TY - JOUR

T1 - Chromosome-Length Assembly of the Baikal Seal (Pusa sibirica) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal

AU - Yakupova, Aliya

AU - Tomarovsky, Andrey

AU - Totikov, Azamat

AU - Beklemisheva, Violetta

AU - Logacheva, Maria

AU - Perelman, Polina L

AU - Komissarov, Aleksey

AU - Dobrynin, Pavel

AU - Krasheninnikova, Ksenia

AU - Tamazian, Gaik

AU - Serdyukova, Natalia A

AU - Rayko, Mike

AU - Bulyonkova, Tatiana

AU - Cherkasov, Nikolay

AU - Pylev, Vladimir

AU - Peterfeld, Vladimir

AU - Penin, Aleksey

AU - Balanovska, Elena

AU - Lapidus, Alla

AU - Dna Zoo Consortium, null

AU - OBrien, Stephen J

AU - Graphodatsky, Alexander

AU - Koepfli, Klaus-Peter

AU - Kliver, Sergei

N1 - 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.

PY - 2023/2/28

Y1 - 2023/2/28

N2 - 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.

AB - 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.

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-85151109751&origin=inward&txGid=3b07e79949b583d81b00307ee29b6093

UR - https://www.mendeley.com/catalogue/618dcd80-1391-3535-a4ad-b369cf569fae/

U2 - 10.3390/genes14030619

DO - 10.3390/genes14030619

M3 - Article

C2 - 36980891

VL - 14

JO - Genes

JF - Genes

SN - 2073-4425

IS - 3

M1 - 619

ER -