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

Authors

• Aliya Yakupova, ITMO University
• Andrey Tomarovsky, ITMO University; Novosibirsk State University; Institute of Molecular and Cellular Biology SB RAS
• Azamat Totikov, ITMO University; Novosibirsk State University; Institute of Molecular and Cellular Biology SB RAS
• Violetta R. Beklemisheva, Institute of Molecular and Cellular Biology SB RAS
• Maria Logacheva, Skolkovo Institute of Science and Technology
• Polina Perelman, Institute of Molecular and Cellular Biology SB RAS
• Aleksey Komissarov, ITMO University
• Pavel Dobrynin, ITMO University; Vavilov Institute of General Genetics RAS
• Ksenia Krasheninnikova, Wellcome Sanger Institute
• Gaik Tamazian, Peter the Great Saint Petersburg Polytechnic University
• Natalya A. Serdyukova, Institute of Molecular and Cellular Biology SB RAS
• Michael Rayko, Saint Petersburg State University
• Tatiana Bulyonkova, A.P. Ershov Institute of Informatics Systems SB RAS
• Nikolay Cherkasov, Peter the Great Saint Petersburg Polytechnic University
• Vladimir Pylev, Research Centre for Medical Genetics
• Vladimir Peterfeld, Baikal Branch of State Research and Industrial Center of Fisheries
• Aleksey Penin, Institute for Information Transmission Problems of the Russian Academy of Sciences
• Elena Balanovska, Research Centre for Medical Genetics
• Alla L. Lapidus, St. Petersburg State University
• DNA Zoo Consortium, Baylor College of Medicine
• Stephen James O'Brien, Nova Southeastern UniversityFollow
• Alexander S. Graphodatsky, Institute of Molecular and Cellular Biology SB RAS
• Klaus-Peter Koepfli, George Mason University; Smithsonian’s National Zoo and Conservation Biology Institute
• Sergey Kliver, University of Copenhagen

ORCID

0000-0001-7353-8301

ResearcherID

N-1726-2015

Document Type

Article

Publication Title

Genes

ISSN

2073-4425

Publication Date

2-28-2023

Keywords

Pusa sibirica, conservation, pinnipeds, demography, heterozygosity

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.

DOI

10.3390/genes14030619

Volume

14

Issue

3

First Page

619

Comments

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.

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 International License.

NSUWorks Citation

Yakupova, Aliya; Andrey Tomarovsky; Azamat Totikov; Violetta R. Beklemisheva; Maria Logacheva; Polina Perelman; Aleksey Komissarov; Pavel Dobrynin; Ksenia Krasheninnikova; Gaik Tamazian; Natalya A. Serdyukova; Michael Rayko; Tatiana Bulyonkova; Nikolay Cherkasov; Vladimir Pylev; Vladimir Peterfeld; Aleksey Penin; Elena Balanovska; Alla L. Lapidus; DNA Zoo Consortium; Stephen James O'Brien; Alexander S. Graphodatsky; Klaus-Peter Koepfli; and Sergey Kliver. 2023. "Chromosome-Length Assembly of the Baikal Seal (Pusa sibirica) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal." Genes 14, (3): 619. doi:10.3390/genes14030619.