Table 1 Current reference genome assemblies of important U.S. aquaculture species published through NCBI GenBank®. An asterisk (*) indicates the assembly is presently included in the data mining system AquaMine (v1.2; https://aquamine.elsiklab.missouri.edu/; Elsik Lab, University of Missouri) or planned for the next release (**)

Anoplopoma fimbria**

Sablefish

Afim_UVic_2022

GCA_027596085.2

Flores et al., 2023 [31]

Clupea harengus*

Atlantic herring

Ch_v2.0.2

GCA_900700415.2

Pettersson et al., 2019 [42]

Coregonus clupeaformis*

Lake whitefish

ASM2061545v1

GCA_020615455.1

Mérot et a. 2023 [43]

Crassostrea virginica*

Eastern oyster

C_virginica-3.0

GCA_002022765.4

Gómez-Chiarri et al., 2015 [44]

Esox lucius*

Northern pike

Eluc_v4

GCA_004634155.1

Rondeau et al., 2014 [45]

Esox lucius**

Northern pike

fEsoLuc1.pri

GCA_011004845.1

Rhie et al., 2021 [46]

Etheostoma cragini*

Arkansas darter

CSU_Ecrag_1.0

GCA_013103735.1

Reid et al., 2021 [47]

Gadus morhua*

Atlantic cod

gadMor3.0

GCA_902167405.1

Tørresen et al., 2017 [48]

Haliotis rufescens*

Red abalone

xgHalRufe1.0.p

GCA_023055435.1

Griffiths et al., 2022 [49]

Hippoglossus hippoglossus*

Atlantic halibut

fHipHip1.pri

GCA_009819705.1

Einfeldt et al., 2021 [50]

Hippoglossus stenolepis*

Pacific halibut

HSTE1.2

GCA_022539355.2

Jasonowicz et al., 2022 [51]

Homarus americanus*

American lobster

GMGI_Hamer_2.0

GCA_018991925.1

Polinski et al., 2021 [52]

Ictalurus furcatus**

Blue catfish

Billie_1.0

GCA_023375685.2

Waldbieser et al., 2023 [40]

Ictalurus punctatus*

Channel catfish

IpCoco_1.2

GCA_001660625.2

Liu et al., 2016 [39]

Ictalurus punctatus**

Channel catfish

Coco_2.0

GCA_001660625.3

Waldbieser et al., 2023 [40]

Lampris incognitus**

Smalleye Pacific opah

fLamInc1.hap2

GCA_029633865.1

Rhie et al., 2021 [46]

Lepisosteus oculatus*

Spotted gar

LepOcu1

GCA_040954835.1

Braasch et al., 2016 [53]

Magallana gigas*

Pacific oyster

cgigas_uk_roslin_v1

GCA_902806645.1

Peñaloza et al., 2021 [32]

Magallana gigas**

Pacific oyster

xbMagGiga1.1

GCA_963853765.1

Mrowicki et al., 2024 [33]

Mercenaria mercenaria*

Hard Clam/Northern quahog

ASM1480567v1.1

GCA_014805675.2

Song et al., 2021 [54]

Mercenaria mercenaria**

Hard Clam/Northern quahog

MADL_Memer_1

GCA_021730395.1

Farhat et al. 2022 [55]

Micropterus salmoides*

Largemouth bass

ASM1485139v1

GCA_014851395.1

Sun et al., 2021 [56]

Misgurnus anguillicaudatus**

Pond loach

HAU_Mang_1.0

GCA_027580225.1

Sun et al., 2023 [57]

Morone saxatilis*

Striped bass

NCSU_SB_2.0

GCA_004916995.1

Not published. NCSU, Raleigh, NC

Mugil cephalus*

Flathead mullet/Striped mullet

CIBA_Mcephalus_1.1

GCA_022458985.1

Shekhar et al., 2022 [58]

Oncorhynchus gorbuscha*

Pink salmon

OgorEven_v1.0

GCA_021184085.1

Christensen et al., 2021 [59]

Oncorhynchus keta*

Chum salmon

Oket_V1

GCA_012931545.1

Rondeau et al., 2021 [60]

Oncorhynchus keta**

Chum salmon

Oket_V2

GCA_023373465.1

Rondeau et al., 2023 [61]

Oncorhynchus kisutch*

Coho salmon

Okis_V2

GCA_002021735.2

Kim et al., 2016 [62]

Oncorhynchus mykiss*

Rainbow trout

USDA_OmyKA_1.1

GCA_013265735.3

Gao et al., 2021 [38]

Oncorhynchus nerka*

Sockeye salmon

Oner_1.0

GCA_006149115.2

Christensen et al., 2020 [63]

Oncorhynchus nerka**

Sockeye salmon

Oner_Uvic_2.0

GCA_034236695.1

Christensen et al., 2020 [63]

Oncorhynchus tshawytscha*

Chinook salmon

Otsh_v2.0

GCA_018296145.1

Christensen et al., 2018 [64]

Oreochromis niloticus*

Nile tilapia

O_niloticus_UMD_NMBU

GCA_001858045.3

Conte et al., 2019 [65]

Ostrea edulis**

European oyster

xbOstEdul1.1

GCA_947568905.1

Gundappa et al., 2022 [66]

Penaeus monodon*

Giant tiger prawn

NSTDA_Pmon_1

GCA_015228065.1

Van Quyen et al., 2020 [67]

Penaeus vannamei*

Pacific white shrimp

ASM378908v1

GCA_003789085.1

Zhang et al., 2019 [68]

Perca flavescens*

Yellow perch

PFLA_1.0

GCA_004354835.1

Feron et al., 2020 [69]

Procambarus clarkii*

Red swamp crawfish

ASM2042438v2

GCA_020424385.2

Xu et al., 2021 [70]

Ruditapes philippinarum**

Manila clam

ASM2657151v2

GCA_026571515.2

Xu et al., 2022 [71]

Salmo salar*

Atlantic salmon (European)

Ssal_v3.1

GCA_905237065.2

Lien et al., 2016 [72]

Salmo salar

Atlantic salmon (N. American)

USDA_NASsal_1.1

GCA_021399835.1

Gao et al., 2023 [35]

Salvelinus fontinalis**

Brook trout

ASM2944872v1

GCA_029448725.1

Pasquier et al., 2016 [73]

Seriola dumerili*

Greater amberjack

Sdu_1.0

GCA_002260705.1

Araki et al., 2018 [74]

Seriola lalandi dorsalis*

California yellowtail

Sedor1

GCA_002814215.1

Purcell et al., 2018 [75]

Syngnathus scovelli**

Gulf pipefish

RoL_Ssco_1.1

GCA_024217435.4

Ramesh et al., 2023 [76]

Thunnus albacares**

Yellowfin tuna

fThuAlb1.1

GCA_914725855.1

Ciezarek et al., 2016 [77]

Trachinotus carolinus

Florida pompano

FAU_TrCaro_1

GCA_040938265.1

Not published. FAU, Boca Raton, FL

Xiphias gladius*

Swordfish

ASM1685928v1

GCA_016859285.1

Wu et al., 2021 [78]