Data Category | Description | Organism (* US Aquaculture Species) | Source | PubMed | Link |
---|---|---|---|---|---|
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 |