{"id":"https://openalex.org/W7213318749","doi":"https://doi.org/10.64898/2026.09.10.750547","title":"From pelagic to reef: Genomic basis of morphological adaption during life-history transition in the orbicular batfish ( Platax orbicularis )","display_name":"From pelagic to reef: Genomic basis of morphological adaption during life-history transition in the orbicular batfish ( Platax orbicularis )","publication_year":2026,"publication_date":"2026-09-15","ids":{"openalex":"https://openalex.org/W7213318749","doi":"https://doi.org/10.64898/2026.09.10.750547"},"language":"en","primary_location":{"id":"doi:10.64898/2026.09.10.750547","doi":"https://doi.org/10.64898/2026.09.10.750547","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.10.750547","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/15/2026.09.10.750547.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":null,"license_id":null,"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"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/15/2026.09.10.750547.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5151517466","display_name":"Yuxuan Zhang","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Yuxuan Zhang","raw_affiliation_strings":["Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China","State Key Lab of Marine Environment Health, City University of Hong Kong, Kowloon Tong, Hong Kong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China","institution_ids":["https://openalex.org/I168719708"]},{"raw_affiliation_string":"State Key Lab of Marine Environment Health, City University of Hong Kong, Kowloon Tong, Hong Kong, China","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101745441","display_name":"Yanwen Shao","orcid":"https://orcid.org/0009-0002-4863-3504","observed_orcids":["https://orcid.org/0009-0002-4863-3504"]},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Yanwen Shao","raw_affiliation_strings":["Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100376847","display_name":"Liang Zhong","orcid":"https://orcid.org/0000-0002-4514-9074","observed_orcids":["https://orcid.org/0000-0002-4514-9074"]},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Liang Zhong","raw_affiliation_strings":["Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003632285","display_name":"Runsheng Li","orcid":"https://orcid.org/0000-0003-1563-1844","observed_orcids":["https://orcid.org/0000-0003-1563-1844"]},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Runsheng Li","raw_affiliation_strings":["Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China"],"raw_orcid":"https://orcid.org/0000-0003-1563-1844","affiliations":[{"raw_affiliation_string":"Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103284818","display_name":"Wenlong  Colin Cai","orcid":"https://orcid.org/0000-0003-0562-6363","observed_orcids":["https://orcid.org/0000-0003-0562-6363"]},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":true,"raw_author_name":"Wenlong Cai","raw_affiliation_strings":["Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China","State Key Lab of Marine Environment Health, City University of Hong Kong, Kowloon Tong, Hong Kong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China","institution_ids":["https://openalex.org/I168719708"]},{"raw_affiliation_string":"State Key Lab of Marine Environment Health, City University of Hong Kong, Kowloon Tong, Hong Kong, China","institution_ids":["https://openalex.org/I168719708"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5103284818"],"corresponding_institution_ids":["https://openalex.org/I168719708"],"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/T10268","display_name":"Developmental Biology and Gene Regulation","score":0.6693999767303467,"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/T10268","display_name":"Developmental Biology and Gene Regulation","score":0.6693999767303467,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.17900000512599945,"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/T12319","display_name":"Fish Biology and Ecology Studies","score":0.07429999858140945,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/platax-orbicularis","display_name":"Platax orbicularis","score":1.0},{"id":"https://openalex.org/keywords/metamorphosis","display_name":"metamorphosis","score":0.984000027179718},{"id":"https://openalex.org/keywords/life-history-transitions","display_name":"life-history transitions","score":0.8899999856948853},{"id":"https://openalex.org/keywords/chromosome-level-genome-assembly","display_name":"chromosome-level genome assembly","score":0.777999997138977},{"id":"https://openalex.org/keywords/comparative-genomics","display_name":"comparative genomics","score":0.7990000247955322},{"id":"https://openalex.org/keywords/developmental-reprogramming","display_name":"developmental reprogramming","score":0.7099999785423279},{"id":"https://openalex.org/keywords/cell-cycle","display_name":"cell cycle","score":0.6079999804496765},{"id":"https://openalex.org/keywords/ossification","display_name":"ossification","score":0.8420000076293945},{"id":"https://openalex.org/keywords/extracellular-matrix-remodeling","display_name":"extracellular matrix remodeling","score":0.9679999947547913},{"id":"https://openalex.org/keywords/positive-selection","display_name":"positive selection","score":0.847000002861023},{"id":"https://openalex.org/keywords/hox-genes","display_name":"Hox genes","score":0.9589999914169312},{"id":"https://openalex.org/keywords/adaptive-evolution","display_name":"adaptive evolution","score":0.6679999828338623},{"id":"https://openalex.org/keywords/teleosts","display_name":"teleosts","score":0.7459999918937683},{"id":"https://openalex.org/keywords/larval-to-juvenile-transition","display_name":"larval to juvenile transition","score":0.5339999794960022}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8636000156402588},{"id":"https://openalex.org/C136397037","wikidata":"https://www.wikidata.org/wiki/Q33753","display_name":"Metamorphosis","level":3,"score":0.8499000072479248},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.7041000127792358},{"id":"https://openalex.org/C111039654","wikidata":"https://www.wikidata.org/wiki/Q253149","display_name":"Hox gene","level":4,"score":0.6539999842643738},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6068999767303467},{"id":"https://openalex.org/C77942228","wikidata":"https://www.wikidata.org/wiki/Q191468","display_name":"Pelagic zone","level":2,"score":0.5430999994277954},{"id":"https://openalex.org/C139807058","wikidata":"https://www.wikidata.org/wiki/Q352374","display_name":"Adaptation (eye)","level":2,"score":0.5123999714851379},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.4684000015258789},{"id":"https://openalex.org/C168601633","wikidata":"https://www.wikidata.org/wiki/Q1044484","display_name":"Evolutionary developmental biology","level":2,"score":0.42910000681877136},{"id":"https://openalex.org/C153991713","wikidata":"https://www.wikidata.org/wiki/Q17142856","display_name":"Niche","level":2,"score":0.4162999987602234},{"id":"https://openalex.org/C173758957","wikidata":"https://www.wikidata.org/wiki/Q129270","display_name":"Larva","level":2,"score":0.4153999984264374},{"id":"https://openalex.org/C2776817793","wikidata":"https://www.wikidata.org/wiki/Q6553369","display_name":"Lineage (genetic)","level":3,"score":0.40849998593330383},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.40529999136924744},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.3840999901294708},{"id":"https://openalex.org/C153026981","wikidata":"https://www.wikidata.org/wiki/Q519888","display_name":"Allometry","level":2,"score":0.3815000057220459},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.3465999960899353},{"id":"https://openalex.org/C169503297","wikidata":"https://www.wikidata.org/wiki/Q961088","display_name":"Heterochrony","level":3,"score":0.33880001306533813},{"id":"https://openalex.org/C115961737","wikidata":"https://www.wikidata.org/wiki/Q1516282","display_name":"Juvenile","level":2,"score":0.30889999866485596},{"id":"https://openalex.org/C91721477","wikidata":"https://www.wikidata.org/wiki/Q778612","display_name":"Fin","level":2,"score":0.30660000443458557},{"id":"https://openalex.org/C183074962","wikidata":"https://www.wikidata.org/wiki/Q213713","display_name":"Developmental biology","level":2,"score":0.3000999987125397},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.29319998621940613},{"id":"https://openalex.org/C90856448","wikidata":"https://www.wikidata.org/wiki/Q431","display_name":"Zoology","level":1,"score":0.2840000092983246},{"id":"https://openalex.org/C62142553","wikidata":"https://www.wikidata.org/wiki/Q200312","display_name":"Convergent evolution","level":4,"score":0.2784000039100647},{"id":"https://openalex.org/C105176652","wikidata":"https://www.wikidata.org/wiki/Q1147112","display_name":"Comparative genomics","level":5,"score":0.27799999713897705},{"id":"https://openalex.org/C161078062","wikidata":"https://www.wikidata.org/wiki/Q1068690","display_name":"Functional genomics","level":5,"score":0.26249998807907104},{"id":"https://openalex.org/C37291498","wikidata":"https://www.wikidata.org/wiki/Q193603","display_name":"Ontogeny","level":2,"score":0.2621999979019165},{"id":"https://openalex.org/C19843653","wikidata":"https://www.wikidata.org/wiki/Q213907","display_name":"Model organism","level":3,"score":0.2533999979496002}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.09.10.750547","doi":"https://doi.org/10.64898/2026.09.10.750547","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.10.750547","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/15/2026.09.10.750547.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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.09.10.750547","doi":"https://doi.org/10.64898/2026.09.10.750547","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.10.750547","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/15/2026.09.10.750547.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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G5771860720","display_name":null,"funder_award_id":"7020090","funder_id":"https://openalex.org/F4320309893","funder_display_name":"City University of Hong Kong"}],"funders":[{"id":"https://openalex.org/F4320309893","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23"},{"id":"https://openalex.org/F4320319065","display_name":"Aromatic Plant Research Center","ror":"https://ror.org/05eebgw43"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7213318749.pdf","grobid_xml":"https://content.openalex.org/works/W7213318749.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2268825415","https://openalex.org/W4362721149","https://openalex.org/W2395916326","https://openalex.org/W3013819449","https://openalex.org/W2811191634","https://openalex.org/W2000275880","https://openalex.org/W2943872042","https://openalex.org/W3215571824","https://openalex.org/W4393111939","https://openalex.org/W4385067636"],"abstract_inverted_index":{"Abstract":[0],"Metamorphosis":[1],"enables":[2],"teleosts":[3],"to":[4],"transition":[5],"between":[6],"ecological":[7,92],"niches,":[8],"driving":[9],"lineage-specific":[10],"morphological":[11],"innovations.":[12],"The":[13],"orbicular":[14,199],"batfish":[15],"(":[16,127,133,142,165],"Platax":[17],"orbicularis)":[18],"exemplifies":[19],"this,":[20],"transforming":[21],"from":[22],"a":[23,27,38,60],"pelagic":[24],"larva":[25],"into":[26,189],"reef-associated":[28],"juvenile":[29],"with":[30,45,51,91],"extreme":[31],"allometric":[32],"fin":[33,99,117,181],"elongation.":[34,118],"Here,":[35],"we":[36,54],"generated":[37],"chromosome-level":[39],"genome":[40],"assembly":[41],"of":[42,77,84,97,110,160,196,205],"715.46":[43],"Mb,":[44],"99.4%":[46],"completeness.":[47],"Integrating":[48],"comparative":[49],"genomics":[50],"tissue-specific":[52],"transcriptomics,":[53],"demonstrate":[55],"that":[56],"such":[57],"transformation":[58],"is":[59],"systemic":[61],"process":[62],"shaped":[63],"by":[64,107],"both":[65],"long-term":[66],"evolutionary":[67,191],"adaptation":[68],"and":[69,81,86,129,135,138,144,153,193,201,208],"short-term":[70],"developmental":[71,114,178],"reprogramming.":[72],"Comparative":[73],"analyses":[74],"revealed":[75],"expansion":[76],"development-related":[78],"gene":[79],"families":[80],"significant":[82],"evolution":[83,207],"immune-":[85],"sensory-related":[87],"families,":[88],"likely":[89],"associated":[90],"niche":[93],"transition.":[94],"Spatiotemporal":[95],"clustering":[96],"metamorphosing":[98],"transcriptomes":[100],"identified":[101],"rapid":[102],"cell":[103,125],"cycle":[104,126],"activation":[105],"accompanied":[106],"sustained":[108],"suppression":[109],"basal":[111],"metabolism,":[112],"indicating":[113],"trade-offs":[115],"during":[116],"Several":[119],"differentially":[120,175],"expressed":[121],"genes":[122],"involved":[123],"in":[124,180,198,211],"ankfn1":[128],"mcph1":[130],"),":[131,137],"ossification":[132],"cyp24a1":[134],"sema4d":[136],"extracellular":[139],"matrix":[140],"remodeling":[141],"sdc4":[143],"serpine1":[145],")":[146,173],"exhibited":[147],"positive":[148],"selection,":[149],"suggesting":[150],"coordinated":[151],"regulatory":[152],"protein-level":[154],"adaptation.":[155],"Among":[156],"an":[157],"extensive":[158],"repertoire":[159],"49":[161],"hox":[162],"genes,":[163],"four":[164],"hoxb6b":[166],",":[167,169,171],"hoxc8a":[168],"hoxd9b":[170],"hoxd10a":[172],"were":[174],"expressed,":[176],"implicating":[177],"regulators":[179],"remodeling.":[182],"Together,":[183],"our":[184],"findings":[185],"offer":[186],"new":[187],"insights":[188],"the":[190,203],"context":[192],"molecular":[194],"mechanisms":[195],"metamorphosis":[197,209],"batfish,":[200],"advance":[202],"understanding":[204],"adaptive":[206],"innovations":[210],"teleosts.":[212]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-09-16T00:00:00"}