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

/ 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.

WOS,
Смотреть статью

Держатели документа:
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]

/ M. I. Popkova, V. V. Shishov, E. A. Vaganov [et al.] // Forests. - 2020. - Vol. 11, Is. 12. - Ст. 1343, DOI 10.3390/f11121343. - Cited References:58. - This work was supported by the Russian Ministry of Science and Higher Education (projects #FSRZ-2020-0010 and #FSRZ-2020-0014) and the Russian Science Foundation [Grant 18-14-00072]. M. Popkova received a Merit scholarship for foreign students from Fonds de Recherche du Quebec-Nature et Technologie (FRQNT) for completing this work. MVF was supported by RFBR and Krasnoyarsk Region (project number 18-45-240001 r_a). V.V.S. appreciates the support of the project #FEFE-2020-0014 (Russian Ministry of Science and Higher Education). . - ISSN 1999-4907РУБ Forestry

Аннотация: Plants exhibit morphological and anatomical adaptations to cope the environmental constraints of their habitat. How can mechanisms for adapting to contrasting environmental conditions change the patterns of tree rings formation? In this study, we explored differences in climatic conditions of permafrost and non-permafrost zones and assessed their influence on radial growth and wood traits of Larix gmelinii Rupr (Rupr) and Larix sibirica L., respectively. We quantified the contribution of xylem cell anatomy to the tree-ring width variability. Comparison of the anatomical tree-ring parameters over the period 1963-2011 was tested based on non-parametric Mann-Whitney U test. The generalized linear modeling shows the common dependence between TRW and the cell structure characteristics in contrasting environments, which can be defined as non-specific to external conditions. Thus, the relationship between the tree-ring width and the cell production in early- and latewood are assessed as linear, whereas the dependence between the radial cell size in early- and latewood and the tree-ring width becomes significantly non-linear for both habitats. Moreover, contribution of earlywood (EW) and latewood (LW) cells to the variation of TRW (in average 56.8% and 24.4% respectively) was significantly higher than the effect of cell diameters (3.3% (EW) and 17.4% (LW)) for the environments. The results show that different larch species from sites with diverging climatic conditions converge towards similar xylem cell structures and relationships between xylem production and cell traits. The work makes a link between climate and tree-ring structure, and promotes a better understanding the anatomical adaptation of larch species to local environment conditions.

WOS

Держатели документа:
Siberian Fed Univ, Lab Complex Res Forest Dynam Eurasia, Krasnoyarsk 660041, Russia.
Chinese Acad Sci, Environm & Res Ctr, South China Bot Garden, Guangzhou 510650, Peoples R China.
Reshetnev Siberian State Univ Sci & Technol, Sci Lab Forest Hlth, Krasnoyarsk 660041, Russia.
Siberian Fed Univ, Rectorate, Krasnoyarsk 660041, Russia.
VN Sukachev Inst Forest SB RAS, Fed Res Ctr, Krasnoyarsk 660036, Russia.
Siberian Fed Univ, Inst Ecol & Geog, Lab Ecosyst Biogeochem, Krasnoyarsk 660041, Russia.
Swiss Fed Res Inst WSL, Landscape Dynam, CH-8903 Birmensdorf, Switzerland.
Siberian Fed Univ, Khakass Tech Inst, Abakan 655017, Russia.
Chinese Acad Sci, Key Lab Vegetat Restorat & Management Degraded Ec, South China Bot Garden, Guangzhou 510650, Peoples R China.
Univ Quebec Chicoutimi, Dept Sci Fondamentales, Chicoutimi, PQ G7H 2B1, Canada.

Доп.точки доступа:
Popkova, Margarita, I; Shishov, Vladimir V.; Vaganov, Eugene A.; Fonti, Marina, V; Kirdyanov, Alexander, V; Babushkina, Elena A.; Huang, Jian-Guo; Rossi, Sergio; Russian Ministry of Science and Higher Education [FSRZ-2020-0010, FSRZ-2020-0014, FEFE-2020-0014]; Russian Science FoundationRussian Science Foundation (RSF) [18-14-00072]; Fonds de Recherche du Quebec-Nature et Technologie (FRQNT); RFBRRussian Foundation for Basic Research (RFBR) [18-45-240001 r_a]; Krasnoyarsk Region [18-45-240001 r_a]