Department of Diversity and Evolution of Genomes
Laboratory of Comparative Genomics

Head of the Laboratory
Former research workers:
Andreyushkova Daria
Bishani Ali
Dementieva Polina, PhD
Kichigin Ilya
Kliver Sergei
Popova Kseniya
Sarachakov Aleksandr
Vorobieva Nadezhda, PhD
- Structure of supernumerary chromosomes
- System of chromosomal sex determination
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The staff of the Laboratory are among the contributors of a large international consortium DNA Zoo |
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Yakupova A, Tomarovsky A, Totikov A, Beklemisheva V, Logacheva M, Perelman PL, Komissarov A, Dobrynin P, Krasheninnikova K, Tamazian G, Serdyukova NA, Rayko M, Bulyonkova T, Cherkasov N, Pylev V, Peterfeld V, Penin A, Balanovska E, Lapidus A, Consortium DZ, O'Brien SJ, Graphodatsky A, Koepfli K-P, Kliver S. Chromosome-length assembly of the Baikal seal (Pusa sibirica) genome reveals a historically large population prior to isolation in lake Baikal. (doi: 10.3390/genes14030619) Genes 14(3): 619, 2023
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Beklemisheva VR, Lemskaya NA, Prokopov DY, Perelman PL, Romanenko SA, Proskuryakova AA, Serdyukova NA, Utkin YA, Nie W, Ferguson-Smith MA, Fentang Y, Graphodatsky AS. Maps of constitutive-heterochromatin distribution for four martes species (Mustelidae, Carnivora, Mammalia) show the formative role of macrosatellite repeats in interspecific variation of chromosome structure. (doi: 10.3390/genes14020489) Genes 14(2): 489, 2023
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Lisachov A, Rumyantsev A, Prokopov D, Ferguson-Smith M, Trifonov V. Conservation of major satellite DNAs in snake heterochromatin. (doi: 10.3390/ani13030334) Animals 13(3): 334, 2023
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Dumas F, Perelman PL, Biltueva L, Roelke M. Retrotransposon mapping in spider monkey genomes of the family Atelidae (Platyrrhini, Primates) shows a high level of LINE-1 amplification. (doi: 10.4081/jbr.2022.10725) J Biol Res 95(2): 10725, 2022
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Interesova EA, Babkina IB, Romanov VI, Pozdnyak IV, Davletshina GI, Trifonov VA. New data on small lampreys of the genus Lethenteron (Petromyzontidae) of the Tom river, a typical habitat of the Siberian brook lamprey Lethenteron kessleri. (doi: 10.1134/S003294522206011X) J Ichthyol 62(7): 1230-1236, 2022
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Karamysheva TV, Gayner TA, Elisaphenko EA, Trifonov VA, Zakirova EG, Orishchenko KE, Prokhorovich MA, Lopatkina ME, Skryabin NA, Lebedev IN, Rubtsov NB. The Precise breakpoint mapping in paracentric inversion 10q22.2q23.3 by comprehensive cytogenomic analysis, multicolor banding, and single-copy chromosome sequencing. (doi.org/10.3390/biomedicines10123255) Biomedicines 10(12): 3255, 2022
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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). (doi: 10.3390/ijms232415838) Int J Mol Sci 23(24): 15838, 2022
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Ochkalova S, Korchagin V, Vergun A, Urin A, Zilov D, Ryakhovsky S, Girnyk A, Martirosyan I, Zhernakova DV, Arakelyan M, Danielyan F, Kliver S, Brukhin V, Komissarov A, Ryskov A. First genome of rock lizard Darevskia valentini involved in formation of several parthenogenetic species. (doi: 10.3390/genes13091569) Genes 13(9): 1569, 2022
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Romanenko SA, Prokopov DY, Proskuryakova AA, Davletshina GI, Tupikin AE, Kasai F, Ferguson-Smith MA, Trifonov VA. The cytogenetic map of the Nile crocodile (Crocodylus niloticus, Crocodylidae, Reptilia) with fluorescence in situ localization of major repetitive DNAs. (doi: 10.3390/ijms232113063) Int J Mol Sci 23(21): 13063, 2022
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Romanenko S, Trifonov V. Chapter 3. Generation of microdissection-derived painting probes from single copy chromosomes. In: Liehr T (ed.) Cytogenetics and Molecular Cytogenetics, CRC Press, Boca Raton, FL, USA, 2022, pp 27-34 (doi: 10.1201/9781003223658)
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Milioto V, Perelman PL, Paglia LL, Biltueva L, Roelke M, Dumas F. Mapping retrotransposon LINE-1 sequences into two Cebidae species and Homo sapiens genomes and a short review on primates. (doi: 10.3390/genes13101742) Genes 13(10): 1742, 2022
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Interesova EA, Romanov VI, Davletshina GI, Fedorova VS, Trifonov VA. Dissemination of Misgurnus nikolskyi (Cobitidae) in the south of Western Siberia. (doi: 10.1134/S2075111722030067) Russ J Biol Invasions 13(3): 301-304, 2022
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de Ferran V, ..., Kliver S, Serdyukova N, ..., Eizirik E. Phylogenomics of the world’s otters. (doi: 10.1016/j.cub.2022.06.036) Curr Biol 32(16): 3650-3658.e4, 2022
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Derežanin L, Blažytė A, Dobrynin P, Duchêne DA, Grau JH, Jeon S, Kliver S, Koepfli K-P, Meneghini D, Preick M, Tomarovsky A, Totikov A, Fickel J, Förster DW. Multiple types of genomic variation contribute to adaptive traits in the mustelid subfamily Guloninae. (doi: 10.1111/mec.16443) Mol Ecol 31(10): 2898-2919, 2022
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Molodtseva AS, Makunin AI, Salomashkina VV, Kichigin IG, Vorobieva NV, Vasiliev SK, Shunkov MV, Tishkin AA, Grushin SP, Anijalg P, Tammeleht E, Keis M, Boeskorov GG, Mamaev N, Okhlopkov IM, Kryukov AP, Lyapunova EA, Kholodova MV, Seryodkin IV, Saarma U, Trifonov VA, Graphodatsky AS. Phylogeography of ancient and modern brown bears from eastern Eurasia. (doi: 10.1093/biolinnean/blac009) Biol J Linn Soc 135(4): 722-733, 2022
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Rajičić M, Makunin A, Adnađević T, Trifonov V, Vujošević M, Blagojević J. B chromosomes’ sequences in yellow-necked mice Apodemus flavicollis — exploring the transcription. (doi: 10.3390/life12010050) Life 12(1): 50, 2022
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Volleth M, Müller S, Heller K-G, Trifonov V, Liehr T, Yong H-S, Baker RJ, Khan FAA, Sotero-Caio CG. Cytogenetic analyses detect cryptic diversity in Megaderma spasma from Malaysia. (10.3161/15081109ACC2021.23.2.001) Acta Chiropterologica 23(2): 271–284, 2021
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Shevchenko AK, Zhernakova DV, Malov SV, Komissarov A, Kolchanova SM, Tamazian G, Antonik A, Cherkasov N, Kliver S, Turenko A, Rotkevich M, Evsyukov I, Vlahov D, Thami PK, Gaseitsiwe S, Novitsky V, Essex M, O’Brien SJ. Genome-wide association study reveals genetic variants associated with HIV-1C infection in a Botswana study population. (doi: 10.1073/pnas.2107830118) Proc Natl Acad Sci USA 118(47): e2107830118, 2021
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Nikitin SV, Knyazev SP, Trifonov VA, Proskuryakova AA, Shmidt YuD, Shatokhin KS, Zaporozhets VI, Bashur DS, Korshunova EV, Ermolaev VI. Unusual congenital polydactyly in mini-pigs from the breeding group of the Institute of Cytology and Genetics (Novosibirsk, Russia). (doi: 10.18699/VJ21.074) Vavilov J Genet Breed 25(6): 652-660, 2021
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Tamazian G, Dobrynin P, Zhuk A, Zhernakova DV, Perelman PL, Serdyukova NA, Graphodatsky AS, Komissarov A, Kliver S, Cherkasov N, Scott AF, Mohr DW, Koepfli K-P, O’Brien SJ, Krasheninnikova K. Draft de novo genome assembly of the elusive jaguarundi, Puma yagouaroundi. (doi: 10.1093/jhered/esab036) J Heredity 112(6): 540-548, 2021
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Sharakhova M, Trifonov V. Chromosome-centric view of genome organization and evolution. (doi: 10.3390/genes12081237) Genes 12(8): 1237, 2021
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Totikov A, Tomarovsky A, Prokopov D, Yakupova A, Bulyonkova T, Derezanin L, Rasskazov D, Wolfsberger WW, Koepfli K-P, Oleksyk TK, Kliver S. Chromosome-level genome assemblies expand capabilities of genomics for conservation biology. (doi: 10.3390/genes12091336) Genes 12(9): 1336, 2021
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Hempel E, Westbury MV, Grau JH, Trinks A, Paijmans JLA, Kliver S, Barlow A, Mayer F, Müller J, Chen L, Koepfli K-P, Hofreiter M, Bibi F. Diversity and paleodemography of the addax (Addax nasomaculatus), a Saharan antelope on the verge of extinction. (doi: 10.3390/genes12081236) Genes 12(8): 1236, 2021
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Romanenko SA, Smorkatcheva AV, Kovalskaya YM, Prokopov DY, Lemskaya NA, Gladkikh OL, Polikarpov IA, Serdyukova NA, Trifonov VA, Molodtseva AS, O’Brien PCM, Golenishchev FN, Ferguson-Smith MA, Graphodatsky AS. 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, 2021, pp 193-209 (doi: 10.3390/books978-3-0365-0157-4)
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Buggiotti L, Yurchenko AA, Yudin NS, Vander Jagt CJ, Vorobieva NV, Kusliy MA, Vasiliev SK, Rodionov AN, Boronetskaya OI, Zinovieva NA, Graphodatsky AS, Daetwyler HD, Larkin DM. Demographic history, adaptation, and NRAP convergent evolution at amino acid residue 100 in the world northernmost cattle from Siberia. (doi: 10.1093/molbev/msab078) Mol Biol Evol 38(8): 3093-3110, 2021
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Lisachov AP, Tishakova KV, Romanenko SA, Molodtseva AS, Prokopov DYu, Pereira JC, Ferguson-Smith MA, Borodin PM, Trifonov VA. Whole-chromosome fusions in the karyotype evolution of Sceloporus (Iguania, Reptilia) are more frequent in sex chromosomes than autosomes. (doi: 10.1098/rstb.2020.0099) Philos Trans R Soc Lond B Biol Sci 376(1833): 20200099, 2021
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Karamysheva T, Romanenko S, Makunin A, Rajičić M, Bogdanov A, Trifonov V, Blagojević J, Vujošević M, Orishchenko K, Rubtsov N. New data on organization and spatial localization of B-chromosomes in cell nuclei of the yellow-necked mouse Apodemus flavicollis. (doi: 10.3390/cells10071819) Cells 10(7): 1819, 2021
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Volleth M, Khan FAA, Müller S, Baker RJ, Arenas-Viveros D, Stevens RD, Trifonov V, Liehr T, Heller K-G, Sotero-Caio CG. Cytogenetic investigations in Bornean Rhinolophoidea revealed cryptic diversity in Rhinolophus sedulus entailing classification of Peninsular Malaysia specimens as a new species. (doi: 10.3161/15081109ACC2021.23.1.001) Acta Chiropterologica 23(1): 1-20, 2021
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Romanenko SA, Malikov VG, Mahmoudi A, Golenishchev FN, Lemskaya NA, Pereira JC, Trifonov VA, Serdyukova NA, Ferguson-Smith MA, Aliabadian M, Graphodatsky AS. New data on comparative cytogenetics of the mouse-like hamsters (Calomyscus Thomas, 1905) from Iran and Turkmenistan. (doi: 10.3390/genes12070964) Genes 12(7): 964, 2021
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Höhne C, Prokopov D, Kuhl H, Du K, Klopp C, Wuertz S, Trifonov V, Stöck M. The immune system of sturgeons and paddlefish (Acipenseriformes): a review with new data from a chromosome‐scale sturgeon genome. (doi: org/10.1111/raq.12542) Rev Aquacult 13(3): 1709-1729, 2021
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Pobedintseva MA, Reshetnikova SN, Serdyukova NA, Bishani A, Trifonov VA, Interesova EA. Genetic diversity of the prussian carp Carassius gibelio (Cyprinidae) in the middle Ob basin. (doi: 10.1134/S1022795421040116) Russ J Genet 57(4): 446-452, 2021
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Lisachov A, Andreyushkova D, Davletshina G, Prokopov D, Romanenko S, Galkina S, Saifitdinova A, Simonov E, Borodin P, Trifonov V. Amplified fragments of an autosome-borne gene constitute a significant component of the W sex chromosome of Eremias velox (Reptilia, Lacertidae). (doi: 10.3390/genes12050779) Genes 12(5): 779, 2021
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Bishani A, Prokopov DYu, Romanenko SA, Molodtseva AS, Perelman PL, Interesova EA, Beklemisheva VR, Graphodatsky AS, Trifonov VA. Evolution of tandemly arranged repetitive DNAs in three species of Cyprinoidei with different ploidy levels. (doi: 10.1159/000513274) Cytogenet Genome Res 161: 32-42, 2021
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Kolchanova S, Komissarov A, Kliver S, Mazo-Vargas A, Afanador Y, Velez-Valentín J, de la Rosa RV, Castro-Marquez S, Rivera-Colon I, Majeske AJ, Wolfsberger WW, Hains T, Corvelo A, Martinez-Cruzado J-C, Glenn TC, Robinson O, Koepfli K-P, Oleksyk TK. Molecular phylogeny and evolution of Amazon parrots in the Greater Antilles. (doi: 10.3390/genes12040608) Genes 12(4): 608, 2021
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Kusliy MA, Vorobieva NV, Tishkin AA, Makunin AI, Druzhkova AS, Trifonov VA, Iderkhangai T-O, Graphodatsky AS. Traces of late Bronze and early Iron Age Mongolian horse mitochondrial lineages in modern populations. (doi: 10.3390/genes12030412) Genes 12(3): 412, 2021
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Evdokimov A., Popov A., Ryabchikova E., Koval O., Romanenko S., Trifonov V., Petruseva I., Lavrik I., Lavrik O. Uncovering molecular mechanisms of regulated cell death in the naked mole rat. (doi: 10.18632/aging.202577) Aging (Albany NY) 13(3): 3239-3253, 2021
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Pan Q, ..., Trifonov V, ..., Guiguen Y. The rise and fall of the ancient northern pike master sex determining gene. (doi: 10.7554/eLife.62858) eLife 10: e62858, 2021
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Iannucci A, Makunin AI, Lisachov AP, Ciofi C, Stanyon R, Svartman M, Trifonov VA. Bridging the gap between vertebrate cytogenetics and genomics with single-chromosome sequencing (ChromSeq). (doi: 10.3390/genes12010124) Genes 12(1): 124, 2021
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Jevit MJ, Davis BW, Castaneda C, Hillhouse A, Juras R, Trifonov VA, Tibary A, Pereira JC, Ferguson-Smith MA, Raudsepp T. An 8.22 Mb assembly and annotation of the alpaca (Vicugna pacos) Y chromosome. (doi: 10.3390/genes12010105) Genes 12(1): 105, 2021
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Trifonov V. Origin and evolution of mammalian B chromosomes. 4th B Chromosome Conference. 20-23 July 2019, Botucatu, Brazil
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Trifonov VA. Polyploidy and genome evolution of ray-finned fishes. International Conference “Chromosome – 2018”, 20-24 August 2018, Novosibirsk, Russia
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Kichigin IG. Studying anolis and gekkota sex chromosomes by isolated chromosome sequencing. International Conference “Chromosome – 2018”, 20-24 August 2018, Novosibirsk, Russia
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Trifonov V. Evolutionary sex chromosome translocations in amniotes. 23rd International Colloquium on Animal Cytogenetics and Genomics, June 9-12, 2018, Saint-Petersburg, Russia
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Trivonof V. Whole genome duplications in vertebrate evolution. 11th European Cytogenetics Conference, 1-4 July 2017, Florence, Italy
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Trifonov V. Evolutionary plasticity of sturgeon genomes. 21st International Chromosome Conference. 10-13 July 2016, Foz do Iguaçu, Brazil
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Trifonov VA. Application of molecular cytogenetic technologies for the study of sex chromosomes. Meeting intended to facilitate design of strategies to study the impact of mitonuclear incompatibilities in the diversification of animals. 14-16 October 2015, University of A Coruña, Spain
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Trifonov VA. Molecular composition and evolution of cervid B chromosomes. 3rd B-Chromosome Conference, 7-9 April 2014, Gatersleben, Germany
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Trifonov VA. Amplification of genes on mammalian B chromosomes. The 19th International Chromosome Conference. 2-6 September 2013, Bologna, Italy
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Biltueva LS. Karyotype evolution of Eulipotyphla. The genome homology of Sorex species revealed by comparative chromosome painting and banding data. VIth European Congress of Mammology, 19-23 July 2011, Paris, France
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Trifonov VA. Amplification of genes on mammalian B chromosomes. Second Conference of Brazilian Cytogenetics, 28-30 August 2011, Aguas de Lindoia, Brazil
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Trifonov VA. Isolation and analysis of coding sequences from B-chromosomes of the Red Fox (Vulpes vulpes) and Siberian Roe Deer (Capreolus pygargus). 2nd Congress of the International Cytogenetics and Genome Society and Digital Scientific UK Users Group Meeting, 25-29 June 2006, Canterbury, UK
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Biltueva L. Karyotypic relationships in the Insectivora. The 8th Meeting of the International Sorex araneus Cytogenetic Committee (ISACC). 8-12 August 2008, York, UK
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Cambridge Resource Centre for Comparative Genomics, University of Cambridge, UK
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National Cancer Institute at Frederick, MD, USA
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Cornell University, Ithaca, NY, USA
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University of North Carolina at Chapel Hill, NC, USA
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Institut für Humangenetik, Jena, Germany
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Julius-Maximilians-Universität Würzburg, Germany
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Muséum national d'histoire naturelle, Paris, France
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Università degli Studi di Firenze, Florence, Italy
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Università Politécnica delle Marche, Ancona, Italy
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Kunming Institute of Zoology, China
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Zhejiang Ocean University, China
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Universidade de São Paulo, Câmpus de Rio Claro, Brasil
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Universidade Estadual Paulista, São Paulo, Brazi
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Universidade Federal de Minas Gerais, Belo Horizonte, Brasil
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Institute for Biological Research "Siniša Stanković", Belgrade, Serbia
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Univerzita Karlova, Praha, Czech Republick