release-updates
Data CategoryDescriptionOrganism (* US Aquaculture Species)SourcePubMedLink

Assembly

Genome Assembly Astyanax mexicanus (Mexican tetra/Mexican cavefish) AstMex3_surface Warren et al. - PubMed 33664263 NCBI FTP
Clupea harengus (Atlantic herring) Ch_v2.0.2 Pettersson et al. - PubMed 31649060 NCBI FTP
Coregonus clupeaformis (Lake whitefish) ASM2061545v1 Mérot et al. - PubMed 35416336 NCBI FTP
Crassostrea gigas (Pacific oyster)* cgigas_uk_roslin_v1 Peñaloza et al. - PubMed 33764468 NCBI FTP
Crassostrea virginica (Eastern oyster)* C_virginica-3.0 Gómez-Chiarri et al. - PubMed 25982405 NCBI FTP
Danio rerio (Zebrafish) GRCz11 Howe et al. - PubMed 23594743 NCBI FTP
Drosophila melanogaster (Fruit fly) Release_6_plus_ISO1_MT Hoskins et al. - PubMed 25589440 NCBI FTP
Esox lucius (Northern pike) Eluc_v4 Rondeau et al. - PubMed 25069045 NCBI FTP
Etheostoma cragini (Arkansas darter) CSU_Ecrag_1.0 Reid et al. - PubMed 33058399 NCBI FTP
Gadus morhua (Atlantic cod) gadMor3.0 Tørresen et al. - PubMed 28100185 NCBI FTP
Gasterosteus aculeatus aculeatus (Three-spined stickleback) GAculeatus_UGA_version5 Nath et al. - PubMed 33598708 NCBI FTP
Haliotis rufescens (Red abalone)* xgHalRufe1.0.p Griffiths et al. - PubMed 36190478 NCBI FTP
Hippoglossus hippoglossus (Atlantic halibut) fHipHip1.pri Einfelt et al. - PubMed 33655659 NCBI FTP
Hippoglossus stenolepis (Pacific halibut) HSTE1.2 Jasonowicz et al. - PubMed 35569134 NCBI FTP
Homarus americanus (American lobster) GMGI_Hamer_2.0 Polinski et al. - PubMed 34162536 NCBI FTP
Homo sapiens (Human) T2T-CHM13v2.0 Nurk et al. - PubMed 35357919 NCBI FTP
Ictalurus punctatus (Channel catfish)* IpCoco_1.2 Liu et al. - PubMed 27249958 NCBI FTP
Lepisosteus oculatus (spotted gar) LepOcu1 Braasch et al. - PubMed 26950095 NCBI FTP
Lottia gigantea (Owl limpet) Helro1 Simakov et al. - PubMed 23254933 NCBI FTP
Mercenaria mercenaria (Northern quahog) ASM1480567v1.1 Song et al. - PubMed 33487168 NCBI FTP
Micropterus salmoides (Largemouth bass) ASM1485139v1 Sun et al. - PubMed 32985096 NCBI FTP
Morone saxatilis (Striped sea bass)* NCSU_SB_2.0 Not published. North Carolina State University NCBI FTP
Mugil cephalus (Flathead mullet/Striped mullet) CIBA_Mcephalus_1.1 Shekhar et al. - PubMed 35783261 NCBI FTP
Oncorhynchus gorbuscha (Pink salmon) OgorEven_v1.0 Christensen et al. - PubMed 34919547 NCBI FTP
Oncorhynchus keta (Chum salmon) Oket_V1 Rondeau EB et al. - bioRxiv 2021.12.27.474290 NCBI FTP
Oncorhynchus kisutch (Coho salmon)* Okis_V2 Kim et al. - PubMed 26614614 NCBI FTP
Oncorhynchus mykiss (Rainbow trout)* USDA_OmyKA_1.1 Gao et al. - PubMed 33616628 NCBI FTP
Oncorhynchus nerka (Sockeye salmon) Oner_1.0 Christensen et al. - PubMed 33119641 NCBI FTP
Oncorhynchus tshawytscha (Chinook salmon) Otsh_v2.0 Christensen et al. - PubMed 29621340 NCBI FTP
Oreochromis niloticus (Nile tilapia)* O_niloticus_UMD_NMBU Conte et al. - PubMed 30942871 NCBI FTP
Penaeus monodon (Giant tiger prawn)* NSTDA_Pmon_1 Van Quyen et al. - PubMed 32033920 NCBI FTP
Penaeus vannamei (Pacific white shrimp)* ASM378908v1 Zhang et al. - PubMed 30664654 NCBI FTP
Perca flavescens (Yellow perch)* PFLA_1.0 Feron et al. - PubMed 31903688 NCBI FTP
Procambarus clarkii (Red swamp crawfish) ASM2042438v2 Xu et al. - PubMed 34303807 NCBI FTP
Salmo salar (Atlantic salmon)* Ssal_v3.1 Lien et al. - PubMed 27088604 NCBI FTP
Salvelinus sp. IW2-2015 (Salvelinus fish) ASM291031v2 Christensen et al. - PubMed 30212580 (retracted)
Christensen et al. - PubMed 33561157
NCBI FTP
Seriola dumerili (Greater amberjack) Sdu_1.0 Araki et al. - PubMed 29785397 NCBI FTP
Seriola lalandi dorsalis (Calfornia amberjack/Yellowtail amberjack)* Sedor1 Purcell et al. - 29310588 NCBI FTP
Xiphias gladius (Swordfish) ASM1685928v1 Wu et al. - PubMed 33533895 NCBI FTP

Genes

NCBI Genes (RefSeq) Astyanax mexicanus NCBI Astyanax mexicanus Annotation Release 103; 21-July-2022 Li et al. - PubMed 33270901 NCBI FTP
Clupea harengus NCBI Clupea harengus Annotation Release 102; 27-July-2021 NCBI FTP
Coregonus clupeaformis NCBI Coregonus clupeaformis Annotation Release 101; 30-November-2021 NCBI FTP
Crassostrea gigas NCBI Crassostrea gigas Annotation Release 102; 04-May-2020 NCBI FTP
Crassostrea virginica NCBI Crassostrea virginica Annotation Release 100; 14-September-2017 NCBI FTP
Danio rerio NCBI Danio rerio Annotation Release 106; 26-June-2017 NCBI FTP
Drosophila melanogaster Annotation for GCF_000001215.4 Release 6 plus ISO1 MT; 2021/10/02 NCBI FTP
Esox lucius NCBI Esox lucius Annotation Release 103; 10-May-2019 NCBI FTP
Etheostoma cragini NCBI Etheostoma cragini Annotation Release 100; 04-June-2020 NCBI FTP
Gadus morhua NCBI Gadus morhua Annotation Release 100; 13-August-2019 NCBI FTP
Gasterosteus aculeatus aculeatus NCBI Gasterosteus aculeatus Annotation Release 100; 18-March-2021 NCBI FTP
Haliotis rufescens NCBI Haliotis rufescens Annotation Release 101; 26-May-2022 NCBI FTP
Hippoglossus hippoglossus NCBI Hippoglossus hippoglossus Annotation Release 100; 20-May-2020 NCBI FTP
Hippoglossus stenolepis NCBI Hippoglossus stenolepis Annotation Release 101; 04-April-2022 NCBI FTP
Homarus americanus NCBI Homarus americanus Annotation Release 100; 17-July-2021 NCBI FTP
Homo sapiens NCBI Homo sapiens Annotation Release 110; 06-April-2022 NCBI FTP
Ictalurus punctatus NCBI Ictalurus punctatus Annotation Release 100; 06-July-2016 NCBI FTP
Lepisosteus oculatus NCBI Lepisosteus oculatus Annotation Release 101; 08-January-2016 NCBI FTP
Lottia gigantea Annotation for GCF_000327385.1 Helro1; 2020/10/14 NCBI FTP
Mercenaria mercenaria Mercenaria mercenaria Annotation Release 100.20221206; 07-December-2022 NCBI FTP
Micropterus salmoides NCBI Micropterus salmoides Annotation Release 100; 30-December-2020 NCBI FTP
Morone saxatilis NCBI Morone saxatilis Annotation Release 100; 27-July-2020 NCBI FTP
Mugil cephalus NCBI Mugil cephalus Annotation Release 100; 07-April-2022 NCBI FTP
Oncorhynchus gorbuscha NCBI Oncorhynchus gorbuscha Annotation Release 100; 02-February-2022 NCBI FTP
Oncorhynchus keta NCBI Oncorhynchus keta Annotation Release 100; 08-August-2020 NCBI FTP
Oncorhynchus kisutch NCBI Oncorhynchus kisutch Annotation Release 101; 09-December-2019 NCBI FTP
Oncorhynchus mykiss NCBI Oncorhynchus mykiss Annotation Release 101; 30-October-2020 NCBI FTP
Oncorhynchus nerka NCBI Oncorhynchus nerka Annotation Release 100; 01-July-2019 NCBI FTP
Oncorhynchus tshawytscha NCBI Oncorhynchus tshawytscha Annotation Release 101; 08-July-2021 NCBI FTP
Oreochromis niloticus NCBI Oreochromis niloticus Annotation Release 104; 26-July-2018 NCBI FTP
Penaeus monodon NCBI Penaeus monodon Annotation Release 100; 24-November-2020 NCBI FTP
Penaeus vannamei NCBI Penaeus vannamei Annotation Release 100; 14-December-2018 NCBI FTP
Perca flavescens NCBI Perca flavescens Annotation Release 100; 01-April-2019 NCBI FTP
Procambarus clarkii NCBI Procambarus clarkii Annotation Release 100; 11-January-2022 NCBI FTP
Salmo salar NCBI Salmo salar Annotation Release 102; 07-January-2022 NCBI FTP
Salvelinus alpinus NCBI Salvelinus alpinus Annotation Release 101; 25-February-2018 NCBI FTP
Seriola dumerili NCBI Seriola dumerili Annotation Release 100; 05-October-2017 NCBI FTP
Seriola lalandi dorsalis NCBI Seriola lalandi dorsalis Annotation Release 100; 26-December-2017 NCBI FTP
Xiphias gladius NCBI Xiphias gladius Annotation Release 100; 18-March-2021 NCBI FTP
Ensembl Genes Clupea harengus Ensembl Release 109; February 2023 Martin et al. - PubMed 36318249 Ensembl FTP
Danio rerio Ensembl FTP
Esox lucius Ensembl FTP
Gadus morhua Ensembl FTP
Ictalurus punctatus Ensembl FTP
Lepisosteus oculatus Ensembl FTP
Oncorhynchus kisutch Ensembl FTP
Oncorhynchus mykiss Ensembl FTP
Oreochromis niloticus Ensembl FTP
Salmo salar Ensembl FTP
Seriola dumerili Ensembl FTP
Seriola lalandi dorsalis Ensembl FTP
Crassotrea gigas Ensembl Metazoa Release 56; February 2023 Ensembl FTP
Lottia gigantea Ensembl FTP
Hippoglossus hippoglossus Ensembl Rapid Release 2022_03 Ensembl FTP
Homo sapiens Ensembl Rapid Release 2022_07 Ensembl FTP
Oncorhynchus nerka Ensembl Rapid Release 2020_06 Ensembl FTP

Homology

Orthologues and paralogues from Ensembl Compara Astyanax mexicanus
Clupea harengus
Danio rerio
Esox lucius
Gadus morhua
Homo sapiens
Ictalurus punctatus
Oncorhynchus kisutch
Oncorhynchus mykiss
Oreochromis niloticus
Salmo salar
Seriola dumerili
Seriola lalandi dorsalis
Ensembl Compara; Ensembl Release 109; February 2023 Martin et al. - PubMed 36318249 Ensembl BioMart
Clusters of Orthologues from AquaMine All species AquaMine-Ortho v1.2; Feb 2023 Not yet published AquaMine Download
Clusters of Orthologues from OrthoDB Astyanax mexicanus
Clupea harengus
Crassostrea gigas
Crassostrea virginica
Danio rerio
Esox lucius
Homo sapiens
Ictalurus punctatus
Lottia gigantea
Oncorhynchus kisutch
Oncorhynchus mykiss
Oncorhynchus tshawytscha
Salmo salar
Salvelinus sp. IW2-2015
Seriola dumerili
Seriola lalandi dorsalis
OrthoDB Release 10.1; 21 January 2020 Zdobnov et al. - PubMed 33196836 OrthoDB Download
Recriprocal Best Hits All species AquaMine-RBH v1.2; May 2023 Not yet published AquaMine Download

Proteins

Protein annotation from Uniprot (number of proteins shown in parentheses) Astyanax mexicanus (113477)
Clupea harengus (41068)
Coregonus clupeaformis (120)
Crassostrea gigas (83441)
Crassostrea virginica (50432)
Danio rerio (47704)
Drosophila melanogaster (42762)
Esox lucius (72462)
Etheostoma cragini (39)
Gadus morhua (63307)
Gasterosteus aculeatus aculeatus (8)
Haliotis rufescens (173)
Hippoglossus hippoglossus (215)
Hippoglossus stenolepis (50)
Homarus americanus (24677)
Homo sapiens (207780)
Ictalurus punctatus (45715)
Lepisosteus oculatus (22599)
Lottia gigantea (23776)
Mercenaria mercenaria (68)
Micropterus salmoides (332)
Morone saxatilis (200)
Mugil cephalus (440)
Oncorhynchus gorbuscha (446)
Oncorhynchus keta (326)
Oncorhynchus kisutch (115693)
Oncorhynchus mykiss (165231)
Oncorhynchus nerka (218)
Oncorhynchus tshawytscha (96680)
Oreochromis niloticus (75978)
Penaeus monodon (854)
Penaeus vannamei (26428)
Perca flavescens (22044)
Procambarus clarkii (904)
Salmo salar (86907)
Salvelinus sp. IW2-2015 (1094)
Seriola dumerili (32505)
Seriola lalandi dorsalis (33062)
Xiphias gladius (261)
UniProt release 2023_02 UniProt Consortium - PubMed 36408920 UniProt FTP

Gene Ontology

Gene Ontology Annotations All species AquaMine-GO-Annotation v1.2; May 2023 Not yet published AquaMine Download
Clupea harengus
Danio rerio
Esox lucius
Gadus morhua
Ictalurus punctatus
Lepisosteus oculatus
Oncorhynchus kisutch
Oncorhynchus mykiss
Oreochromis niloticus
Salmo salar
Seriola dumerili
Seriola lalandi dorsalis
Ensembl Release 109; February 2023 Martin et al. - PubMed 36318249 Ensembl BioMart
Crassotrea gigas
Lottia gigantea
Ensembl Metazoa Release 56; February 2023 Ensembl Metazoa BioMart
See UniProt Protein List UniProt release 2023_02 UniProt Consortium - PubMed 36408920 UniProt FTP
Gene Ontology Gene Ontology Consortium GO release 2023-05-10 Gene Ontology Consortium - PubMed 36866529 GOC Download

Pathways

Pathway information from KEGG Astyanax mexicanus
Crassostrea gigas
Danio rerio
Drosophila melanogaster
Esox lucius
Gasterosteus aculeatus aculeatus
Hippoglossus hippoglossus
Homarus americanus
Homo sapiens
Ictalurus punctatus
Lottia gigantea
Micropterus salmoides
Oncorhynchus mykiss
Oncorhynchus tshawytscha
Oreochromis niloticus
Penaeus vannamei
Perca flavescens
Salmo salar
Salvelinus alpinus
Seriola dumerili
Seriola lalandi dorsalis
Xiphias gladius
KEGG Release 105.0; January 1, 2023 Kanehisha et al. - PubMed 36300620 KEGG Download
Pathway Information from Reactome Danio rerio
Drosophila melanogaster
Homo sapiens
Reactome Version 83; December 7, 2022 Gillespie et al. - PubMed 34788843 Reactome Download

Gene Expression

RNA-seq based Gene Expression Levels Haliotis rufescens PRJNA488641 Masonbrink et al. - PubMed 30657886 NCBI BioProject
Oncorhynchus kisutch PRJNA292718 Kim et al. - PubMed 26614614 NCBI BioProject
Oncorhynchus mykiss PRJNA389609 Salem et al. - PubMed 25793877 NCBI BioProject
PRJEB37848 NCBI BioProject
Oreochromis niloticus PRJNA78915 Brawand et al. - PubMed 25186727 NCBI BioProject
Penaeus monodon PRJNA421400 Huerlimann et al. - PubMed 30202061 NCBI BioProject
Salmo salar PRJNA470665 Mohamed et al. - PubMed 30271423 NCBI BioProject
PRJNA260929 Lien et al - PubMed 27088604 NCBI BioProject

Variation

Single Nucelotide Variants from EVA Oncorhynchus mykiss European Variation Archive RS Release 4; 21 Nov 2022 Cezard et al. - PubMed 34718739 EVA Download
Oreochromis niloticus EVA Download
Seriola dumerili EVA Download

Publications

A mapping from genes to publications Crassostrea gigas
Crassostrea virginica
Ictalurus punctatus
Morone saxatilis
Oncorhynchus kisutch
Oncorhynchus mykiss
Oreochromis niloticus
Penaeus monodon
Penaeus vannamei
Perca flavescens
Salmo salar
Salvelinus alpinus
Seriola lalandi dorsalis
NCBI PubMed Sayers et al. - PubMed 36370100 NCBI PubMed FTP