevna

/ 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.

WOS

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

/ 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.

Scopus

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.

WOS

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

/ C. Lopez-Vaamonde, N. Kirichenko, A. Cama [et al.] // Front. ecol. evol. - 2021. - Vol. 9. - Ст. 626752, DOI 10.3389/fevo.2021.626752 . - ISSN 2296-701X
Аннотация: Gracillariidae is the most species-rich leaf-mining moth family with over 2,000 described species worldwide. In Europe, there are 263 valid named species recognized, many of which are difficult to identify using morphology only. Here we explore the use of DNA barcodes as a tool for identification and species discovery in European gracillariids. We present a barcode library including 6,791 COI sequences representing 242 of the 263 (92%) resident species. Our results indicate high congruence between morphology and barcodes with 91.3% (221/242) of European species forming monophyletic clades that can be identified accurately using barcodes alone. The remaining 8.7% represent cases of non-monophyly making their identification uncertain using barcodes. Species discrimination based on the Barcode Index Number system (BIN) was successful for 93% of species with 7% of species sharing BINs. We discovered as many as 21 undescribed candidate species, of which six were confirmed from an integrative approach; the other 15 require additional material and study to confirm preliminary evidence. Most of these new candidate species are found in mountainous regions of Mediterranean countries, the South-Eastern Alps and the Balkans, with nine candidate species found only on islands. In addition, 13 species were classified as deep conspecific lineages, comprising a total of 27 BINs with no intraspecific morphological differences found, and no known ecological differentiation. Double-digest restriction-site associated DNA sequencing (ddRAD) analysis showed strong mitonuclear discrepancy in four out of five species studied. This discordance is not explained by Wolbachia-mediated genetic sweeps. Finally, 26 species were classified as “unassessed species splits” containing 71 BINs and some involving geographical isolation or ecological specialization that will require further study to test whether they represent new cryptic species. © Copyright © 2021 Lopez-Vaamonde, Kirichenko, Cama, Doorenweerd, Godfray, Guiguet, Gomboc, Huemer, Landry, Lastuvka, Lastuvka, Lee, Lees, Mutanen, van Nieukerken, Segerer, Triberti, Wieser and Rougerie.

Scopus

Держатели документа:
INRAE, URZF, Orleans, France
IRBI, UMR 7261, CNRS-Universite de Tours, Tours, France
Sukachev Institute of Forest, Siberian Branch of Russian Academy of Sciences, Federal Research Center “Krasnoyarsk Science Center SB RAS, Krasnoyarsk, Russian Federation
Siberian Federal University, Krasnoyarsk, Russian Federation
La Chapelle sur Loire, France
Department of Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii, Honolulu, HI, United States
Naturalis Biodiversity Center, Leiden, Netherlands
Department of Zoology, University of Oxford, Oxford, United Kingdom
Department of Biology, The Pennsylvania State University, University Park, PA, United States
Gancani, Beltinci, Slovenia
Tiroler Landesmuseen Betriebsges.m.b.H, Sammlungs- und Forschungszentrum, Hall in Tirol, Austria
Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
Prostejov, Czech Republic
Faculty of Agronomy, Mendel University, Brno, Czech Republic
Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
Department of Life Sciences, Natural History Museum, London, United Kingdom
Staatliche Naturwissenschaftliche Sammlungen Bayerns, Zoologische Staatssammlung Munchen (SNSB-ZSM), Munich, Germany
Museo Civico di Storia Naturale, Zoologia, Verona, Italy
Landesmuseum fur Karnten, Abteilung Zoologie, Sammlungs- und Wissenschaftszentrum, Klagenfurt, Austria
Institut de Systematique, Museum national d’Histoire naturelle, CNRS, Sorbonne Universite, EPHE, Universite des Antilles, Paris, France

Доп.точки доступа:
Lopez-Vaamonde, C.; Kirichenko, N.; Cama, A.; Doorenweerd, C.; Godfray, H. C.J.; Guiguet, A.; Gomboc, S.; Huemer, P.; Landry, J. -F.; Lastuvka, A.; Lastuvka, Z.; Lee, K. M.; Lees, D. C.; Mutanen, M.; van Nieukerken, E. J.; Segerer, A. H.; Triberti, P.; Wieser, C.; Rougerie, R.

/ C. Lopez-Vaamonde, N. Kirichenko, A. Cama [et al.] // Front. Ecol. Evol. - 2021. - Vol. 9. - Ст. 626752, DOI 10.3389/fevo.2021.626752. - Cited References:88. - This work was funded by the Studium (France) to both NK and DL to work as research fellows at INRAE Orleans; the Russian Foundation for Basic Research (No. 19-04-01029-a) and the basic project of Sukachev Institute of Forest SB RAS (project No. 0287-2021-0011) to NK; the Region Centre (France) project ENDOFEED (201000047141) to CL-V; the Ministry of Agriculture (France) project PASSIFOR to CL-V and RR; the Academy of Finland (grant number: 277984) to MM and the Kvantum Institute to KL; Kone foundation, Finnish Cultural foundation for financing the FinBOL (Finnish Barcode of Life) 2011-2015, and the Academy of Finland for financing FinBOL through the FinBIF national infrastructure project since 2014; Agriculture & Agri-Food Canada, Science and Technology Branch (projects Nos. J-000977 and J-002279) to J-FL; Promotion of Educational Policies, University and Research Department of the Autonomous Province of Bolzano - South Tyrol and Austrian Federal Ministry of Science, Research and Economics in the framework of ABOL (Austrian Barcode of Life) to PH. CD's salary and all DNA sequencing at Naturalis Biodiversity Center was funded through the Dutch Economic Restructuring Fund (FES). AS was supported by the Bavarian Ministry of Science and Art (Germany) project BFB and the Federal Ministry of Education and Research (Germany) project GBOL. Funding for DNA barcoding was also partly provided by the Government of Canada through Genome Canada, the Ontario Genomics Institute in support of the International Barcode of Life project, and by the National Science and Engineering Research Council of Canada. . - ISSN 2296-701XРУБ Ecology

Аннотация: Gracillariidae is the most species-rich leaf-mining moth family with over 2,000 described species worldwide. In Europe, there are 263 valid named species recognized, many of which are difficult to identify using morphology only. Here we explore the use of DNA barcodes as a tool for identification and species discovery in European gracillariids. We present a barcode library including 6,791 COI sequences representing 242 of the 263 (92%) resident species. Our results indicate high congruence between morphology and barcodes with 91.3% (221/242) of European species forming monophyletic clades that can be identified accurately using barcodes alone. The remaining 8.7% represent cases of non-monophyly making their identification uncertain using barcodes. Species discrimination based on the Barcode Index Number system (BIN) was successful for 93% of species with 7% of species sharing BINs. We discovered as many as 21 undescribed candidate species, of which six were confirmed from an integrative approach; the other 15 require additional material and study to confirm preliminary evidence. Most of these new candidate species are found in mountainous regions of Mediterranean countries, the South-Eastern Alps and the Balkans, with nine candidate species found only on islands. In addition, 13 species were classified as deep conspecific lineages, comprising a total of 27 BINs with no intraspecific morphological differences found, and no known ecological differentiation. Double-digest restriction-site associated DNA sequencing (ddRAD) analysis showed strong mitonuclear discrepancy in four out of five species studied. This discordance is not explained by Wolbachia-mediated genetic sweeps. Finally, 26 species were classified as "unassessed species splits" containing 71 BINs and some involving geographical isolation or ecological specialization that will require further study to test whether they represent new cryptic species.

WOS

Держатели документа:
URZF, INRAE, Orleans, France.
Univ Tours, IRBI, UMR 7261, CNRS, Tours, France.
RAS, SB, Sukachev Inst Forest, Fed Res Ctr,Krasnoyarsk Sci Ctr, Krasnoyarsk, Russia.
Siberian Fed Univ, Krasnoyarsk, Russia.
Univ Hawaii, Coll Trop Agr & Human Resources, Dept Plant & Environm Protect Sci, Honolulu, HI USA.
Nat Biodivers Ctr, Leiden, Netherlands.
Univ Oxford, Dept Zool, Oxford, England.
Penn State Univ, Dept Biol, University Pk, PA 16802 USA.
Gancani, Beltinci, Slovenia.
Tiroler Landesmuseen BetriebsgesmbH Sammlungs & F, Hall In Tirol, Austria.
Agr & Agri Food Canada, Ottawa Res & Dev Ctr, Ottawa, ON, Canada.
Mendel Univ Brno, Fac Agron, Brno, Czech Republic.
Univ Oulu, Ecol & Genet Res Unit, Oulu, Finland.
Nat Hist Museum, Dept Life Sci, London, England.
Staatliche Nat Wissensch Sammlungen Bayerns, Zool Staatssammlung Munchen SNSB ZSM, Munich, Germany.
Museo Civ Storia Nat, Zool, Verona, Italy.
Landesmuseum Karnten, Abt Zool Sammlungs & Wissensch Zentrum, Klagenfurt, Austria.
Univ Antilles, Inst Systemat Evolut Biodivers ISYEB, Museum Natl Hist Nat, CNRS,Sorbonne Univ,EPHE, Paris, France.

Доп.точки доступа:
Lopez-Vaamonde, Carlos; Kirichenko, Natalia; Cama, Alain; Doorenweerd, Camiel; Godfray, H. Charles J.; Guiguet, Antoine; Gomboc, Stanislav; Huemer, Peter; Landry, Jean-Francois; Lastuvka, Ales; Lastuvka, Zdenek; Lee, Kyung Min; Lees, David C.; Mutanen, Marko; van Nieukerken, Erik J.; Segerer, Andreas H.; Triberti, Paolo; Wieser, Christian; Rougerie, Rodolphe; Studium (France); Russian Foundation for Basic ResearchRussian Foundation for Basic Research (RFBR) [19-04-01029-a]; basic project of Sukachev Institute of Forest SB RAS [0287-2021-0011]; Region Centre (France) project ENDOFEED [201000047141]; Ministry of Agriculture (France) project PASSIFOR; Academy of FinlandAcademy of FinlandEuropean Commission [277984]; Kone foundation; Finnish Cultural foundationFinnish Cultural Foundation; Agriculture & Agri-Food Canada, Science and Technology Branch [J-000977, J-002279]; Promotion of Educational Policies, University and Research Department of the Autonomous Province of Bolzano - South TyrolPronvincia Autonoma di Bolzano; Austrian Federal Ministry of Science, Research and Economics in the framework of ABOL; Dutch Economic Restructuring Fund (FES); Bavarian Ministry of Science and Art (Germany) project BFB; Federal Ministry of Education and Research (Germany) project GBOL; Government of Canada through Genome CanadaGenome Canada; Ontario Genomics Institute in support of the International Barcode of Life project; National Science and Engineering Research Council of CanadaNatural Sciences and Engineering Research Council of Canada (NSERC); Kvantum Institute; Academy of FinlandAcademy of FinlandEuropean Commission

/ R. Linnakoski, S. Sutela, MPA Coetzee [et al.] // Sci Rep. - 2021. - Vol. 11, Is. 1. - Ст. 7336, DOI 10.1038/s41598-021-86343-7. - Cited References:88. - Tuija Hytonen, Alex Nordlund and Runlei Chang are thanked for excellent technical assistance and Pyry Veteli for providing Finnish isolates of Armillaria. The CSC - IT Center for Science, Finland, is acknowledged for providing computational resources. This work was funded by the Academy of Finland (decision number 309896). We are grateful to the 1KFG project (CSP 1974) for access to unpublished genome data. The genome sequence data were produced by the US Department of Energy Joint Genome Institute in collaboration with the user community, and we acknowledge the JGI team and the people who generated the material and RNA for the project: Francis M. Martin, Laszlo Nagy, Neha Sahu, Sara Hortal Botifoll, Johanna Wong-Bajracharya and Jonathan M. Plett. . - ISSN 2045-2322РУБ Multidisciplinary Sciences

Аннотация: Species of Armillaria are distributed globally and include some of the most important pathogens of forest and ornamental trees. Some of them form large long-living clones that are considered as one of the largest organisms on earth and are capable of long-range spore-mediated transfer as well as vegetative spread by drought-resistant hyphal cords called rhizomorphs. However, the virus community infecting these species has remained unknown. In this study we used dsRNA screening and high-throughput sequencing to search for possible virus infections in a collection of Armillaria isolates representing three different species: Armillaria mellea from South Africa, A. borealis from Finland and Russia (Siberia) and A. cepistipes from Finland. Our analysis revealed the presence of both negative-sense RNA viruses and positive-sense RNA viruses, while no dsRNA viruses were detected. The viruses included putative new members of virus families Mymonaviridae, Botourmiaviridae and Virgaviridae and members of a recently discovered virus group tentatively named "ambiviruses" with ambisense bicistronic genomic organization. We demonstrated that Armillaria isolates can be cured of viruses by thermal treatment, which enables the examination of virus effects on host growth and phenotype using isogenic virus-infected and virus-free strains.

WOS

Держатели документа:
Nat Resources Inst Finland Luke, Helsinki, Finland.
Univ Pretoria, Forestry & Agr Biotechnol Inst FABI, Dept Biochem Genet & Microbiol, Pretoria, South Africa.
VN Sukachev Inst Forest SB RAS, Lab Reforestat Mycol & Plant Pathol, Krasnoyarsk, Russia.
Reshetnev Siberian State Univ Sci & Technol, Dept Chem Technol Wood & Biotechnol, Krasnoyarsk, Russia.

Доп.точки доступа:
Linnakoski, Riikka; Sutela, Suvi; Coetzee, Martin P. A.; Duong, Tuan A.; Pavlov, Igor N.; Litovka, Yulia A.; Hantula, Jarkko; Wingfield, Brenda D.; Vainio, Eeva J.; Litovka, Yulia; Academy of FinlandAcademy of FinlandEuropean Commission [309896]; 1KFG project [CSP 1974]

/ R. Linnakoski, S. Sutela, M. P.A. Coetzee [et al.] // Ботанический журнал. - 2021. - Т. 106, № 4. - P353-362, DOI 10.31857/S0006813621040116 . - ISSN 0006-8136
Аннотация: Species of Armillaria are distributed globally and include some of the most important pathogens of forest and ornamental trees. Some of them form large long-living clones that are considered as one of the largest organisms on earth and are capable of long-range spore-mediated transfer as well as vegetative spread by drought-resistant hyphal cords called rhizomorphs. However, the virus community infecting these species has remained unknown. In this study we used dsRNA screening and high-throughput sequencing to search for possible virus infections in a collection of Armillaria isolates representing three different species: Armillaria mellea from South Africa, A. borealis from Finland and Russia (Siberia) and A. cepistipes from Finland. Our analysis revealed the presence of both negative-sense RNA viruses and positive-sense RNA viruses, while no dsRNA viruses were detected. The viruses included putative new members of virus families Mymonaviridae, Botourmiaviridae and Virgaviridae and members of a recently discovered virus group tentatively named “ambiviruses” with ambisense bicistronic genomic organization. We demonstrated that Armillaria isolates can be cured of viruses by thermal treatment, which enables the examination of virus effects on host growth and phenotype using isogenic virus-infected and virus-free strains. © 2021, The Author(s).

Scopus

Держатели документа:
Natural Resources Institute Finland (Luke), Helsinki, Finland
Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
Laboratory of Reforestation, Mycology and Plant Pathology, V.N. Sukachev Institute of Forest SB RAS, Krasnoyarsk, Russian Federation
Department of Chemical Technology of Wood and Biotechnology, Reshetnev Siberian State University of Science and Technology, Krasnoyarsk, Russian Federation

Доп.точки доступа:
Linnakoski, R.; Sutela, S.; Coetzee, M. P.A.; Duong, T. A.; Pavlov, I. N.; Litovka, Y. A.; Hantula, J.; Wingfield, B. D.; Vainio, E. J.

/ I. Franic, S. Prospero, K. Adamson [et al.] // Sci. Data. - 2022. - Vol. 9, Is. 1. - Ст. 62, DOI 10.1038/s41597-022-01162-3. - Cited References:37. - We gratefully acknowledge the financial support of the Swiss National Science Foundation (Project C15.0081) grant number 174644 and the Swiss Federal Office for the Environment (Grant 00.0418.PZ/ P193-1077). This work was supported by COST Action "Global Warning" (FP1401). CABI is an international intergovernmental organisation, and R.E., M.K., H.L. and I.F. gratefully acknowledge the core financial support from our member countries (and lead agencies) including the United Kingdom (Foreign, Commonwealth & Development Office), China (Chinese Ministry of Agriculture and Rural Affairs), Australia (Australian Centre for International Agricultural Research), Canada (Agriculture and Agri-Food Canada), Netherlands (Directorate General for International Cooperation), and Switzerland (Swiss Agency for Development and Cooperation). See https://www.cabi.org/aboutcabi/who-we-work-with/key-donors/ for full details. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. M.B. and M.K.H. were financially supported by the Slovak Research and Development Agency (Project APVV-19-0116). H.B. would like to thank the botanist Jorge Capelo who helped with Myrtaceae identification and INIAV IP for supporting her contribution to this study. Contributions of M. de G. and B.P. were financed through Slovenian Research Agency (P4-0107) and by the Slovenian Ministry of Agriculture, Forestry and Food (Public Forestry Service). G.C, C.B.E. and A.F.M. were supported by OTKA 128008 research grant provided by the National Research, Development and Innovation Office. Contributions of K.A. and R.D. were supported by the Estonian Science Foundation grant PSG136. M.J.J., C.L.M. and H.P.R. were financially supported by the 15. Juni Fonden (Grant 2017-N-123). P.B., B.G. and M.Ka. were financially supported by the Ministry of Science and Higher Education of the Republic of Poland for the University of Agriculture in Krakow (SUB/040013-D019). C.N. was financially supported by the Slovak Research and Development Agency (Grant APVV-15-0531). N.K. was partially supported by Russian Foundation for Basic Research (Grants 15-29-02645, 19-04-01029). R.OH. was supported by funding from DAERA, and assistance from David Craig, AFBI. T.P. thanks the South African Department of Forestry, Fisheries and the Environment (DFFE) for funding noting that this publication does not necessarily represent the views or opinions of DFFE or its employees. In preparing the publication, materials of the bioresource scientific collection of the CSBG SB RAS "Collections of living plants indoors and outdoors" USU_440534 (Novosibirsk, Russia) were used. M.Z. was financially supported by Ministry of education, science and technological development of the Republic of Serbia (Contract 451-03-68/2020-14/200197). We acknowledge the Genetic Diversity Centre (GDC) at ETH Zurich for providing computational infrastructure and acknowledge the contribution of McGill University and Genome Quebec Innovation Center (Montreal, Quebec, Canada) for pair-end sequencing on Illumina MiSeq. . - ISSN 2052-4463РУБ Multidisciplinary Sciences

Аннотация: International trade in plants and climate change are two of the main factors causing damaging tree pests (i.e. fungi and insects) to spread into new areas. To mitigate these risks, a large-scale assessment of tree-associated fungi and insects is needed. We present records of endophytic fungi and insects in twigs of 17 angiosperm and gymnosperm genera, from 51 locations in 32 countries worldwide. Endophytic fungi were characterized by high-throughput sequencing of 352 samples from 145 tree species in 28 countries. Insects were reared from 227 samples of 109 tree species in 18 countries and sorted into taxonomic orders and feeding guilds. Herbivorous insects were grouped into morphospecies and were identified using molecular and morphological approaches. This dataset reveals the diversity of tree-associated taxa, as it contains 12,721 fungal Amplicon Sequence Variants and 208 herbivorous insect morphospecies, sampled across broad geographic and climatic gradients and for many tree species. This dataset will facilitate applied and fundamental studies on the distribution of fungal endophytes and insects in trees.

WOS

Держатели документа:
CABI, Delemont, Switzerland.
Swiss Fed Inst Forest Snow & Landscape Res WSL, Birmensdorf, Switzerland.
Univ Bern, Inst Plant Sci, Bern, Switzerland.
Estonian Univ Life Sci, Inst Forestry & Rural Engn, Tartu, Estonia.
Sapienza Univ Rome, Dept Environm Biol, Rome, Italy.
French Natl Res Inst Agr Food & Environm URZF INR, Forest Zool Res Unit, Orleans, France.
Hellen Agr Org Demeter, Forest Res Inst, Thessaloniki, Greece.
Meise Bot Garden, Meise, Belgium.
Slovak Acad Sci, Inst Forest Ecol, Nitra, Slovakia.
Natl Res Inst Rural Engn Water & Forests INRGREF, Ariana, Tunisia.
Agr Univ Krakow, Dept Forest Ecosyst Protect, Krakow, Poland.
Inst Nacl Invest Agr & Vet IP INIAV IP, Oeiras, Portugal.
ITQB NOVA, GREEN IT Bioresources Sustainabil, Oeiras, Portugal.
Silva Tarouca Res Inst Landscape & Ornamental Gar, Pruhonice, Czech Republic.
Norwegian Inst Bioecon Res, NIBIO, As, Norway.
NMBU Norwegian Univ Life Sci, As, Norway.
Murdoch Univ, Harry Butler Inst, Murdoch, WA, Australia.
Nat Res Ctr, Inst Bot, Vilnius, Lithuania.
Swedish Univ Agr Sci, Southern Swedish Forest Res Ctr, Alnarp, Sweden.
Inst Invest Forestales & Agr Bariloche INTA CONIC, San Carlos De Bariloche, Rio Negro, Argentina.
Clemson Univ, Dept Forestry & Environm Conservat, Clemson, SC USA.
Univ Sopron, Forest Res Inst, Dept Forest Protect, Matrafured, Hungary.
Ukrainian Res Inst Forestry & Forest Meliorat, Kharkiv, Ukraine.
Slovenian Forestry Inst, Ljubljana, Slovenia.
Univ Valladolid INIA, Sustainable Forest Management Res Inst, Palencia, Spain.
Univ Valladolid, Dept Vegetal Prod & Forest Resources, Palencia, Spain.
Isparta Univ Appl Sci, Isparta, Turkey.
La Trobe Univ, Sch Appl Syst Biol, Melbourne, Vic, Australia.
Agribio Ctr, Agr Victoria Res, Bundoora, Vic, Australia.
Ukrainian Res Inst Mt Forestry, Ivano Frankivsk, Ukraine.
Zhejiang A&F Univ, Coll Forestry & Biotechnol, Hangzhou, Peoples R China.
Swiss Fed Inst Technol, Inst Terr Ecosyst, Zurich, Switzerland.
Swiss Fed Inst Technol, Inst Agr Sci, Zurich, Switzerland.
Univ Copenhagen, Dept Geosci & Nat Resource Management, Copenhagen, Denmark.
Russian Acad Sci, Sukachev Inst Forest, Krasnoyarsk Sci Ctr SB RAS, Fed Res Ctr,Siberian Branch, Krasnoyarsk, Russia.
Siberian Fed Univ, Krasnoyarsk, Russia.
Croatian Forest Res Inst, Jastrebarsko, Croatia.
Ukrainian Natl Forestry Univ, Lvov, Ukraine.
Univ Montenegro, Biotech Fac, Podgorica, Montenegro.
CABI, Beijing, Peoples R China.
Fera Sci Ltd, Natl Agrifood Innovat Campus, York, N Yorkshire, England.
Royal Bot Gardens Victoria, Melbourne, Vic, Australia.
Minist Agr Nat & Food Qual, Netherlands Food & Consumers Prod Safety Author, Natl Plant Protect Org, Wageningen, Netherlands.
CNR, Natl Res Council, Inst Sustainable Plant Protect IPSP, Sesto Fiorentino, Italy.
Forestry Res Inst Zvolen, Natl Forest Ctr, Zvolen, Slovakia.
Dept Agr Food & Marine, Dublin, Ireland.
AgriFood & Biosciences Inst AFBI, Belfast, Antrim, North Ireland.
Cankiri Karatekin Univ, Fac Forestry, Cankiri, Turkey.
Univ Pretoria, Forestry & Agr Biotechnol Inst FABI, Pretoria, South Africa.
Tanzania Forestry Res Inst TAFORI, Lushoto, Tanzania.
Russian Acad Sci, Siberian Branch, Cent Siberian Bot Garden, Novosibirsk, Russia.
Nat Resources Inst Finland, Suonenjoki, Finland.
US Forest Serv, USDA, Southern Res Stn, Athens, GA USA.
Univ Tuscia, DIBAF, Viterbo, Italy.
Univ Georgia, DB Warnell Sch Forestry & Nat Resources, Athens, GA USA.
Linnaeus Univ, Forestry & Wood Technol, Vaxjo, Sweden.
Univ Novi Sad, Inst Lowland Forestry & Environm ILFE, Novi Sad, Serbia.
Kirstenbosch Res Ctr, South African Natl Biodivers Inst, Cape Town, South Africa.

Доп.точки доступа:
Franic, Iva; Prospero, Simone; Adamson, Kalev; Allan, Eric; Attorre, Fabio; Auger-Rozenberg, Marie Anne; Augustin, Sylvie; Avtzis, Dimitrios; Baert, Wim; Barta, Marek; Bauters, Kenneth; Bellahirech, Amani; Boron, Piotr; Braganca, Helena; Brestovanska, Tereza; Brurberg, May Bente; Burgess, Treena; Burokiene, Daiva; Cleary, Michelle; Corley, Juan; Coyle, David R.; Csoka, Gyorgy; Cerny, Karel; Davydenko, Kateryna; de Groot, Maarten; Diez, Julio Javier; Lehtijarvi, R.; Drenkhan, Rein; Edwards, Jacqueline; Elsafy, Mohammed; Eotvos, Csaba bela; Falko, Roman; Fan, Jianting; Feddern, Nina; Furjes-Miko, Agnes; Gossner, Martin M.; Grad, Bartlomiej; Hartmann, Martin; Havrdova, Ludmila; Horakova, Miriam Kadasi; Hrabetova, Marketa; Justesen, Mathias Just; Kacprzyk, Magdalena; Kenis, Marc; Kirichenko, Natalia; Kovac, Marta; Kramarets, Volodymyr; Lackovic, Nikola; Lantschner, Maria Victoria; Lazarevic, Jelena; Leskiv, Marianna; Li, Hongmei; Madsen, Corrie Lynne; Malumphy, Chris; Matosevic, Dinka; Matsiakh, Iryna; May, Tom W.; Meffert, Johan; Migliorini, Duccio; Nikolov, Christo; O'Hanlon, Richard; Oskay, Funda; Paap, Trudy; Parpan, Taras; Piskur, Barbara; Ravn, Hans Peter; Richard, John; Ronse, Anne; Roques, Alain; Ruffner, Beat; Sivickis, Karolis; Soliani, Carolina; Talgo, Venche; Tomoshevich, Maria; Uimari, Anne; Ulyshen, Michael; Vettraino, Anna Maria; Villari, Caterina; Wang, Yongjun; Witzell, Johanna; Zlatkovic, Milica; Eschen, Rene; Diez, Julio; Braganca, Maria Helena Pires; Swiss National Science FoundationSwiss National Science Foundation (SNSF)European Commission [C15.0081, 174644]; Swiss Federal Office for the Environment [00.0418.PZ/ P193-1077]; COST Action "Global Warning" [FP1401]; United Kingdom (Foreign, Commonwealth & Development Office); China (Chinese Ministry of Agriculture and Rural Affairs); Australia (Australian Centre for International Agricultural Research); Canada (Agriculture and Agri-Food Canada); Netherlands (Directorate General for International Cooperation); Switzerland (Swiss Agency for Development and Cooperation); Slovak Research and Development AgencySlovak Research and Development Agency [APVV-19-0116, APVV-15-0531]; Slovenian Research AgencySlovenian Research Agency - Slovenia [P4-0107]; Slovenian Ministry of Agriculture, Forestry and Food (Public Forestry Service); OTKA by the National Research, Development and Innovation Office [128008]; Estonian Science Foundation grant [PSG136]; 15. Juni Fonden [2017-N-123]; Ministry of Science and Higher Education of the Republic of PolandMinistry of Science and Higher Education, Poland [SUB/040013-D019]; Russian Foundation for Basic ResearchRussian Foundation for Basic Research (RFBR) [15-29-02645, 19-04-01029]; DAERA; South African Department of Forestry, Fisheries and the Environment (DFFE); Ministry of education, science and technological development of the Republic of SerbiaMinistry of Education, Science & Technological Development, Serbia [451-03-68/2020-14/200197]

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

ГРНТИ

68.47.03

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

РИНЦ

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

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