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

, 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 thi...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:Genes 2023-02, Vol.14 (3), p.619
Hauptverfasser: 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
Format: Artikel
Sprache:eng
Schlagworte:
Online-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
container_end_page
container_issue 3
container_start_page 619
container_title Genes
container_volume 14
creator 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
description , 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_str_mv 10.3390/genes14030619
format Article
fullrecord <record><control><sourceid>gale_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_10048373</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A743765279</galeid><sourcerecordid>A743765279</sourcerecordid><originalsourceid>FETCH-LOGICAL-c400t-62c8df5fecbb766267111ca0cc7a7cd35cd3a8a4b13b872013237e655941e3e83</originalsourceid><addsrcrecordid>eNpdkstq3DAUhkVpaUKaZbdF0E26cKu77FWZDG0SGOjQy1rImmOPEluaSnYgb9FHroZM0qQCXdD_nf_oiIPQW0o-ct6QTz0EyFQQThRtXqBjRjSvhGDy5ZPzETrN-ZqUIQgjRL5GR1w1Nakbeoz-LLcpjjHHEaoVhH7a4kXOMLbDHY4dnraAz62_sQP-AWU5w-s5W5x965N3Fn_AFxBKLP4Ot0XP2OJLn6e4F4disbKpB7yOu3mwk48Br5OPCU8RX-V4uPKhYDcPed6gV10xgtPDfoJ-ff3yc3lZrb5dXC0Xq8oJQqZKMVdvOtmBa1utFFOaUuoscU5b7TZclmlrK1rK21ozQjnjGpSUjaDAoeYn6PO9725uR9g4CFOyg9klP9p0Z6L15rkS_Nb08dbQ8o8117w4nB0cUvw9Q57M6LODYbAB4pwN0w2TpFayKej7_9DrOKdQ6ttTQknOFPlH9XYA40MXS2K3NzULLbhWssCFqu4pl2LOCbrHN1Ni9l1hnnVF4d89LfSRfugB_hfBObKv</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2794653260</pqid></control><display><type>article</type><title>Chromosome-Length Assembly of the Baikal Seal ( Pusa sibirica ) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal</title><source>MDPI - Multidisciplinary Digital Publishing Institute</source><source>MEDLINE</source><source>Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals</source><source>PubMed Central</source><source>PubMed Central Open Access</source><creator>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</creator><creatorcontrib>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 ; DNA Zoo Consortium</creatorcontrib><description>, 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.</description><identifier>ISSN: 2073-4425</identifier><identifier>EISSN: 2073-4425</identifier><identifier>DOI: 10.3390/genes14030619</identifier><identifier>PMID: 36980891</identifier><language>eng</language><publisher>Switzerland: MDPI AG</publisher><subject>Analysis ; Animals ; Chromosome 6 ; Chromosomes ; Demography ; Environmental aspects ; Environmental conditions ; Females ; Fisheries ; Fishing ; Genetic diversity ; Genomes ; Genomics ; Heterozygosity ; Karyotype ; Karyotypes ; Lakes ; Marine mammals ; Mitochondrial DNA ; Phylogenetics ; Population ; Population decline ; Pusa sibirica ; Seals, Earless - genetics ; Single-nucleotide polymorphism ; Species</subject><ispartof>Genes, 2023-02, Vol.14 (3), p.619</ispartof><rights>COPYRIGHT 2023 MDPI AG</rights><rights>2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2023 by the authors. 2023</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c400t-62c8df5fecbb766267111ca0cc7a7cd35cd3a8a4b13b872013237e655941e3e83</cites><orcidid>0000-0001-9541-8319 ; 0000-0003-1236-631X ; 0000-0001-7281-0676 ; 0000-0002-3882-8300 ; 0000-0003-1486-0864 ; 0000-0001-6981-7316 ; 0000-0002-9122-4143 ; 0000-0002-8282-1085 ; 0000-0002-0982-5100 ; 0000-0002-2931-1123 ; 0000-0003-0427-8731</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10048373/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10048373/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/36980891$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Yakupova, Aliya</creatorcontrib><creatorcontrib>Tomarovsky, Andrey</creatorcontrib><creatorcontrib>Totikov, Azamat</creatorcontrib><creatorcontrib>Beklemisheva, Violetta</creatorcontrib><creatorcontrib>Logacheva, Maria</creatorcontrib><creatorcontrib>Perelman, Polina L</creatorcontrib><creatorcontrib>Komissarov, Aleksey</creatorcontrib><creatorcontrib>Dobrynin, Pavel</creatorcontrib><creatorcontrib>Krasheninnikova, Ksenia</creatorcontrib><creatorcontrib>Tamazian, Gaik</creatorcontrib><creatorcontrib>Serdyukova, Natalia A</creatorcontrib><creatorcontrib>Rayko, Mike</creatorcontrib><creatorcontrib>Bulyonkova, Tatiana</creatorcontrib><creatorcontrib>Cherkasov, Nikolay</creatorcontrib><creatorcontrib>Pylev, Vladimir</creatorcontrib><creatorcontrib>Peterfeld, Vladimir</creatorcontrib><creatorcontrib>Penin, Aleksey</creatorcontrib><creatorcontrib>Balanovska, Elena</creatorcontrib><creatorcontrib>Lapidus, Alla</creatorcontrib><creatorcontrib>Dna Zoo Consortium</creatorcontrib><creatorcontrib>OBrien, Stephen J</creatorcontrib><creatorcontrib>Graphodatsky, Alexander</creatorcontrib><creatorcontrib>Koepfli, Klaus-Peter</creatorcontrib><creatorcontrib>Kliver, Sergei</creatorcontrib><creatorcontrib>DNA Zoo Consortium</creatorcontrib><title>Chromosome-Length Assembly of the Baikal Seal ( Pusa sibirica ) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal</title><title>Genes</title><addtitle>Genes (Basel)</addtitle><description>, 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.</description><subject>Analysis</subject><subject>Animals</subject><subject>Chromosome 6</subject><subject>Chromosomes</subject><subject>Demography</subject><subject>Environmental aspects</subject><subject>Environmental conditions</subject><subject>Females</subject><subject>Fisheries</subject><subject>Fishing</subject><subject>Genetic diversity</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Heterozygosity</subject><subject>Karyotype</subject><subject>Karyotypes</subject><subject>Lakes</subject><subject>Marine mammals</subject><subject>Mitochondrial DNA</subject><subject>Phylogenetics</subject><subject>Population</subject><subject>Population decline</subject><subject>Pusa sibirica</subject><subject>Seals, Earless - genetics</subject><subject>Single-nucleotide polymorphism</subject><subject>Species</subject><issn>2073-4425</issn><issn>2073-4425</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNpdkstq3DAUhkVpaUKaZbdF0E26cKu77FWZDG0SGOjQy1rImmOPEluaSnYgb9FHroZM0qQCXdD_nf_oiIPQW0o-ct6QTz0EyFQQThRtXqBjRjSvhGDy5ZPzETrN-ZqUIQgjRL5GR1w1Nakbeoz-LLcpjjHHEaoVhH7a4kXOMLbDHY4dnraAz62_sQP-AWU5w-s5W5x965N3Fn_AFxBKLP4Ot0XP2OJLn6e4F4disbKpB7yOu3mwk48Br5OPCU8RX-V4uPKhYDcPed6gV10xgtPDfoJ-ff3yc3lZrb5dXC0Xq8oJQqZKMVdvOtmBa1utFFOaUuoscU5b7TZclmlrK1rK21ozQjnjGpSUjaDAoeYn6PO9725uR9g4CFOyg9klP9p0Z6L15rkS_Nb08dbQ8o8117w4nB0cUvw9Q57M6LODYbAB4pwN0w2TpFayKej7_9DrOKdQ6ttTQknOFPlH9XYA40MXS2K3NzULLbhWssCFqu4pl2LOCbrHN1Ni9l1hnnVF4d89LfSRfugB_hfBObKv</recordid><startdate>20230228</startdate><enddate>20230228</enddate><creator>Yakupova, Aliya</creator><creator>Tomarovsky, Andrey</creator><creator>Totikov, Azamat</creator><creator>Beklemisheva, Violetta</creator><creator>Logacheva, Maria</creator><creator>Perelman, Polina L</creator><creator>Komissarov, Aleksey</creator><creator>Dobrynin, Pavel</creator><creator>Krasheninnikova, Ksenia</creator><creator>Tamazian, Gaik</creator><creator>Serdyukova, Natalia A</creator><creator>Rayko, Mike</creator><creator>Bulyonkova, Tatiana</creator><creator>Cherkasov, Nikolay</creator><creator>Pylev, Vladimir</creator><creator>Peterfeld, Vladimir</creator><creator>Penin, Aleksey</creator><creator>Balanovska, Elena</creator><creator>Lapidus, Alla</creator><creator>Dna Zoo Consortium</creator><creator>OBrien, Stephen J</creator><creator>Graphodatsky, Alexander</creator><creator>Koepfli, Klaus-Peter</creator><creator>Kliver, Sergei</creator><general>MDPI AG</general><general>MDPI</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>LK8</scope><scope>M7P</scope><scope>P64</scope><scope>PHGZM</scope><scope>PHGZT</scope><scope>PIMPY</scope><scope>PKEHL</scope><scope>PQEST</scope><scope>PQGLB</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0001-9541-8319</orcidid><orcidid>https://orcid.org/0000-0003-1236-631X</orcidid><orcidid>https://orcid.org/0000-0001-7281-0676</orcidid><orcidid>https://orcid.org/0000-0002-3882-8300</orcidid><orcidid>https://orcid.org/0000-0003-1486-0864</orcidid><orcidid>https://orcid.org/0000-0001-6981-7316</orcidid><orcidid>https://orcid.org/0000-0002-9122-4143</orcidid><orcidid>https://orcid.org/0000-0002-8282-1085</orcidid><orcidid>https://orcid.org/0000-0002-0982-5100</orcidid><orcidid>https://orcid.org/0000-0002-2931-1123</orcidid><orcidid>https://orcid.org/0000-0003-0427-8731</orcidid></search><sort><creationdate>20230228</creationdate><title>Chromosome-Length Assembly of the Baikal Seal ( Pusa sibirica ) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal</title><author>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</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c400t-62c8df5fecbb766267111ca0cc7a7cd35cd3a8a4b13b872013237e655941e3e83</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Analysis</topic><topic>Animals</topic><topic>Chromosome 6</topic><topic>Chromosomes</topic><topic>Demography</topic><topic>Environmental aspects</topic><topic>Environmental conditions</topic><topic>Females</topic><topic>Fisheries</topic><topic>Fishing</topic><topic>Genetic diversity</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Heterozygosity</topic><topic>Karyotype</topic><topic>Karyotypes</topic><topic>Lakes</topic><topic>Marine mammals</topic><topic>Mitochondrial DNA</topic><topic>Phylogenetics</topic><topic>Population</topic><topic>Population decline</topic><topic>Pusa sibirica</topic><topic>Seals, Earless - genetics</topic><topic>Single-nucleotide polymorphism</topic><topic>Species</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Yakupova, Aliya</creatorcontrib><creatorcontrib>Tomarovsky, Andrey</creatorcontrib><creatorcontrib>Totikov, Azamat</creatorcontrib><creatorcontrib>Beklemisheva, Violetta</creatorcontrib><creatorcontrib>Logacheva, Maria</creatorcontrib><creatorcontrib>Perelman, Polina L</creatorcontrib><creatorcontrib>Komissarov, Aleksey</creatorcontrib><creatorcontrib>Dobrynin, Pavel</creatorcontrib><creatorcontrib>Krasheninnikova, Ksenia</creatorcontrib><creatorcontrib>Tamazian, Gaik</creatorcontrib><creatorcontrib>Serdyukova, Natalia A</creatorcontrib><creatorcontrib>Rayko, Mike</creatorcontrib><creatorcontrib>Bulyonkova, Tatiana</creatorcontrib><creatorcontrib>Cherkasov, Nikolay</creatorcontrib><creatorcontrib>Pylev, Vladimir</creatorcontrib><creatorcontrib>Peterfeld, Vladimir</creatorcontrib><creatorcontrib>Penin, Aleksey</creatorcontrib><creatorcontrib>Balanovska, Elena</creatorcontrib><creatorcontrib>Lapidus, Alla</creatorcontrib><creatorcontrib>Dna Zoo Consortium</creatorcontrib><creatorcontrib>OBrien, Stephen J</creatorcontrib><creatorcontrib>Graphodatsky, Alexander</creatorcontrib><creatorcontrib>Koepfli, Klaus-Peter</creatorcontrib><creatorcontrib>Kliver, Sergei</creatorcontrib><creatorcontrib>DNA Zoo Consortium</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest Central (New)</collection><collection>ProQuest One Academic (New)</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Middle East (New)</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Applied &amp; Life Sciences</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Genes</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Yakupova, Aliya</au><au>Tomarovsky, Andrey</au><au>Totikov, Azamat</au><au>Beklemisheva, Violetta</au><au>Logacheva, Maria</au><au>Perelman, Polina L</au><au>Komissarov, Aleksey</au><au>Dobrynin, Pavel</au><au>Krasheninnikova, Ksenia</au><au>Tamazian, Gaik</au><au>Serdyukova, Natalia A</au><au>Rayko, Mike</au><au>Bulyonkova, Tatiana</au><au>Cherkasov, Nikolay</au><au>Pylev, Vladimir</au><au>Peterfeld, Vladimir</au><au>Penin, Aleksey</au><au>Balanovska, Elena</au><au>Lapidus, Alla</au><au>Dna Zoo Consortium</au><au>OBrien, Stephen J</au><au>Graphodatsky, Alexander</au><au>Koepfli, Klaus-Peter</au><au>Kliver, Sergei</au><aucorp>DNA Zoo Consortium</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Chromosome-Length Assembly of the Baikal Seal ( Pusa sibirica ) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal</atitle><jtitle>Genes</jtitle><addtitle>Genes (Basel)</addtitle><date>2023-02-28</date><risdate>2023</risdate><volume>14</volume><issue>3</issue><spage>619</spage><pages>619-</pages><issn>2073-4425</issn><eissn>2073-4425</eissn><abstract>, 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.</abstract><cop>Switzerland</cop><pub>MDPI AG</pub><pmid>36980891</pmid><doi>10.3390/genes14030619</doi><orcidid>https://orcid.org/0000-0001-9541-8319</orcidid><orcidid>https://orcid.org/0000-0003-1236-631X</orcidid><orcidid>https://orcid.org/0000-0001-7281-0676</orcidid><orcidid>https://orcid.org/0000-0002-3882-8300</orcidid><orcidid>https://orcid.org/0000-0003-1486-0864</orcidid><orcidid>https://orcid.org/0000-0001-6981-7316</orcidid><orcidid>https://orcid.org/0000-0002-9122-4143</orcidid><orcidid>https://orcid.org/0000-0002-8282-1085</orcidid><orcidid>https://orcid.org/0000-0002-0982-5100</orcidid><orcidid>https://orcid.org/0000-0002-2931-1123</orcidid><orcidid>https://orcid.org/0000-0003-0427-8731</orcidid><oa>free_for_read</oa></addata></record>
fulltext fulltext
identifier ISSN: 2073-4425
ispartof Genes, 2023-02, Vol.14 (3), p.619
issn 2073-4425
2073-4425
language eng
recordid cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_10048373
source MDPI - Multidisciplinary Digital Publishing Institute; MEDLINE; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; PubMed Central Open Access
subjects Analysis
Animals
Chromosome 6
Chromosomes
Demography
Environmental aspects
Environmental conditions
Females
Fisheries
Fishing
Genetic diversity
Genomes
Genomics
Heterozygosity
Karyotype
Karyotypes
Lakes
Marine mammals
Mitochondrial DNA
Phylogenetics
Population
Population decline
Pusa sibirica
Seals, Earless - genetics
Single-nucleotide polymorphism
Species
title Chromosome-Length Assembly of the Baikal Seal ( Pusa sibirica ) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal
url https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-19T15%3A45%3A21IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Chromosome-Length%20Assembly%20of%20the%20Baikal%20Seal%20(%20Pusa%20sibirica%20)%20Genome%20Reveals%20a%20Historically%20Large%20Population%20Prior%20to%20Isolation%20in%20Lake%20Baikal&rft.jtitle=Genes&rft.au=Yakupova,%20Aliya&rft.aucorp=DNA%20Zoo%20Consortium&rft.date=2023-02-28&rft.volume=14&rft.issue=3&rft.spage=619&rft.pages=619-&rft.issn=2073-4425&rft.eissn=2073-4425&rft_id=info:doi/10.3390/genes14030619&rft_dat=%3Cgale_pubme%3EA743765279%3C/gale_pubme%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2794653260&rft_id=info:pmid/36980891&rft_galeid=A743765279&rfr_iscdi=true