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Contract number
Time span of the project

As of 01.11.2022

Number of staff members
scientific publications
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

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

Scientific results:

  1. For the first time we have provided an exhaustive phylogenetic description, conducted a   phylogenetic research an testing of the bracket fungus Porodaedalea niemela that can be found on the northernmost border of boreal forests on the Taymyr peninsula, we also were the first to sequence and annotate the genome of the fungus (Konstantin V. Krutovskiy is head of the genomics project for this fungus, which is performed  in collaboration with  the US Department of Energy.
  2. On the basis of full-genome data obtained in Konstantin V. Krutovskiy’s projects we have developed new polymorphic markers for population-genetic, phylogenetic and genogeographic research of Pinus sylvestris, Pinus sibirica and Lárix sibírica.
  3. For the first time on the crossroads of dendrochronology  and genomics we have studied the relation of the dynamics of velocity and the stability of individual growth, and individual heterozygosity in mountain hemlock and Siberian larch with the use of full-genome markers. The result demonstrate the major instability of growth in fast-growing trees.
  4. For the first time we have sequenced and annotated the genome of the whale and conducted an analysis of the genes that are probably related to high life expectancy of this species.
  5. For the first time we have sequenced and annotated the nuclear, mitochondrial and chloroplast genomes of the most significant tree species of boreal forests of Siberia, the Siberian larch and the cedar (Konstantin V. Krutovskiy leads the genomics project, which has been supported with a mega-grant from the Government of  Russia) as well as the chloroplast genome of the Karelian birch.
  6. For the first time we completely sequenced and assembled the mitochondrial genome of the woolly mammoth.
  7. For the first time we have studied mobile genetic elements in the mitochondrial genome of four species of honey fungus.
  8. For the first time we have sequenced, assembled and annotated the genome of the boreal honey fungus, Armillaria borealis.

Implemented results of research: 

  • The Laboratory has developed, patented and implemented a new method for assembling large genomes.
  • We have obtained and annotated the genome of the larch, which is used as the reference genome in full-genome association research and genome selection.      

Education and career development:

  • We have created a new department of genetics and bioinformatics at the Siberian Federal University.
  • The Laboratory has developed a master’s and postgraduate degree program for the Department of Genomics and Bioinformatics of the Siberian Federal University.
  • We have developed new courses in bioinformatics, molecular ecology and genomics. 

Organizational and structural changes: 

We have created the Science and Education Center for Genome Research of the Institute of Basic Biology and Biotechnology of the Siberian Federal University (Krasnoyarsk) which can be later developed into a center for the collective use of scientific equipment for genome research. 

Other results:
The Laboratory participates in the development of the first Russian third-generation DNA sequencer in collaboration with the «GAMMA-DNA» startup that has received a grant from the Skolkovo Foundation. Head of the Laboratory Konstantin V. Krutovskiy is one of the six authors of the original sequencing method that has been protected by an international patent and one of the 9 participants of the project.


  • We are conducting joint research with the Vavilov Institute of General Genetics of the Russian Academy of Sciences, the Voronezh State University of Forestry and Technologies named after G.F. Morozov, a branch of the Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, the Sukachev Institute of Forest of the Siberian Branch of the Russian Academy of Sciences, the Russian Center for Forest Protection and the Center for Forest Protection of the Krasnoyarsk Region.
  • We are pursuing international cooperation and joint research with the University of Göttingen and the Institute of Forest Genetics in Germany.
  • Participation in projects of the international consortium in alpine forest genomics (AforGeN) and evolution genomics (EvolTree). 

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bondar, e. i., s. i. feranchuk, k. a. miroshnikova, v. v. sharov, d. a. kuzmin, n. v. oreshkova, k. v. krutovsky
2022 Annotation of Siberian larch (Larix sibirica Ledeb.) nuclear genome – one of the most cold resistant tree species in the only seasonal senescence Genus in Pinaceae. Plants 11(15): 2062. https://doi.org/10.3390/plants11152062 (IF = 4.658/4.827; Q1Scopus/Q1WoS)
batalova, a. y., y. a. putintseva, m. g. sadovsky, k. v. krutovsky
2022 Comparative genomics of seasonal senescence in forest trees. International Journal of Molecular Sciences 23(7): 3761. https://doi.org/10.3390/ijms23073761 (IF = 5.924/6.132; Q1Scopus/Q1WoS)
kirichenko, a. d., a. a. poroshina, d. yu. sherbakov, m. g. sadovsky, k. v. krutovsky
2021. Comparative analysis of alignment-free genome clustering and whole genome alignment-based phylogenomic relationship of coronaviruses. PLoS One 17(3): e0264640. https://doi.org/10.1371/journal.pone.0264640 (IF = 3.240/3.788; Q1Scopus/ Q2WoS)
bondar, e. i., m. troukhan, k. v. krutovsky, t. v. tatarinova.
2022. Genome-wide prediction of transcription start sites in conifers. International Journal of Molecular Sciences 23(3), 1735; https://doi.org/10.3390/ijms23031735 (IF = 5.924/6.132; Q1/Q1)
titievsky, a.; putintseva, y.a.; taranenko, e.a.; baskin, s.; oreshkova, n.v.; brodsky, e.; sharova, a. v.; sharov, v.v.; panov, j.; kuzmin, d.a.; brodsky, l.; krutovsky, k.v.
2021 Comparative genomics analysis of repetitive elements in ten gymnosperm species: “dark repeatome” and its abundance in conifer and Gnetum species. Life 11(11): 1234; https://doi.org/10.3390/life11111234 (IF = 3.817(2 years)/na; Q1Scopus/Q2WoS)
putintseva yu.a., e.i. bondar, e.p. simonov, v.v. sharov, n.v. oreshkova, d.a. kuzmin, yu.m. konstantinov, v.n. shmakov, v.i. belkov, m.s. sadovsky, o. keech, k.v. krutovsky
2020 Siberian larch (Larix sibirica Ledeb.) mitochondrial genome assembled using both short and long nucleotide sequence reads is currently the largest known mitogenome. BMC Genomics 21: 654; https://doi.org/10.1186/s12864-020-07061-4 (IF = 3.594; Q2)
akulova v.s., v.v. sharov, a.i. aksyonova, yu.a. putintseva, n.v. oreshkova, s.i. feranchuk, d.a. kuzmin, i.n. pavlov, y. a. litovka, k.v. krutovsky
2020 De novo sequencing, assembly and functional annotation of Armillaria borealis genome. BMC Genomics 21(Suppl 7): 534; https://doi.org/10.1186/s12864-020-06964-6 (IF = 3.594; Q2)
kolesnikova a., y. a. putintseva, e. p. simonov, v. v. biriukov, n. v. oreshkova, i. n. pavlov, v. v. sharov, d. a. kuzmin, s. v. makolov, j. anderson, k. v. krutovsky
2019 Mobile genetic elements explain size variation in the mitochondrial genomes of four closely-related Armillaria species. BMC Genomics 20:351; https://doi.org/10.1186/s12864-019-5732-z (IF = 3.729; Q1)
bondar, e. i., y. a. putintseva, n. v. oreshkova, k. v. krutovsky
2019 Siberian larch (Larix sibirica Ledeb.) chloroplast genome and development of polymorphic chloroplast markers. BMC Bioinformatics 20(Suppl. 1): 38; https://doi.org/10.1186/s12859-018-2571-x (IF = 2.213; Q1)
kuzmin, d. a., s. i. feranchuk, v. v. sharov, a. n. cybin, s. v. makolov, y. a. putintseva, n. v. oreshkova, k. v. krutovsky
2019 Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb.). BMC Bioinformatics 20(Suppl. 1): 37; https://doi.org/10.1186/s12859-018-2570-y (IF = 2.213; Q1)
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