{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,22]],"date-time":"2026-08-22T12:59:12Z","timestamp":1787403552715,"version":"build-2736575974"},"reference-count":73,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2023,12,19]],"date-time":"2023-12-19T00:00:00Z","timestamp":1702944000000},"content-version":"vor","delay-in-days":356,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002367","name":"Chinese Academy of Sciences","doi-asserted-by":"publisher","award":["XDB42000000"],"award-info":[{"award-number":["XDB42000000"]}],"id":[{"id":"10.13039\/501100002367","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,12,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The Pacific geoduck Panopea generosa (class Bivalvia, order Adapedonta, family Hiatellidae, genus Panopea) is the largest known burrowing bivalve with considerable commercial value. Pacific geoduck and other geoduck clams play important roles in maintaining ecosystem health for their filter feeding habit and coupling pelagic and benthic processes. Here, we report a high-quality chromosome-level genome assembly of P. generosa to characterize its phylogeny and molecular mechanisms of its life strategies. The assembled P. generosa genome consists of 19 chromosomes with a size of 1.47 Gb, a contig N50 length of 1.6 Mb, and a scaffold N50 length of 73.8 Mb. The BUSCO test of the genome assembly showed 93.0% completeness. Constructed chromosome synteny revealed many occurrences of inter- and intrachromosomal rearrangements between P. generosa and Sinonovacula constricta. Of the 35,034 predicted protein-coding genes, 30,700 (87.6%) could be functionally annotated in public databases, indicating the high quality of genome annotation. Comparison of gene copy numbers of gene families among P. generosa and 11 selected species identified 507 rapidly expanded P. generosa gene families that are functionally enriched in immune and gonad development and may be involved in its complex survival strategies. In particular, genes carrying the copine domains underwent additional duplications in P. generosa, which might be important for neuronal development and immune response. The availability of a fully annotated chromosome-level genome provides a valuable dataset for genetic breeding of P. generosa.<\/jats:p>","DOI":"10.1093\/gigascience\/giad105","type":"journal-article","created":{"date-parts":[[2023,12,19]],"date-time":"2023-12-19T14:53:28Z","timestamp":1702997608000},"source":"Crossref","is-referenced-by-count":4,"title":["Chromosome-level genome assembly of the Pacific geoduck <i>Panopea generosa<\/i> reveals major inter- and intrachromosomal rearrangements and substantial expansion of the copine gene family"],"prefix":"10.1093","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2267-4287","authenticated-orcid":false,"given":"Jing","family":"Wang","sequence":"first","affiliation":[{"name":"CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences , Qingdao 266071 ,","place":["China"]},{"name":"Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology , Qingdao 266237 ,","place":["China"]},{"name":"Center for Ocean Mega-Science, Chinese Academy of Sciences , Qingdao 266071 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0395-0557","authenticated-orcid":false,"given":"Qing","family":"Xu","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences , Qingdao 266071 ,","place":["China"]},{"name":"Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology , Qingdao 266237 ,","place":["China"]},{"name":"Center for Ocean Mega-Science, Chinese Academy of Sciences , Qingdao 266071 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8582-0678","authenticated-orcid":false,"given":"Min","family":"Chen","sequence":"additional","affiliation":[{"name":"Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences , Yantai 264003 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3244-5384","authenticated-orcid":false,"given":"Yang","family":"Chen","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences , Qingdao 266071 ,","place":["China"]},{"name":"Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology , Qingdao 266237 ,","place":["China"]},{"name":"Center for Ocean Mega-Science, 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Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology , Qingdao 266237 ,","place":["China"]},{"name":"Center for Ocean Mega-Science, Chinese Academy of Sciences , Qingdao 266071 ,","place":["China"]},{"name":"Department of Molecular Biology and Biochemistry, Simon Fraser University , Burnaby, British Columbia V5A 1S6 ,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,12,19]]},"reference":[{"key":"2024111706450575000_bib1","doi-asserted-by":"crossref","first-page":"85","DOI":"10.4002\/040.056.0206","article-title":"Distribution limits of the geoduck clams Panopea generosa and P. globosa on the Pacific coast of Mexico","volume":"56","author":"Gonz\u00e1lez-Pel\u00e1ez","year":"2013","journal-title":"Malacologia"},{"key":"2024111706450575000_bib2","doi-asserted-by":"crossref","first-page":"169","DOI":"10.4002\/040.052.0111","article-title":"The proper name for the 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