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Laboratory of Genetics of plant-microbial interactions №9

Laboratory of Genetics of plant-microbial interactions №9

Head of the laboratory : Zhukov Vladimir Alexandrovich

Phone: +7 (812) 470 51 83

The team of the Laboratory of Genetics of Plant-microbial interactions under the leadership of PhD Zhukov Vladimir Alexandrovich performs research on deciphering the molecular genetic mechanisms of mutually beneficial symbioses formed by legumes with nodule bacteria, fungi of arbuscular mycorrhiza and beneficial rhizospheric/endophytic bacteria. Bioinformatics methods are used in research to analyze "big data" obtained using "omix" approaches - NGS sequencing of transcriptomes and genomes, metabolomics and proteomics.

The instrument park, which includes a powerful computing server and data storage, allows solving scientific problems at the modern level, claiming to be a world priority, and carrying out all molecular biological procedures: synthesis of libraries for NGS sequencing (Illumina and Oxford Nanopore), PCR (including in real time), sample preparation for metabolomic and transcriptomic analysis , etc .

The laboratory staff performs research within the framework of the State Assignment, NCMU "Agrotechnologies of the Future", two grants from the Russian National Science Foundation (including jointly with the N.I. Vavilov Research Institute).

The laboratory was previously headed by Doctor of Biological Sciences, Professor, acad. I.A. Tikhonovich of the Russian Academy of Sciences (in the period 1984 – 2001) and D.B.N. A.Y. Borisov (in the period 2001 – 2014). Since September 2014, the laboratory has been headed by Candidate of Biological Sciences Zhukov Vladimir Alexandrovich.

The laboratory cooperates with St. Petersburg State University (Departments of Genetics and Biotechnology, Biochemistry, Physiology and Biochemistry of Plants), the V.L. Komarov Botanical Institute, Sirius University, the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR).

We invite students and postgraduates to cooperate in the preparation of qualification papers (bachelor's/ master's degrees, PhD thesis, PhD dissertations). Possible topics of work can be found here. Information about admission to the graduate school of the Federal State Budgetary Educational Institution ARRIAM – here.

 

Основные направления

  • Исследование молекулярно-генетических основ мутуалистических симбиозов гороха посевного

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  • Транскриптомика симбиотических систем

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  • Геномика надорганизменных систем

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  • Выявление генетических основ эффективности симбиозов, формируемых бобовыми растениями, и разработка способов ее повышения в полевых условиях

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Staff

GRANTS 

 

CURRENTLY BEING PERFORMED

The Government of the Russian Federation

  • AWCSC "AGROTECHNOLOGIES OF THE FUTURE"

The laboratory's research topic is Comparative genomics of economically significant legume plant species aimed at identifying key determinants that determine the effectiveness of plant-microbial interactions.

Russian Science Foundation

  • RSF (22-16-00109) Molecular genetic basis of symbiotic responsiveness of seed peas (Pisum sativum L.). 2022-2024. Head: Zhukov V.A..

 

COMPLETED

Russian Science Foundation

  • RSF (20-16-00107) Metabolomic and transcriptomic changes in seeds and leaves of seed peas (Pisum sativum L.) during the formation of complex plant-microbial systems. 2020-2022. Supervisor: Stark O.Y.
  • RSF (17-76-30016) Scientific foundations for the creation of an effective technology for stabilizing plant growth and development in a multicomponent plant-microbial system. 2017-2020. Supervisor: Tikhonovich I.A.
  • RSF (16-16-00118-P) Transcriptome variability in legume forms with different efficiency of nitrogen and phosphorus nutrition. 2019-2020. Head: Zhukov V.A.
  • RSF (16-16-00118) Transcriptome variability in legume forms with different efficiency of nitrogen and phosphorus nutrition. 2016-2018. Supervisor: Zhukov V.A.
  • RSF (14-24-00135) Differentiation of symbiotic compartments of nitrogen-fixing nodules of legumes: coordinated changes in transcriptional activity of symbiont genomes and hormonal status of symbiotic tissues (2014-2016). Head: Tikhonovich I.A.

 

Russian Foundation for Basic Research

  • RFBR (20-04-01136) New mechanisms of systemic regulation of the development of arbuscular mycorrhiza in seed peas. 2020-2022. Supervisor: Stark O.Y.
  • RFBR (19-316-90058 – Graduate students) Regulation of the development of arbuscular mycorrhizal symbiosis due to alternative splicing and microRNAs in seed peas (Pisum sativum L.). 2019-2022. Supervisor: Zhukov V.A.
  • RFBR (19-316-51014 – Scientific mentoring) "Symbiogenomics": genetic and metabolic integration in the supra-organizational symbiotic system "seed peas - nodule bacteria". 2019-2021. Head: Zhukov V.A.
  • RFBR (19-016-00194) Bacterial endophytic community of the aboveground part of the seed pea (Pisum sativum L.): patterns of formation and growth-stimulating activity. 2019-2021. Head: Zhukov V.A.
  • RFBR (16-04-01859) The genetic mechanisms underlying the colonization process of seed peas (Pisum sativum L.) by arbuscular mycorrhizal fungi and nodule bacteria. 2016-2018. Supervisor: Stark O.Y.
  • RFBR (15-29-02737) Biodiversity of leguminous plants by receptors of substances affecting the effectiveness of symbiosis with rhizobia. 2015-2016. Head: Lutova L.A.
  • RFBR (14-04-01442) The Sym31 gene of pea (Pisum sativum L.) is a key regulator of the differentiation of nodule bacteria into a symbiotic form. 2014-2016. Head: Zhukov V.A.

 

St. Petersburg State University

  • Event 1. Study of the mechanisms of nitrate-mediated regulation of the development of symbiotic nodules in seeded peas (Pisum sativum L.) and low-cut alfalfa (Medicago truncatula Gaertn.) using genomic technologies. 2020-2022. Head: Zhukov V.A..

Publications

  1. Zorin E.A., Kliukova M.S., Afonin A.M., Gribchenko E.S., Gordon M.L., Sulima A.S., Zhernakov A.I., Kulaeva O.A., Romanyuk D.A., Kusakin P.G., Tsyganova A.V., Tsyganov V.E., Tikhonovich I.A., Zhukov V.A. (2022) A variable gene family encoding nodule-specific cysteine-rich peptides in pea (Pisum sativum L.). Front Plant Sci., 13: 884726. https://doi.org/10.3389/fpls.2022.884726.
  2. Sulima A.S., Zhukov V.A. (2022). War and Peas: Molecular Bases of Resistance to Powdery Mildew in Pea (Pisum sativum L.) and Other Legumes. Plants, 11(3), 339. https://doi.org/10.3390/plants11030339.
  3. Zhukov V.A.; Zhernakov A.I.; Sulima A.S.; Kulaeva O.A.; Kliukova M.S.; Afonin A.M.; Shtark O.Y.; Tikhonovich I.A. (2021). Association Study of Symbiotic Genes in Pea (Pisum sativum L.) Cultivars Grown in Symbiotic Conditions. Agronomy, 11(11), 2368. https://doi.org/10.3390/agronomy11112368. 
  4. Afonin A.M., Gribchenko E.S., Zorin E.A., Sulima A.S., Zhukov V.A. (2021). DNA methylation patterns differ between free-living rhizobium leguminosarum RCAM1026 and bacteroids formed in symbiosis with pea (Pisum sativum L.). Microorganisms, 9(12), 2458. https://doi.org/10.3390/microorganisms9122458.
  5. Zhukov V., Zorin E., Zhernakov A., Afonin A., Akhtemova G., Bovin A., Dolgikh A., Gorshkov A., Gribchenko E., Ivanova K., Kirienko A., Kitaeva A., Kliukova M., Kulaeva O., Kusakin P., Leppyanen I., Pavlova O., Romanyuk D., Rudaya E., Serova T., Shtark O., Sulima A., Tsyganova A., Vasileva E., Dolgikh E., Tsyganov V., Tikhonovich I. (2021). Transcriptomic analysis of sym28 and sym29 supernodulating mutants of pea (Pisum sativum L.) under complex inoculation with beneficial microorganisms. Biological Communications, 66(3): 181–197.   https://doi.org/10.21638/spbu03.2021.301. 
  6. Solovev Y.V., Igolkina A.A., Kuliaev P.O., Sulima A.S., Zhukov V.A., Porozov Y.B., Pidko E.A., Andronov E.E. (2021). Towards Understanding Afghanistan Pea Symbiotic Phenotype Through the Molecular Modeling of the Interaction Between LykX-Sym10 Receptor Heterodimer and Nod Factors Frontiers in Plant Science, 12, 642591. https://doi.org/10.3389/fpls.2021.642591.
  7. Shtark O., Puzanskiy R., Avdeeva G., Yemelyanov V., Shavarda A., Romanyuk D., Kliukova M., Kirpichnikova A., Tikhonovich I., Zhukov V., Shishova, M. (2021). Metabolic Alterations in Pisum sativum Roots during Plant Growth and Arbuscular Mycorrhiza Development. Plants, 10(6), 1033. https://doi.org/10.3390/plants10061033.
  8. Afonin A.M., Gribchenko E.S., Zorin E.A., Sulima A.S., Romanyuk D.A., Zhernakov A.I., Shtark O.Y., Akhtemova G.A., Zhukov V.A. (2021). Unique transcriptome features of pea (Pisum sativum L.) lines with differing responses to beneficial soil microorganisms. Ecological genetics, 19(2), 131-141. https://doi.org/10.17816/ecogen54703.
  9. Zorin E.A., Afonin A.M., Kulaeva O.A., Gribchenko E.S., Shtark O.Y., Zhukov V.A. (2020). Transcriptome Analysis of Alternative Splicing Events Induced by Arbuscular Mycorrhizal Fungi (Rhizophagus irregularis) in Pea (Pisum sativum L.) Roots. Plants, 9(12), 1700. https://doi.org/10.3390/plants9121700.
  10. Afonin A.M., Leppyanen I.V., Kulaeva O.A., Shtark O.Y., Tikhonovich I.A., Dolgikh E.A., Zhukov V.A. (2020). A high coverage reference transcriptome assembly of pea (Pisum sativum L.) mycorrhizal roots. Vavilovskii zhurnal genetiki i selektsii, 24(4), 331–339. https://doi.org/10.18699/VJ20.625.
  11. Mamontova T., Afonin A.M., Ihling C., Soboleva A., Lukasheva E., Sulima A.S., Shtark O.Y., Akhtemova G.A., Povydysh M.N., Sinz A., Frolov A., Zhukov V.A., Tikhonovich I.A. (2019) Profiling of Seed Proteome in Pea (Pisum sativum L.) Lines Characterized with High and Low Responsivity to Combined Inoculation with Nodule Bacteria and Arbuscular Mycorrhizal Fungi. Molecules, 24(8):1603. https://doi.org/10.3390/molecules24081603.
  12. Shtark O.Y., Puzanskiy R.K., Avdeeva G.S., Yurkov A.P., Smolikova G.N., Yemelyanov V.V., Kliukova M.S., Shavarda A.L., Kirpichnikova A.A., Zhernakov A.I., Afonin A.M., Tikhonovich I.A., Zhukov V.A., Shishova M.F. (2019) Metabolic alterations in pea leaves during arbuscular mycorrhiza development. PeerJ. 7:e7495. https://doi.org/10.7717/peerj.7495.
  13. Zhernakov A.I., Shtark O.Y., Kulaeva O.A., Fedorina J.V., Afonin A.M., Kitaeva A.B., Tsyganov V.E., Afonso-Grunz F., Hoffmeier K., Rotter B., Winter P., Tikhonovich I.A., Zhukov V.A. (2019) Mapping-by-sequencing using NGS-based 3'-MACE-Seq reveals a new mutant allele of the essential nodulation gene Sym33 (IPD3) in pea (Pisum sativum L.). PeerJ. 7:6662. https://doi.org/10.7717/peerj.6662.
  14. Sulima A.S., Zhukov V.A., Kulaeva O.A., Vasileva E.N., Borisov A.Y., Tikhonovich I.A. (2019). New sources of Sym2A allele in the pea (Pisum sativum L.) carry the unique variant of candidate LysM-RLK gene LykX. PeerJ, 7, e8070. https://doi.org/10.7717/peerj.8070.
  15. Magne K., Couzigou J.M., Schiessl K., Liu S., George J., Zhukov V.A., Sahl L., Boyer F., Iantcheva A., Mysore K.S., Wen J., Citerne S., Oldroyd G., Ratet P. (2018) MTNODULE ROOT1 and MTNODULE ROOT2 are essential for indeterminate nodule identity. Plant Physiology, 178(1), 295-316. https://doi.org/10.1104/pp.18.00610.
  16. Osmolovskaya N., Shumilina J., Kim A., Didio A., Grishina T., Bilova T., Keltsieva O.A., Zhukov V., Tikhonovich I., Tarakhovskaya E., Frolov A., Wessjohann L.A. (2018) Methodology of Drought Stress Research: Experimental Setup and Physiological Characterization. International journal of molecular sciences, 19(12), 4089. doi: 10.3390/ijms19124089. https://doi.org/10.3390/ijms19124089.
  17. Sulima A.S., Zhukov V.A., Afonin A.A., Zhernakov A.I., Tikhonovich I.A., Lutova L.A. (2017) Selection Signatures in the First Exon of Paralogous Receptor Kinase Genes from the Sym2 Region of the Pisum sativum L. Genome. Frontiers in Plant Science, 8, 1957. https://doi.org/10.3389/fpls.2017.01957.
  18. Kulaeva O.A., Zhernakov A.I., Afonin A.M., Boikov S.S., Sulima A.S., Tikhonovich I.A., Zhukov V.A. (2017) Pea Marker Database (PMD) - A new online database combining known pea (Pisum sativum L.) gene-based markers. PLoS One, 12(10), 0186713. https://doi.org/10.1371/journal.pone.0186713.
  19. Zhukov V.A., Akhtemova G.A., Zhernakov A.I., Sulima A.S., Shtark O.Y., Tikhonovich I.A. (2017). Evaluation of the symbiotic effectiveness of pea (Pisum sativum L.) genotypes in pot experiment. Agric. Biol, 52, 607-614. https://doi.org/10.15389/agrobiology.2017.3.607eng.
  20. Shtark O.Y., Sulima A.S., Zhernakov A.I., Kliukova M.S., Fedorina J.V., Pinaev A.G., Kryukov A.A., Akhtemova G.A., Tikhonovich I.A., Zhukov V.A. (2016). Arbuscular mycorrhiza development in pea (Pisum sativum L.) mutants impaired in five early nodulation genes including putative orthologs of NSP1 and NSP2. Symbiosis, 68(1-3), 129–144. https://doi.org/10.1007/s13199-016-0382-2.

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