{"id":"https://openalex.org/W7203744398","doi":"https://doi.org/10.64898/2026.10.13.758928","title":"Chromosomal-Level Whole Genome Assemblies of Crassostrea Virginica","display_name":"Chromosomal-Level Whole Genome Assemblies of Crassostrea Virginica","publication_year":2026,"publication_date":"2026-10-19","ids":{"openalex":"https://openalex.org/W7203744398","doi":"https://doi.org/10.64898/2026.10.13.758928","pmid":"https://pubmed.ncbi.nlm.nih.gov/42995768","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/13738429"},"language":"en","primary_location":{"id":"doi:10.64898/2026.10.13.758928","doi":"https://doi.org/10.64898/2026.10.13.758928","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.13.758928","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/19/2026.10.13.758928.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref","datacite","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/19/2026.10.13.758928.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5147588488","display_name":"Liam Cawood","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Liam Cawood","raw_affiliation_strings":["Department of Environmental Health Sciences, School of Public Health, Yale University, New Haven, CT 06510, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Environmental Health Sciences, School of Public Health, Yale University, New Haven, CT 06510, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5147491504","display_name":"Shiying Wang","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shiying Wang","raw_affiliation_strings":["Department of Genetics and Pediatrics, School of Medicine, Yale University, New Haven, CT 06510, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics and Pediatrics, School of Medicine, Yale University, New Haven, CT 06510, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5147620456","display_name":"Eli Kleiman","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eli Kleiman","raw_affiliation_strings":["Department of Chronic Disease Epidemiology, School of Public Health, Yale University, New Haven, CT 06510, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chronic Disease Epidemiology, School of Public Health, Yale University, New Haven, CT 06510, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5159101495","display_name":"Zhiyuan Chen","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhiyuan Chen","raw_affiliation_strings":["Department of Ophthalmology, School of Medicine, Yale University, New Haven, CT 06510, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Ophthalmology, School of Medicine, Yale University, New Haven, CT 06510, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5147586512","display_name":"Isabel Kleiman","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Isabel Kleiman","raw_affiliation_strings":["Department of Chronic Disease Epidemiology, School of Public Health, Yale University, New Haven, CT 06510, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chronic Disease Epidemiology, School of Public Health, Yale University, New Haven, CT 06510, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5147566845","display_name":"Nicole Fair","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nicole Fair","raw_affiliation_strings":["Department of Chronic Disease Epidemiology, School of Public Health, Yale University, New Haven, CT 06510, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chronic Disease Epidemiology, School of Public Health, Yale University, New Haven, CT 06510, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5147570911","display_name":"Ruby Brownell","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ruby Brownell","raw_affiliation_strings":["Department of Chronic Disease Epidemiology, School of Public Health, Yale University, New Haven, CT 06510, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chronic Disease Epidemiology, School of Public Health, Yale University, New Haven, CT 06510, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007637663","display_name":"Irina Tikhonova","orcid":"https://orcid.org/0000-0002-5260-0476","observed_orcids":["https://orcid.org/0000-0002-5260-0476"]},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Irina Tikhonova","raw_affiliation_strings":["Center of Genome Analysis, Yale University, West Haven, CT 06516, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of Genome Analysis, Yale University, West Haven, CT 06516, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101549804","display_name":"Zicheng Li","orcid":"https://orcid.org/0000-0003-0386-8422","observed_orcids":["https://orcid.org/0000-0003-0386-8422"]},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zicheng Li","raw_affiliation_strings":["Department of Chronic Disease Epidemiology, School of Public Health, Yale University, New Haven, CT 06510, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chronic Disease Epidemiology, School of Public Health, Yale University, New Haven, CT 06510, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5107846331","display_name":"Josephine Hoh","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Josephine Hoh","raw_affiliation_strings":["Department of Applied Mathematics, Yale University, New Haven, CT 06520, USA","Department of Chronic Disease Epidemiology, School of Public Health, Yale University, New Haven, CT 06510, USA","Department of Ophthalmology, School of Medicine, Yale University, New Haven, CT 06510, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics, Yale University, New Haven, CT 06520, USA","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Department of Chronic Disease Epidemiology, School of Public Health, Yale University, New Haven, CT 06510, USA","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Department of Ophthalmology, School of Medicine, Yale University, New Haven, CT 06510, USA","institution_ids":["https://openalex.org/I32971472"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5107846331"],"corresponding_institution_ids":["https://openalex.org/I32971472"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9340999722480774,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9340999722480774,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11088","display_name":"Marine Bivalve and Aquaculture Studies","score":0.03020000085234642,"subfield":{"id":"https://openalex.org/subfields/1104","display_name":"Aquatic Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.021900000050663948,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/crassostrea-virginica","display_name":"Crassostrea virginica","score":1.0},{"id":"https://openalex.org/keywords/chromosome-level-genome-assembly","display_name":"chromosome-level genome assembly","score":0.9769999980926514},{"id":"https://openalex.org/keywords/reference-genome","display_name":"reference genome","score":0.8989999890327454},{"id":"https://openalex.org/keywords/genome-annotation","display_name":"genome annotation","score":0.6809999942779541},{"id":"https://openalex.org/keywords/repetitive-elements","display_name":"repetitive elements","score":0.9509999752044678},{"id":"https://openalex.org/keywords/protein-coding-genes","display_name":"protein-coding genes","score":0.8330000042915344},{"id":"https://openalex.org/keywords/oyster-aquaculture","display_name":"oyster aquaculture","score":0.8220000267028809},{"id":"https://openalex.org/keywords/oyster-breeding","display_name":"oyster breeding","score":0.7379999756813049},{"id":"https://openalex.org/keywords/long-island-sound","display_name":"Long Island Sound","score":0.8930000066757202}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6123999953269958},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5828999876976013},{"id":"https://openalex.org/C2776845067","wikidata":"https://www.wikidata.org/wiki/Q542708","display_name":"Crassostrea","level":3,"score":0.4499000012874603},{"id":"https://openalex.org/C24432333","wikidata":"https://www.wikidata.org/wiki/Q2068526","display_name":"Whole genome sequencing","level":4,"score":0.4205999970436096},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3716999888420105},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.35920000076293945},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.31360000371932983},{"id":"https://openalex.org/C2776991149","wikidata":"https://www.wikidata.org/wiki/Q468415","display_name":"Eastern oyster","level":4,"score":0.27570000290870667},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.274399995803833},{"id":"https://openalex.org/C168167062","wikidata":"https://www.wikidata.org/wiki/Q1117970","display_name":"Component (thermodynamics)","level":2,"score":0.25850000977516174}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.64898/2026.10.13.758928","doi":"https://doi.org/10.64898/2026.10.13.758928","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.13.758928","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/19/2026.10.13.758928.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmh:oai:pubmedcentral.nih.gov:13738429","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13738429/","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13738429/pdf/nihpp-2026.10.13.758928v1.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"bioRxiv","raw_type":"Text"},{"id":"pmid:42995768","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42995768","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"bioRxiv : the preprint server for biology","raw_type":"Journal Article"},{"id":"doi:10.5281/zenodo.22014056","doi":"https://doi.org/10.5281/zenodo.22014056","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.22014056","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article-journal"},{"id":"doi:10.5281/zenodo.22014057","doi":"https://doi.org/10.5281/zenodo.22014057","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.22014057","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.64898/2026.10.13.758928","doi":"https://doi.org/10.64898/2026.10.13.758928","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.13.758928","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/19/2026.10.13.758928.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[{"display_name":"Life below water","score":0.5769000053405762,"id":"https://metadata.un.org/sdg/14"}],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320308380","display_name":"Yale University","ror":"https://ror.org/03v76x132"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337612","display_name":"Yale Liver Center","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7203744398.pdf","grobid_xml":"https://content.openalex.org/works/W7203744398.grobid-xml"},"referenced_works_count":4,"referenced_works":["https://openalex.org/W272882622","https://openalex.org/W2115378282","https://openalex.org/W2127820364","https://openalex.org/W4313880060"],"related_works":["https://openalex.org/W3136251000","https://openalex.org/W3133530615","https://openalex.org/W6908449292","https://openalex.org/W7215042343","https://openalex.org/W4413641519","https://openalex.org/W4408058565","https://openalex.org/W3011945045","https://openalex.org/W4367054102","https://openalex.org/W4404764623","https://openalex.org/W272882622"],"abstract_inverted_index":{",":[0],"is":[1,101],"an":[2],"ecologically":[3],"important":[4],"foundation":[5],"species":[6],"and":[7,16,25,38,50,62,77,94,113,125,137],"a":[8,40,56,63],"valuable":[9],"aquaculture":[10],"organism.":[11],"To":[12],"support":[13],"genomic":[14],"studies":[15,132],"future":[17,131],"breeding":[18,136],"applications,":[19],"we":[20],"generated":[21],"PacBio":[22],"HiFi,":[23],"Illumina,":[24],"Hi-C":[26],"sequencing":[27,107],"data":[28,108],"from":[29,34,84],"wild":[30],"adult":[31],"oysters,":[32],"collected":[33],"Long":[35],"Island":[36],"Sound":[37],"assembled":[39],"chromosome-level":[41],"reference":[42,71],"genome.":[43],"The":[44,69],"final":[45],"assembly":[46,115],"spans":[47],"529.0":[48],"Mb":[49,61],"consists":[51],"of":[52,59,66,98,103,127],"10":[53],"chromosomes":[54],"with":[55],"scaffold":[57],"N50":[58,65],"55.46":[60],"contig":[64],"16.0":[67],"Mb.":[68],"resulting":[70],"genome":[72,75,100],"achieved":[73],"99.7%":[74],"completeness":[76],"reduced":[78],"duplicated":[79],"universal":[80],"single-copy":[81],"ortholog":[82],"content":[83],"18.7%":[85],"to":[86],"1.1%.":[87],"Genome":[88],"annotation":[89],"identified":[90],"33,259":[91],"protein-coding":[92],"genes":[93],"revealed":[95],"that":[96],"43.2%":[97],"the":[99,114],"composed":[102],"repetitive":[104],"elements.":[105],"All":[106],"underwent":[109],"stringent":[110],"quality":[111],"control,":[112],"results":[116],"were":[117],"validated":[118],"through":[119],"multiple":[120],"technical":[121],"evaluations.":[122],"These":[123],"dataset":[124],"resources":[126],"oyster":[128],"genomics":[129],"provided":[130],"such":[133],"as":[134],"effective":[135],"sustainable":[138],"farming.":[139]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-08-20T00:00:00"}