Vladimir Trifonov


Present position:

guest researcher

Research area:

Molecular & Cytogenetic Evolution of Asexual Aquatic Organisms





Academic History

  • since end of March 2023: guest researcher at Research Department for Limnology, Mondsee, of the University of Innsbruck
  • since 2012: Head of Laboratory of Comparative Genomics, Department of Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology Novosibirsk SB RAS
  • 1997-2001PhD (Molecular Biology) at Novosibirsk State University
  • 1992-1997 Diploma (Molecular Biology) at Novosibirsk State University Faculty of Natural Sciences


Research interests

  • Structure of supernumerary chromosomes
  • System of chromosomal sex determination



  • Crossing over patterns in the squamate genomes (autosomes and sex chromosomes):

    Goal: Meiotic recombination rate and recombination landscapes of individual chromosomes vary greatly among vertebrate taxa, but the evolutionary and adaptive significance of this variation is still poorly understood. Reptiles are good objects to investigate this issue, since even phylogenetically distant species of them frequently have similar karyotypes with largely syntenic chromosomes and chromosomal arms. Therefore, the evolution if the recombination in reptiles is much less affected by the karyotypic evolution than in mammals, which are more common objects in the studies of the recombination evolution. The project is aimed to investigate the variation in recombination rate and crossover distribution along the chromosomes in different squamate lineages. We will focus on elucidating possible phylogenetic, karyotypic and adaptive factors influencing these traits.
    The main method which we use, the immunoflourescent analysis of the synaptonemal complexes, is also a powerful tool in studying sex chromosomes. In squamates, there are many sex chromosomal systems of independent origin, shared by more or less numerous groups of related species. Our method will allow us to precisely cytologically map the locations of the differentiated and pseudoautosomal regions at the squamate sex chromosomes.

    Methods: Fluorescence In Situ Hybridization, DNA Barcoding, Chromosomes, Immunofluorescence Microscopy, Meiotic Prophase I, Synaptonemal complex analysis

  • Common voles karyotype evolution :
    Goal: The cytogenetic data, obtained from the Non-Robertsonian chromosome hybrid zone arvalis - obscurus by the contact of the two karyotypic forms in East Europe, rise a new interest to geographic distribution, genetic boundaries and the full content for chromosome variants in the Microtus arvalis group, one of the pioneers for chromosome cryptic species discoveries.




The staff of the Laboratory are among the contributors of a large international consortium DNA Zoo


  • Lisachov A., Rumyantsev A., Prokopov D., Ferguson-Smith M., Trifonov V. (2023). Conservation of major satellite DNAs in snake heterochromatin, Animals 13(3): 334, doi: 10.3390/ani13030334

  • Trifonov V.A., Lamatsch D.K., Makunin A.I. (2023). B chromosomes and extrachromosomal DNA, Meeting Abstracts from the 5th B Chromosome Conference. BMC Proc 17(20): S4-O1, https://doi.org/10.1186/s12919-023-00284-9  

  • Da Cruz I., Lamatsch D.K., Rice E., Nanda I., Trifonov V.A., Warren W., Schartl M. (2023). The microchromosome of the Amazon Molly: a nascent B chromosome? Meeting Abstracts from the 5th B Chromosome Conference. BMC Proc 17(20): S1-O2. https://doi.org/10.1186/s12919-023-00284-9

  • Lisachov A., Rumyantsev A., Prokopov D., Ferguson-Smith M., Trifonov V. (2023). Conservation of major satellite DNAs in snake heterochromatin, Animals 13(3): 334, doi: 10.3390/ani13030334

  • Interesova E.A., Babkina I.B., Romanov V.I., Pozdnyak I.V., Davletshina G.I., Trifonov V.A. (2022). New data on small lampreys of the genus Lethenteron (Petromyzontidae) of the Tom river, a typical habitat of the Siberian brook lamprey Lethenteron kessleri,  J Ichthyol 62(7): 1230-1236, doi: 10.1134/S003294522206011X 

  • Karamysheva T.V., Gayner T.A., Elisaphenko E.A., Trifonov V.A., Zakirova E.G., Orishchenko K.E., Prokhorovich M.A., Lopatkina M.E., Skryabin N.A., Lebedev I.N., Rubtsov N.B. (2022). The Precise breakpoint mapping in paracentric inversion 10q22.2q23.3 by comprehensive cytogenomic analysis, multicolor banding, and single-copy chromosome sequencing.  Biomedicines 10(12): 3255, doi.org/10.3390/biomedicines10123255

  • Tishakova KV, Prokopov DY, Davletshina GI, Rumyantsev AV, O’Brien PCM, Ferguson-Smith MA, Giovannotti M, Lisachov AP, Trifonov VA. Identification of Iguania ancestral syntenic blocks and putative sex chromosomes in the veiled chameleon (Chamaeleo calyptratus, Chamaeleonidae, Iguania), Int J Mol Sci 23(24): 15838, doi: 10.3390/ijms232415838 

  • Romanenko SA, Prokopov DY, Proskuryakova AA, Davletshina GI, Tupikin AE, Kasai F, Ferguson-Smith MA, Trifonov VA. (2002). The cytogenetic map of the Nile crocodile (Crocodylus niloticus, Crocodylidae, Reptilia) with fluorescence in situ localization of major repetitive DNAs, Int J Mol Sci 23(21): 13063, doi: 10.3390/ijms232113063 

  • Romanenko S, Trifonov V. Chapter 3. Generation of microdissection-derived painting probes from single copy chromosomes (2022). In: Liehr T (ed.) Cytogenetics and Molecular Cytogenetics, CRC Press, Boca Raton, FL, USA, pp 27-34 doi: 10.1201/9781003223658 

  • Interesova E.A., Romanov V.I., Davletshina G.I., Fedorova V.S., Trifonov V.A. (2022). Dissemination of Misgurnus nikolskyi (Cobitidae) in the south of Western Siberia, Russ J Biol Invasions 13(3): 301-304, doi: 10.1134/S207511172203006

  • Molodtseva A.S., Makunin A.I., Salomashkina V.V., Kichigin I.G., Vorobieva N.V., Vasiliev S.K., Shunkov M.V., Tishkin A.A., Grushin S.P., Anijalg P., Tammeleht E., Keis M., Boeskorov G.G., Mamaev N., Okhlopkov I.M., Kryukov A.P., Lyapunova E.A., Kholodova M.V., Seryodkin I.V., Saarma U., Trifonov V.A., Graphodatsky A.S. (2022). Phylogeography of ancient and modern brown bears from eastern Eurasia, Biol J Linn Soc 135(4): 722-733, doi: 10.1093/biolinnean/blac009 

  • Rajičić M., Makunin A., Adnađević T., Trifonov V., Vujošević M., Blagojević J. (2022). B chromosomes’ sequences in yellow-necked mice Apodemus flavicollis — exploring the transcription, Life 12(1): 50, doi: 10.3390/life12010050

  • Volleth M., Müller S., Heller K.-G., Trifonov V., Liehr T., Yong H.-S., Baker R.J., Khan F.A.A., Sotero-Caio C.G. (2021). Cytogenetic analyses detect cryptic diversity in Megaderma spasma from Malaysia, Acta Chiropterologica 23(2): 271–284, doi: 10.3161/15081109ACC2021.23.2.001

  • Nikitin S.V., Knyazev S.P., Trifonov V.A., Proskuryakova A.A., Shmidt Yu.D., Shatokhin K.S., Zaporozhets V.I., Bashur D.S., Korshunova E.V., Ermolaev V.I. (2021). Unusual congenital polydactyly in mini-pigs from the breeding group of the Institute of Cytology and Genetics (Novosibirsk, Russia), Vavilov J Genet Breed 25(6): 652-660, doi: 10.18699/VJ21.074 

  • Sharakhova M, Trifonov V. (2021). Chromosome-centric view of genome organization and evolutionGenes 12(8): 1237, doi: 10.3390/genes12081237

  • Romanenko S.A., Smorkatcheva A.V., Kovalskaya Y.M., Prokopov D.Y., Lemskaya N.A., Gladkikh O.L., Polikarpov I.A., Serdyukova N.A., Trifonov V.A., Molodtseva A.S., O’Brien P.C.M., Golenishchev F.N., Ferguson-Smith M.A., Graphodatsky A.S. (2021). Complex structure of Lasiopodomys mandarinus vinogradovi sex chromosomes, sex determination, and intraspecific autosomal polymorphism. In: Ruiz-Herrera A, Farré-Belmonte M (eds) Mechanisms Driving Karyotype Evolution and Genomic Architecture, MDPI, Switzerland, pp 193-209 doi: 10.3390/books978-3-0365-0157-4

  • Lisachov A.P., Tishakova K.V., Romanenko S.A., Molodtseva A.S., Prokopov D.Yu., Pereira J.C., Ferguson-Smith M.A., Borodin P.M., Trifonov V.A. (2021). Whole-chromosome fusions in the karyotype evolution of Sceloporus (Iguania, Reptilia) are more frequent in sex chromosomes than autosomes,  Philos Trans R Soc Lond B Biol Sci 376(1833): 20200099, doi: 10.1098/rstb.2020.0099

  • Karamysheva T., Romanenko S., Makunin A., Rajičić M., Bogdanov A., Trifonov V., Blagojević J., Vujošević M., Orishchenko K., Rubtsov N. (2021). New data on organization and spatial localization of B-chromosomes in cell nuclei of the yellow-necked mouse Apodemus flavicollis, Cells 10(7): 1819, doi: 10.3390/cells10071819

  • Volleth M., Khan F.A.A., Müller S., Baker R.J., Arenas-Viveros D., Stevens R.D., Trifonov V., Liehr T., Heller K.-G., Sotero-Caio C.G. (2021). Cytogenetic investigations in Bornean Rhinolophoidea revealed cryptic diversity in Rhinolophus sedulus entailing classification of Peninsular Malaysia specimens as a new species, Acta Chiropterologica 23(1): 1-20, doi: 10.3161/15081109ACC2021.23.1.001

  • Romanenko S.A., Malikov V.G., Mahmoudi A., Golenishchev F.N., Lemskaya N.A., Pereira J.C., Trifonov V.A., Serdyukova N.A., Ferguson-Smith M.A., Aliabadian M., Graphodatsky A.S. (2021). New data on comparative cytogenetics of the mouse-like hamsters (Calomyscus Thomas, 1905) from Iran and Turkmenistan, Genes 12(7): 964, doi: 10.3390/genes12070964

  • Höhne C., Prokopov D., Kuhl H., Du K., Klopp C., Wuertz S., Trifonov V., Stöck M. (2021). The immune system of sturgeons and paddlefish (Acipenseriformes): a review with new data from a chromosome‐scale sturgeon genome, Rev Aquacult 13(3): 1709-1729, doi: org/10.1111/raq.12542

  • Pobedintseva M.A., Reshetnikova S.N., Serdyukova N.A., Bishani A., Trifonov V.A., Interesova E.A. (2021). Genetic diversity of the prussian carp Carassius gibelio (Cyprinidae) in the middle Ob basin, Russ J Genet 57(4): 446-452, doi: 10.1134/S1022795421040116

  • Lisachov A., Andreyushkova D., Davletshina G., Prokopov D., Romanenko S., Galkina S., Saifitdinova A., Simonov E., Borodin P., Trifonov V. (2021): Amplified fragments of an autosome-borne gene constitute a significant component of the W sex chromosome of Eremias velox (Reptilia, Lacertidae), Genes 12(5): 779, doi: 10.3390/genes12050779 

  • Bishani A., Prokopov D.Yu., Romanenko S.A., Molodtseva A.S., Perelman P.L., Interesova E.A., Beklemisheva V.R., Graphodatsky A.S., Trifonov V.A. (2021). Evolution of tandemly arranged repetitive DNAs in three species of Cyprinoidei with different ploidy levels, Cytogenet Genome Res 161: 32-42, doi: 10.1159/000513274

  • Kusliy M.A., Vorobieva N.V., Tishkin A.A., Makunin A.I., Druzhkova A.S., Trifonov V.A., Iderkhangai T.-O., Graphodatsky A.S. (2021). Traces of late Bronze and early Iron Age Mongolian horse mitochondrial lineages in modern populations, Genes 12(3): 412, doi: 10.3390/genes12030412

  • Evdokimov A., Popov A., Ryabchikova E., Koval O., Romanenko S., Trifonov V., Petruseva I., Lavrik I., Lavrik O. (2021). Uncovering molecular mechanisms of regulated cell death in the naked mole rat, Aging (Albany NY) 13(3): 3239-3253, doi: 10.18632/aging.202577 

  • Pan Q., ..., Trifonov V., ..., Guiguen Y. (2021). The rise and fall of the ancient northern pike master sex determining gene, eLife 10: e62858, doi: 10.7554/eLife.62858 

  • Iannucci A., Makunin A.I., Lisachov A.P., Ciofi C., Stanyon R., Svartman M., Trifonov V.A. (2021). Bridging the gap between vertebrate cytogenetics and genomics with single-chromosome sequencing (ChromSeq), Genes 12(1): 124, doi: 10.3390/genes12010124 

  • Jevit M.J., Davis B.W., Castaneda C., Hillhouse A., Juras R., Trifonov V.A., Tibary A., Pereira J.C., Ferguson-Smith M.A., Raudsepp T. (2021). An 8.22 Mb assembly and annotation of the alpaca (Vicugna pacos) Y chromosome, Genes 12(1): 105, doi: 10.3390/genes12010105   

Publications of previous years

Reviewer for BMC Genomics, Development Genes and Evolution, Environments, Journal of Applied Genetics 


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