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

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

doi:10.3390/genes14030619

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

by

Aliya Yakupova

^1,*

,

Andrey Tomarovsky

^1,2,3,

Azamat Totikov

^1,2,3

,

Violetta Beklemisheva

³

,

Maria Logacheva

⁴,

Polina L. Perelman

³

,

Aleksey Komissarov

⁵

,

Pavel Dobrynin

^1,6,

Ksenia Krasheninnikova

⁷,

Gaik Tamazian

⁸

,

Natalia A. Serdyukova

³,

Mike Rayko

⁹,

Tatiana Bulyonkova

¹⁰,

Nikolay Cherkasov

⁸,

Vladimir Pylev

¹¹

,

Vladimir Peterfeld

¹²,

Aleksey Penin

¹³,

Elena Balanovska

¹¹

,

Alla Lapidus

⁹

,

DNA Zoo Consortium

¹⁴,

Stephen J. OBrien

¹⁵,

Alexander Graphodatsky

^3,*

,

Klaus-Peter Koepfli

^16,17

and

Sergei Kliver

¹⁸ Show full author list Hide full author list

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

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^*

Authors to whom correspondence should be addressed.

Genes 2023, 14(3), 619; https://doi.org/10.3390/genes14030619

Submission received: 21 December 2022 / Revised: 31 January 2023 / Accepted: 24 February 2023 / Published: 28 February 2023

(This article belongs to the Collection Feature Papers in ‘Animal Genetics and Genomics’)

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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; pinnipeds; demography; heterozygosity

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MDPI and ACS Style

Yakupova, A.; Tomarovsky, A.; Totikov, A.; Beklemisheva, V.; Logacheva, M.; Perelman, P.L.; Komissarov, A.; Dobrynin, P.; Krasheninnikova, K.; Tamazian, G.; et al. Chromosome-Length Assembly of the Baikal Seal (Pusa sibirica) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal. Genes 2023, 14, 619. https://doi.org/10.3390/genes14030619

AMA Style

Yakupova A, Tomarovsky A, Totikov A, Beklemisheva V, Logacheva M, Perelman PL, Komissarov A, Dobrynin P, Krasheninnikova K, Tamazian G, et al. Chromosome-Length Assembly of the Baikal Seal (Pusa sibirica) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal. Genes. 2023; 14(3):619. https://doi.org/10.3390/genes14030619

Chicago/Turabian Style

Yakupova, Aliya, Andrey Tomarovsky, Azamat Totikov, Violetta Beklemisheva, Maria Logacheva, Polina L. Perelman, Aleksey Komissarov, Pavel Dobrynin, Ksenia Krasheninnikova, Gaik Tamazian, and et al. 2023. "Chromosome-Length Assembly of the Baikal Seal (Pusa sibirica) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal" Genes 14, no. 3: 619. https://doi.org/10.3390/genes14030619

APA Style

Yakupova, A., Tomarovsky, A., Totikov, A., Beklemisheva, V., Logacheva, M., Perelman, P. L., Komissarov, A., Dobrynin, P., Krasheninnikova, K., Tamazian, G., Serdyukova, N. A., Rayko, M., Bulyonkova, T., Cherkasov, N., Pylev, V., Peterfeld, V., Penin, A., Balanovska, E., Lapidus, A., ... Kliver, S. (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. https://doi.org/10.3390/genes14030619

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

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