Chromosome-Length Assembly of the Baikal Seal (Pusa sibirica) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal

Aliya Yakupova; Andrey Tomarovsky; Azamat Totikov; Violetta Beklemisheva; Maria Logacheva; Polina L Perelman; Aleksey Komissarov; Pavel Dobrynin; Ksenia Krasheninnikova; Gaik Tamazian; Natalia A Serdyukova; Mike Rayko; Tatiana Bulyonkova; Nikolay Cherkasov; Vladimir Pylev; Vladimir Peterfeld; Aleksey Penin; Elena Balanovska; Alla Lapidus; Dna Zoo Consortium; Stephen J OBrien; Alexander Graphodatsky; Klaus-Peter Koepfli; Sergei Kliver

doi:10.3390/genes14030619

Chromosome-Length Assembly of the Baikal Seal (Pusa sibirica) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal

Genes (Basel). 2023 Feb 28;14(3):619. doi: 10.3390/genes14030619.

Authors

Aliya Yakupova¹, Andrey Tomarovsky^{1

2

3}, Azamat Totikov^{1

2

3}, Violetta Beklemisheva³, Maria Logacheva⁴, Polina L Perelman³, Aleksey Komissarov⁵, Pavel Dobrynin^{1

6}, Ksenia Krasheninnikova⁷, Gaik Tamazian⁸, Natalia A Serdyukova³, Mike Rayko⁹, Tatiana Bulyonkova¹⁰, Nikolay Cherkasov⁸, Vladimir Pylev¹¹, Vladimir Peterfeld¹², Aleksey Penin¹³, Elena Balanovska¹¹, Alla Lapidus⁹, Dna Zoo Consortium¹⁴, Stephen J OBrien¹⁵, Alexander Graphodatsky³, Klaus-Peter Koepfli^{16

17}, Sergei Kliver¹⁸

Affiliations

¹ Computer Technologies Laboratory, ITMO University, 19701 Saint Petersburg, Russia.
² Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia.
³ Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia.
⁴ Skolkovo Institute of Science and Technology, 121205 Moscow, Russia.
⁵ Applied Genomics Laboratory, SCAMT Institute, ITMO University, 9 Ulitsa Lomonosova, 191002 Saint Petersburg, Russia.
⁶ Human Genetics Laboratory, Vavilov Institute of General Genetics RAS, 119991 Moscow, Russia.
⁷ Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, UK.
⁸ Centre for Computational Biology, Peter the Great Saint Petersburg Polytechnic University, 195251 St. Petersburg, Russia.
⁹ Center for Bioinformatics and Algorithmic Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia.
¹⁰ Laboratory of Mixed Computations, A.P. Ershov Institute of Informatics Systems SB RAS, 630090 Novosibirsk, Russia.
¹¹ Laboratory of Human Population Genetics, Research Centre for Medical Genetics, 115522 Moscow, Russia.
¹² Baikal Branch of State Research and Industrial Center of Fisheries, 670034 Ulan-Ude, Russia.
¹³ Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, Russia.
¹⁴ The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
¹⁵ Guy Harvey Oceanographic Center, Halmos College of Arts and Sciences, NOVA Southeastern University, Fort Lauderdale, FL 33004, USA.
¹⁶ Smithsonian-Mason School of Conservation, George Mason University, 1500 Remount Road, Front Royal, VA 22630, USA.
¹⁷ Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, 1500 Remount Road, Front Royal, VA 22630, USA.
¹⁸ Center for Evolutionary Hologenomics, The Globe Institute, The University of Copenhagen, 5A, Oester Farimagsgade, 1353 Copenhagen, Denmark.

Abstract

Pusa sibirica, the Baikal seal, is the only extant, exclusively freshwater, pinniped species. The pending issue is, how and when they reached their current habitat-the rift lake Baikal, more than three thousand kilometers away from the Arctic Ocean. To explore the demographic history and genetic diversity of this species, we generated a de novo chromosome-length assembly, and compared it with three closely related marine pinniped species. Multiple whole genome alignment of the four species compared with their karyotypes showed high conservation of chromosomal features, except for three large inversions on chromosome VI. We found the mean heterozygosity of the studied Baikal seal individuals was relatively low (0.61 SNPs/kbp), but comparable to other analyzed pinniped samples. Demographic reconstruction of seals revealed differing trajectories, yet remarkable variations in Ne occurred during approximately the same time periods. The Baikal seal showed a significantly more severe decline relative to other species. This could be due to the difference in environmental conditions encountered by the earlier populations of Baikal seals, as ice sheets changed during glacial-interglacial cycles. We connect this period to the time of migration to Lake Baikal, which occurred ~3-0.3 Mya, after which the population stabilized, indicating balanced habitat conditions.

Keywords: Pusa sibirica; conservation; demography; heterozygosity; pinnipeds.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Karyotype
Lakes*
Seals, Earless* / genetics

Grants and funding

The work was supported by a research grant of the Russian Science Foundation (RSF, 19-14-00034-P) and partly by a research grant of the Russian Foundation for Basic Research (RFBR), project number 20-04-00808. A.L. and M.R. were supported by St. Petersburg State University (grant ID PURE: 73023672). N.C. and G.T. were supported by Peter the Great St. Petersburg Polytechnic University in the framework of Russian Federation’s Priority 2030 Strategic Academic Leadership Programme (Agreement 75-15-2021-1333). V.P. and E.B. were funded from the state assignment of Ministry of Science and Higher Education of the Russian Federation for Research Centre for Medical Genetics.