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Contract number
14.Y26.31.0004
Time span of the project
2014-2018

As of 30.01.2020

43
Number of staff members
66
scientific publications
7
Objects of intellectual property
General information

Name of the project: Genomic research of main boreal forest-forming pine species and their most dangerous pathogens in Russia

Strategy for Scientific and Technological Development Priority Level: г


Goals and objectives

Research directions: Full-gemone sequencing and annotation, comparative genetics, bioinformatics

Project objective:

- Creation of a forest genomics laboratory; study of genomes of main forest-forming species of Russia and their most dangerous pathogens (primarily fungi) that cause catastrophic exsiccation of Russian boreal forests

- Development of molecular and genetic markers for determining the origin of wood, monitoring genetic variability of pinewood forests, their adaptation to climate change and for creation of selection and nature preservation programs


The practical value of the study

  • The Laboratory has accumulation of DNAs from haploid and diploid tissue the Siberian larch (Larix sibirica Ledeb.), the Siberian pine (Pinus sylvestris L.) and conducted all the stages of of preparation for sequencing. A library has been created featuring samples of various fragmentations for sequencing.
  • We have completed sequencing, primary assembly and annotation of the genome for L. sibirica (supposed size of the genome is 12,03 Gbp) and P. sibirica (supposed size of the genome is 28,9 Gbp) using an original method for multi-stage assembly of large genomes developed by the Laboratory. Annotation of the genomes has been completed.
  • We have completed de novo assembly and annotation of the transcriptome of the Siberian larch (Larix sibirica Ledeb.) and analysis of its statistical and combinatorics properties.
  • The Laboratory has prepared and sequenced transcriptome libraries from various tissues of needles, buds, young shoots, female cones, xylem etc. for detailed annotation of genomes of conifers. We have also completed bioinformatics processing of transcriptome sequencing data.
  • We have conducted works in scanning nucleotide sequences of haploid megagametophytes for purposes of detecting mutations and polymorphic segregating SNPs.
  • Our researchers have conducted a survey of microsatellite loci in genomes of the Siberian larch, the Siberian pine and the Siberian fir. We have completed design, synthesis and testing of corresponding PCR primers for their amplification. For these species, a catalog of microsatellite (SSR) loci has been created and described.
  • The Laboratory has conducted assembly of mitochondrial genomes by selecting exactly mitochondrial contigs and scaffold of the Siberian larch, the Siberian pine and the common pine.
  • We have conducted complete assembly and annotation of the chloroplast genome of the Siberian larch. The length of the chloroplast genome of L. sibirica amounted to 122561 bp and is close to 122474 bp in the closely related Larix decidua Mill. On the basis of the assembled chloroplast genome of the Siberian larch we have conducted search for polymorphic genetic markers – simple microsatellite repeats (SSRs) and single nucleotide polymorphisms (SNP). Assembly was conducted using the program for mapping Bowtie2 and the genome assembler SPAdes. 13 SNPs have been found, of which two are situated in encoding regions of the genome: tRNA-Arg and Cell division protein FtsH.
  • Our researchers have extensively tested the ddRADseq (double digestion Restriction site Associated DNAs sequencing) method – a method of genotyping by sequencing. Obtained data allows to start the work to bind assemblies obtained from reference trees to genetic maps of linkage.
  • We have conducted detailed comparative analysis of mitochondrial genomes of Armillaria borealis, A. sinapina and A. ostoyae. In all the three genomes we have found duplications of several genes and integrative plasmids.
  • The Laboratory has completed sequencing of A. borealis samples cultivated in various environments for analysis of differential expression of genes and determining the more aggressive ones (and, supposedly, more pathogenic) strains and candidate genes for pathogenicity. We have conducted bioinformatics processing of sequencing data. Quality of sequencing has been assessed. As a result of the assembly we have conducted comparative analysis between fungal strains that are contrastive in terms of level of pathogenicity.
  • Our researchers have conducted bioinformatics processing of data from sequencing of genomes of fungi Armillaria mellea s. l. Quality of assembly has been assessed. We have analyzed repeating elements in genomes of fungi. For the first time, mitochondrial genomes of representatives of the A. mellea s. complex have been assembled. We have started work to investigate species diversity of fungi of the A. mellea s. l. complex. on the territory of Siberia and Far East using genetics approaches.

Implemented results of research: We have obtained 5 certificates of state registration for computer software and one patent.

Education and career development:

  • 16 education courses for the «Genomics and Bioinformatics» master degree program have been developed: «Molecular ecology», «Population Genomics», «Genomics», «Forest Pathology Monitoring», «Forest Protection Technologies», «Introduction to Bioinformatics», «Python Programming», «Human Genetics», «Proteomics», «Genomics and Bioinformatics», «Modern Methods of Analysis of Multi-Dimensional Data in Biology», «Special Case-study “Methods of Molecular Genetic Research”», «Theory of Selection», «Immunogenetics», «Plant Bioengineering», «Practical Bioinformatics».
  • Over the four years of the Laboratory's work, 36 people have completed occupational retraining and career enhancement in the domain of our research from other organization (mostly young specialists from the V. N. Sukachyov Forest Institute of the Siberian Branch of the Russian Academy of Sciences and of the Federal Budgetary Organization for Forest Protection of Russia.

Organizational and structural changes: The Research and Education Center for Genomics Research of the Siberian Federal University is functioning on the grounds of the Laboratory. The Center also acts as a collective usage center of full-geome sequencing equipment.

Other results:

  • The Laboratory participates in development of a first Russian third-generation DNA sequencer in collaboration with the «GANNA-DNA» startup that has received a grant from the «Skolkovo» Foundation. The head of Laboratory Prof. Krutovskiy is one of the six authors of an original method of sequencing that received an international patent and one of the 9 participants of the project.

Collaborations:

  • Yu. P. Alukhov Laboratory of Population Genetics of the N. I. Vavilov Institute of General Genetics of the Russian Academy of Sciences (Russia), Department of Monitoring of the State of Forest Genetic Resources of Center for Protection of Forests of the Krasnoyarsk Krai - branch of the Federal Budgetary Organization for Forest Protection (Russia): joint research and collaborative scientific events
  • Laboratory of Forest Genetics and Selection of the V. N. Sukachyov Institute of Forest of the Siberian Branch of the Russian Academy of Sciences (Russia), Laboratory of Plant Molecular Ecology of the Institute of Plant and Ecology Ecology of the Ural Branch of the Russian Academy of Sciences (Russia), Laboratory of the P. A. Lazarev Museum o the Mammoth of the North-Eastern Federal University (Russia), Laboratory for Identification of Objects of Biological Origin of the Southern Federal University (Russia), Khakass Technical Institute (Russia), Center for High Productivity Computations of the Space and Information Technologies Institute of the Siberian Federal University (Russia), Center of Bioinformatics of the University of Haifa (Israel): joint research
  • Department of Forest Genetics and Selection of the Georg-August University of Göttingen (Germany): joint research and internships of employees and students of the Laboratory at the University of Göttingen


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Kolesnikova A., Putintseva Y.A., Simonov E.P., Biriukov V. V., Oreshkova N.V., Pavlov I.N., Sharov V.V., Kuzmin D.A., Makolov S.V., Anderson J., Krutovsky K.V.
Comparison of mitochondrial genomes of four closely-related Armillaria species indicated mobile genetic elements as a main cause of genome size variation. BMC Genomics (accepted) (2019).
Bondar E.I., Putintseva Y.A., Oreshkova N.V., Krutovsky K.V.
Siberian larch (Larix sibirica Ledeb.) chloroplast genome and development of polymorphic chloroplast markers. BMC Bioinformatics 20(1): 37 (2019).
Kuzmin D.A., Feranchuk S.I., Sharov V.V., Cybin A.N., Makolov S.V., Putintseva Y.A., Oreshkova N.V., Krutovsky K.V.
Stepwise large genome assembly approach: A case of Siberian larch (Larix sibirica Ledeb.). BMC Bioinformatics 20(1): 37 (2019).
Oreshkova N.V., Bondar E.I., Putintseva Yu.A., Sharov V.V., Kuzmin D.A., Krutovsky K.V.
Development of nuclear microsatellite markers with long (three -, four-, five-and six-nucleotide) motives for three larch species based on the de novo whole genome sequencing of Siberian larch (Larix sibirica Ledeb.). Russian Journal of Genetics 55(4): 444-450 (2019).
Semerikov V.L., Semerikova S.A., Putintseva Y.A., Tarakanov V.V., Tikhonova I.V., Vidyakin A.I., Oreshkova N.V., Krutovsky K.V.
Colonization History of Scots Pine in Eastern Europe and North Asia Based on Mitochondrial DNA Variation. Tree Genetics and Genomes 14: 8 (2018).
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