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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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.
In: Genes, Vol. 14, No. 3, 619, 2023.Research output: Contribution to journal › Journal article › Research › peer-review
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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
AU - OBrien, Stephen J.
AU - Graphodatsky, Alexander
AU - Koepfli, Klaus-Peter
AU - Kliver, Sergei
PY - 2023
Y1 - 2023
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.
KW - conservation
KW - demography
KW - heterozygosity
KW - pinnipeds
KW - Pusa sibirica
U2 - 10.3390/genes14030619
DO - 10.3390/genes14030619
M3 - Journal article
C2 - 36980891
AN - SCOPUS:85151109751
VL - 14
JO - Genes
JF - Genes
SN - 2073-4425
IS - 3
M1 - 619
ER -
ID: 341476316