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Laboratory for Biodiversity and the Functional Genomics of the World Ocean

Contract number
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Head of the laboratory

As of 01.11.2022

Number of staff members
scientific publications
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General information

Name of the project: Reconstruction of genealogy of cell systems based on analysis of biodiversity of the World Ocean

Goals and objectives

Research directions: High performance sequencing and analysis of genomes/transcriptomes at the level of single cells (single-cell-Seq), molecular deciphering of the global biodiversity of marine organisms and molecular and genetic analysis of nervous systems at the level of single cells, identification and analysis of cell types based on results of high performance sequencing of transcriptomes of single cells

Project objective: Development of approaches and methods for reconstruction of genealogy of neurons and their ancestor lines on the basis of research of genomics of marine organisms at the level of separate cells; development of criteria of natural classification of neurons in neuron networks for thous types of marine animals that have key importance for understanding of evolution and for biomedicine

The practical value of the study

Scientific results:

  1. During the implementation of the project, we have obtained sequences of  transcriptomes of over 1,5 million individual neurons in representatives of 16 types of animals. We have refined the phylogeny of animals (Ctenophora and Spiralia/Lophotrochozoa) and developed methods of the quantitative assessment of the transcriptome activity of the genome in cells of the researched species as well as criteria of homology of neurons. It has been demonstrated that in the researched species almost all the neurons have a unique RNA profile, non-coding RNA and secretory molecules, which creates the foundations for the development of a natural evolutionary classification of neurons.
  2. We have performed a full-genome sequencing of the Ligophorus vanbenedenii parasitic flatworm. We have developed an algorithm for genome assembly which allowed to resolve a region of tandem repetitions of mitochondrial DNA and to obtain a full ring assembly of the mitochondrial genome of L. vanbenedenii.
  3. On the basis of an analysis of  transcriptomes of gills of the M. galloprovincialis Black sea mollusk, we for the first time found genes in mussels that code all three subfamilies of  glutathione S-transferases (GST), one of the key proteins in the metabolism of xenobiotics. We have studied the exon-intron structure of each gene, determined the features of this structure characteristic of each class of GST. We have conducted a comparison of the levels of expression of the genes coding GST in the conditions of normoxia and hypoxia.
  4. In the process of the cultivation of cells of the Black Sea Mnemiopsis Beroe ovata we isolated a new subspecies of the marine protozoa T. aureum ssp. strugatskii (Thraustochytriaceae, Labyrinthulomycetes family), performed an analysis of its transcriptome, in the composition of which we annotated sequences of the whole range of ferments of the synthesis and degradation of fatty acids. For the first time we have demonstrated the possibility of association of Labyrinthulomycetes with pelagic comb jellies, which allows to forecast the presence of still unknown microbial pathways of an effective transformer of organic matter in pelagic ecosystems.

Education and career development:

  • One Candidate of Sciences dissertation has been prepared and defended.
  • As part of the work of the Research and Education Center «Genomics and Bioinformatics» we are implementing education programs of various levels for professional training and the popularization of academic knowledge in the field of marine biology and functional genomics. Practical classes are conducted with the use of modern laboratory equipment. On the grounds of the Laboratory, students of Sevastopol State University prepare their bachelor’s and master’s theses, three postgraduates of the Institute of Biology of the Southern Seas of the Russian Academy of Sciences perform their research. 
  • Employees of the Laboratory deliver lectures and practical classes as part of the implementation of training programs for the master’s degree programs in Biophysics and Bioinformatics at Sevastopol State University. 


  • Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences (Russia): joint research, internships of employees of the Laboratory, conducting scientific conferences. New data has been collected on the sequence of full genomes of the organisms of Nostoc sp. and Arthrospira platensis (Nordstedt) Gomont (Cyanobacteria), Ligophorus vanbenedenii and Axine belones (Platyhelminthas). We have performed an  analysis of genes of the antioxidant complex of the Black Sea mussel on the basis of transcriptome data. We have conducted the collaborative event, the International School for Young Scientists «Systems Biology and Bioinformatics» (SBB–2020).
  • Sevastopol State University (Russia): personnel training in the domain of bioinformatics analysis, using the equipment of the Laboratory of Molecular and Cell Biophysics to conduct experimental molecular works. New data has been collected using real-time PCR.
  • Nikitsky Botanical Garden – National Research Center of the Russian Academy of Sciences:joint research, internships of employees of the Laboratory, conducting scientific conferences.

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n.v. whelan, k. m. kocot, t. p. moroz, k. mukherjee, p. williams, g. paulay, l.l. moroz, k.m. halanych
Ctenophore relationships and their placement as the sister group to all other animals // Nature Ecology & Evolution. - VOL 1, NOVEMBER 2017. Р. 1737–1746.
e.a. vodiasova , e.s. chelebieva, o.n. kuleshova
The new technologies of high-throughput single-cell RNA sequencing // Vavilov’s Journal of Genetics. - 2019;23(5):508-518 https://doi.org/10.18699/VJ19.520
norekian tp, moroz ll.
Comparative neuroanatomy of ctenophores: Neural and muscular systems in Euplokamis dunlapae and related species. J Comp Neurol. 2019 September 9. DOI: 10.1002/cne.24770
gubanova a., drapun i., garbazey o., krivenko o., vodiasova e. pseudodiaptomus marinus sato
1913 in the Black Sea: morphology, genetic analysis, and variability in seasonal and interannual abundance // PeerJ. 2020. Iss. 8. Articleno. e10153 (26 p.). DOI: 10.7717/peerj.10153
vodiasova e. a., meger y. v., lantushenko a. o.
Identification and characterization of the novel genes encoding glutathione S-transferases in Mytilus galloprovincialis // Comparative Biochemistry and Physiology Part D: Genomics and Proteomics. 2021. Vol. 40. Article no. 100926 (9 p.). https://doi.org/10.1016/j.cbd.2021.100926
andreyeva a. yu., gostyukhina o. l., kladchenko e. s., afonnikov d. a., rasskazov d. a., lantushenko a. o., vodiasova e. a.
Hypoxia exerts oxidative stress and changes in expression of antioxidant enzyme genes in gills of Mytilus galloprovincialis (Lamarck, 1819) // Marine Biology Research. 2021. Vol. 17, iss. 4. P. 369-379. https://doi.org/10.1080/17451000.2021.1967992
dmitrieva e., sanna d., vodiasova e. , prokhorova d., casu m., burreddu c., piras m. c., garippa g., merella p.
Morphological and genetic variability of the cryptic Gyrodactylus sphinx and Gyrodactylus gerasevi n. sp. (Platyhelminthes: Monogenea) from the Mediterranean Sea and Black Sea: two new members of the cross-ocean distributed Gyrodactylus orecchiae species group // Journal of Helminthology. 2022. Vol. 96. Article no. e9 (9 p.). https://doi.org/10.1017/S0022149X21000778
baiandina iu. s., kirin m. p., krivenko o. v.
Black Sea Mnemiopsis leidyi (Ctenophora) adult locomotion and light-induced behavior in laboratory experiments // Journal of Sea Research. 2022. Vol. 180. Article no. 102152 (7 p.). https://doi.org/10.1016/j.seares.2021.102152
konstantinov d. k., menzorov a., krivenko o., doroshkov a. v.
Isolation and transcriptome analysis of a biotechnologically promising Black Sea protist, Thraustochytrium aureum ssp. strugatskii // PeerJ. 2022. Iss. 10. Article no e12737 (19 p.). https://doi.org/10.7717/peerj.12737
gostyukhina o. l., andreyeva a. yu., chelebieva e. s., vodiasova e. a., lantushenko a. o., kladchenko e. s.
Adaptive potential of the Mediterranean mussel Mytilus galloprovincialis to short-term environmental hypoxia // Fish and Shellfish Immunology. 2022. Vol. 131. P. 654-661. https://doi.org/10.1016/j.fsi.2022.10.052
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