{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T17:19:19Z","timestamp":1782321559466,"version":"3.54.5"},"reference-count":115,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2025,10,28]],"date-time":"2025-10-28T00:00:00Z","timestamp":1761609600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"California Conservation Genomics Project","award":["RSI-19-690224"],"award-info":[{"award-number":["RSI-19-690224"]}]},{"name":"National Science Foundation through the Graduate Research Fellowship Program"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,5,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The northern elephant seal (Mirounga angustirostris) is the largest pinniped species in the northern hemisphere. The species is classified as being of least conservation concern by the IUCN\u2014a triumph of conservation efforts despite hunting pressure that nearly led to its extinction more than a century ago. The historical range of the northern elephant seal extended from Baja California to Alaska, but overexploitation caused a severe demographic collapse and genetic bottleneck, with only an estimated 10 to 30 survivors left on Isla Guadalupe, Mexico. As part of the California Conservation Genomics Project, we generated a de novo reference genome and annotation for M. angustirostris, combining PacBio HiFi long-read sequencing data with Dovetail Omni-C chromatin conformation data. Our assembly has a primary haplotype genome length of 2,430,321,998 base pairs (2.4 Gb), with the longest contig of 144\u00a0Mb, contig N50 of 58\u00a0Mb, largest scaffold of 215\u00a0Mb, and scaffold N50 of 154\u00a0Mb. The secondary assembly haplotype consists of 422 scaffolds, spanning 2.45 Gb, with contig N50 of 61.24\u00a0Mb, scaffold N50 of 152.94\u00a0Mb, the largest contig of 204.14\u00a0Mb, and the largest scaffold of 216.16\u00a0Mb. We used the primary assembly and annotation for a preliminary investigation of repeat element content, historical demography, genome-wide heterozygosity, and loss-of-function variants. We found that M. angustirostris has one of the lowest estimates of genetic diversity of any marine mammal and a complex demographic history that may have reduced genetic diversity several times. This newly constructed genome will facilitate future in-depth explorations into the mechanisms behind resilience and recovery after a severe population bottleneck.<\/jats:p>","DOI":"10.1093\/jhered\/esaf083","type":"journal-article","created":{"date-parts":[[2025,10,14]],"date-time":"2025-10-14T13:30:17Z","timestamp":1760448617000},"page":"512-525","source":"Crossref","is-referenced-by-count":1,"title":["Genome assembly and annotation of a deep-diving pinniped, the northern elephant seal (\n                    <i>Mirounga angustirostris<\/i>\n                    )"],"prefix":"10.1093","volume":"117","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8121-717X","authenticated-orcid":false,"given":"Milagros G","family":"Rivera","sequence":"first","affiliation":[{"name":"Department of Ecology and Evolutionary Biology, University of California\u2013Santa Cruz , Santa Cruz, CA ,","place":["United 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University of California\u2013Santa Cruz , Santa Cruz, CA ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William E","family":"Seligmann","sequence":"additional","affiliation":[{"name":"Department of Ecology and Evolutionary Biology, University of California\u2013Santa Cruz , Santa Cruz, CA ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruta","family":"Sahasrabudhe","sequence":"additional","affiliation":[{"name":"DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California\u2013Davis , Davis, CA ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oanh","family":"Nguyen","sequence":"additional","affiliation":[{"name":"DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California\u2013Davis , Davis, CA ,","place":["United 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