Genomes - Applied Genomics Initiative

Reference genomes are the core resource for detailed analysis of population and functional genomics. By capturing a representative genome for a species, all further individuals can be assessed relative to the reference and each genome starts a research journey. Different quality genome assemblies can deliver to different needs and not every species requires chromosome length assemblies.

Scientific name	Common name	Class	Output domain	Assembly status	Assembly level	Contact
Acanthaster planci	Crown-of-thorns starfish	Asteroidea	Environment	Coming soon	Chromosome	David Beale
Achroia grisella	Lesser Wax Moth	Insecta	Environment	Coming soon	Scaffold	Gene Wijffels
Acropora hyacinthus	Coral	Anthozoa	Environment	Coming soon	Scaffold	UQ
Aedes aculeatus	Pointy mosquito	Insecta	Health	Coming soon	Contig	AGI Team
Aedes burpengaryensis	Mosquito	Insecta	Health	Coming soon	Contig	AGI Team
Aedes camptorhynchus	Southern saltmarsh mosquito	Insecta	Health	Data generation	Scaffold	AGI Team
Aedes candidoscutellum	Mosquito	Insecta	Health	Coming soon	Contig	AGI Team
Aedes eidsvoldensis	Mosquito	Insecta	Health	Coming soon	Contig	AGI Team
Aedes flavifrons	Mosquito	Insecta	Health	Coming soon	Contig	AGI Team
Aedes imperfectus	Mosquito	Insecta	Health	Coming soon	Contig	AGI Team
Aedes keefei	Mosquito	Insecta	Health	Coming soon	Contig	AGI Team
Aedes kochi	Mosquito	Insecta	Health	Coming soon	Contig	AGI Team
Aedes notoscriptus	Australian backyard mosquito	Insecta	Health	Data generation	Scaffold	AGI Team
Aedes palmarum	Mosquito	Insecta	Health	Coming soon	Contig	AGI Team
Aedes quinquelineatus	Mosquito	Insecta	Health	Coming soon	Contig	AGI Team
Aedes rubrithorax	Mosquito	Insecta	Health	Coming soon	Contig	AGI Team
Aedes sp. Marks #51	Mosquito	Insecta	Health	Coming soon	Contig	AGI Team
Aedes sp. Marks #85	Mosquito	Insecta	Health	Coming soon	Contig	AGI Team
Aedes vigilax	Saltmarsh mosquito	Insecta	Health	Data generation	Scaffold	AGI Team
Aedes wasselli	Mosquito	Insecta	Health	Coming soon	Contig	AGI Team
Ambassis agassizii	Olive Perchlet	Actinopterygii	Environment	Coming soon	Contig	AGI Team
Anopheles annulipes	Mosquito	Insecta	Health	Coming soon	Contig	AGI Team
Anopheles colledgei	Mosquito	Insecta	Health	Coming soon	Contig	AGI Team
Anopheles corethroides	Mosquito	Insecta	Health	Coming soon	Contig	AGI Team
Anopheles farauti	Mosquito	Insecta	Health	Data generation	Contig	Nigel Beebe
Anopheles pseudostigmaticus	Mosquito	Insecta	Health	Coming soon	Contig	AGI Team
Anopheles stigmaticus	Mosquito	Insecta	Health	Data generation	Contig	AGI Team
Anoplolepis gracilipes	Yellow Crazy Ant	Insecta	Health	Data generation	Contig	Ben Hoffmann
Apis mellifera	European honey bee	Insecta	Ecotoxicology	Coming soon	Contig	Angel Popa
Bactrocera albistrigata	White striped fruit fly	Insecta	Biosecurity	Data generation	Contig	Ronald Lee
Bactrocera aquilonis	Northern Territory fruit fly	Insecta	Biosecurity	Coming soon	Scaffold	Ronald Lee
Bactrocera dorsalis	Oriental fruit fly	Insecta	Biosecurity	Assembled	Scaffold	Ronald Lee
Bactrocera frauenfeldi	Mango fruit fly	Insecta	Biosecurity	Assembled	Scaffold	Ronald Lee
Bactrocera jarvisi	Jarvis’ fruit fly	Insecta	Biosecurity	Coming soon	Chromosome	Ronald Lee
Bactrocera kraussi	Krauss’s fruit fly	Insecta	Biosecurity	Assembled	Scaffold	Ronald Lee
Bactrocera neohumeralis	Lesser Queensland fruit fly	Insecta	Biosecurity	Assembled	Chromosome	Ronald Lee
Bactrocera pallida		Insecta	Biosecurity	Assembled	Scaffold	Ronald Lee
Bactrocera tryoni	Queensland fruit fly	Insecta	Biosecurity	Assembled	Chromosome	Ronald Lee
Bemisia tabaci	Silverleaf whitefly	Insecta	Biosecurity	Data generation	Contig	AGI team
Bidyanus bidyanus	Silver perch	Actinopterygii	Conservation	Coming soon	Contig	AGI Team
Brachymyrmex obscurior	Ant	Insecta	Biosecurity	Coming soon	Contig	Ben Hoffmann
Calliphora hilli	Blow fly	Insecta	Agriculture	Assembled	Contig	Angela McGaughran
Calliphora stygia	Brown blowfly	Insecta	Agriculture	Assembled	Contig	Angela McGaughran
Calliphora vicina	Blue bottle fly	Insecta	Agriculture	Assembled	Contig	Angela McGaughran
Carassius auratus	Gold fish	Actinopterygii	Environment	Coming soon	Contig	AGI Team
Centroberyx affinis	Redfish	Actinopterygii	Environment	Coming soon	Contig	AGI Team
Centroberyx gerrardi	Bight Redfish	Actinopterygii	Environment	Coming soon	Contig	AGI Team
Ceratitis capitata	Mediterranean fruit fly	Insecta	Biosecurity	Coming soon	Contig	AGI Team
Ceriodaphnia dubia	Water flea	Branchiopoda	Ecotoxicology	Public	Contig	Anu Kumar
Chironomus tepperi	Bloodworm	Insecta	Ecotoxicology	Public	Scaffold	Anu Kumar
Chlorella sp.	Algae		Ecotoxicology	Coming soon	Contig	Lisa Golding
Conopomorpha cramerella	Cocoa pod borer	Insecta	Biosecurity	Coming soon	Scaffold	Mars
Coquillettidia xanthogaster	Mosquito	Insecta	Health	Coming soon	Contig	AGI Team
Craterocephalus amniculus	Darling River hardyhead	Actinopterygii	Environment	Coming soon	Contig	AGI Team
Craterocephalus fluviatilis	Murray hardyhead	Actinopterygii	Conservation	Coming soon	Contig	AGI Team
Craterocephalus stercusmuscarum fulvus	Unspecked hardyhead	Actinopterygii	Conservation	Coming soon	Contig	AGI Team
Creontiades dilutus	Green mirid	Insecta	Agriculture	Coming soon	Scaffold	AGI Team
Culex annulirostris	Common banded mosquito	Insecta	Health	Data generation	Chromosome	AGI Team
Culex douglasi	Mosquito	Insecta	Health	Coming soon	Contig	AGI Team
Culex insequens	Mosquito	Insecta	Health	Coming soon	Contig	AGI Team
Culex pseudomelanoconia	Mosquito	Insecta	Health	Coming soon	Contig	AGI Team
Culiseta frenchii	Mosquito	Insecta	Health	Coming soon	Contig	AGI Team
Cyprinus carpio	European carp	Actinopterygii	Environment	Coming soon	Contig	AGI Team
Daphnia carinata		Branchiopoda	Ecotoxicology	Public	Scaffold	Anu Kumar
Dasyuroides byrnei	Marsupial rat	Mammalia	Conservation	Coming soon	Scaffold	Denis-Bauer
Dermolepida albohirtum	Cane beetle	Insecta	Agriculture	Coming soon	Scaffold	AGI Team
Diuraphis noxia	Russian wheat aphid	Insecta	Biosecurity	Coming soon	Contig	AGI Team
Dixella humeralis	Mosquito	Insecta	Environment	Coming soon	Contig	AGI Team
Emydura macquarii	Murray River turtle	Reptilia	Ecotoxicology	Awaiting release	Scaffold	David Beale
Felis catus	Domestic cat	Mammalia	Biosecurity	Coming soon	Contig	AGI Team
Gadopsis bispinosus	Two-spined blackfish	Actinopterygii	Environment	Coming soon	Contig	AGI Team
Gadopsis marmoratus	Southern river blackfish	Actinopterygii	Environment	Coming soon	Contig	AGI Team
Gadopsis marmoratus	Northern river blackfish	Actinopterygii	Environment	Coming soon	Contig	AGI Team
Galaxias arcanus	Riffle galaxias	Actinopterygii	Environment	Coming soon	Contig	AGI Team
Galaxias brevipinnis	Climbing galaxias	Actinopterygii	Environment	Coming soon	Contig	AGI Team
Galaxias fuscus	Barred galaxias	Actinopterygii	Conservation	Coming soon	Contig	AGI Team
Galaxias olidus	Mountain galaxias	Actinopterygii	Environment	Coming soon	Contig	AGI Team
Galaxias oliros	Obscure galaxias	Actinopterygii	Environment	Coming soon	Contig	AGI Team
Galaxias rostratus	Flathead galaxias	Actinopterygii	Environment	Coming soon	Contig	AGI Team
Galleria mellonella	Greater wax moth	Insecta	Circular economy	Assembled	Scaffold	Gene Wijffels
Gambusia holbrooki	Eastern gambusia	Actinopterygii	Environment	Coming soon	Contig	AGI Team
Gastrolobium bilobum	Heart-leaved poison	Magnoliopsida	Biosecurity	Data generation	Scaffold	CSIRO
Gastrolobium calycinum	York Road Poison	Magnoliopsida	Biosecurity	Data generation	Scaffold	CSIRO
Gastrolobium parviflorum	Box poison	Magnoliopsida	Biosecurity	Data generation	Scaffold	CSIRO
Gastrolobium spinosum	Prickly poison	Magnoliopsida	Biosecurity	Data generation	Scaffold	CSIRO
Gastrolobium villosum	Crinkle-leaved Poison	Magnoliopsida	Biosecurity	Data generation	Scaffold	CSIRO
Geotria australis	Pouched lamprey	Hyperoartia	Environment	Coming soon	Contig	AGI Team
Helicoverpa armigera	Cotton bollworm	Insecta	Agriculture	Assembled	Scaffold	AGI Team
Helicoverpa punctigera	Australian bollworm	Insecta	Agriculture	Assembled	Scaffold	AGI Team
Helicoverpa zea	Corn earworm	Insecta	Biosecurity	Assembled	Scaffold	AGI Team
Hermetia illucens	Black soldier fly	Insecta	Circular economy	Coming soon	Scaffold	AGI Team
Hypseleotris sp.	Lake’s carp gudgeon	Actinopterygii	Environment	Coming soon	Contig	AGI Team
Hypseleotris klunzingeri	Western carp gudgeon	Actinopterygii	Environment	Coming soon	Contig	AGI Team
Hypseleotris sp.	Murray-Darling carp gudgeon	Actinopterygii	Environment	Coming soon	Contig	AGI Team
Hypseleotris sp.	Midgley’s carp gudgeon	Actinopterygii	Environment	Coming soon	Contig	AGI Team
Ixodes holocyclus	Australian paralysis tick	Arachnida	Health	Coming soon	Chromosome	Alex Gofton
Kuschelorhynchus macadamiae	Macadamia seed weevil	Insecta	Agriculture	Coming soon	Scaffold	Hermes E. Garcia
Leiopotherapon unicolor	Spangled perch	Actinopterygii	Environment	Coming soon	Contig	AGI Team
Lepisiota frauenfeldi	Browsing Ant	Insecta	Biosecurity	Coming soon	Contig	Ben Hoffmann
Lepisiota incisa	African black sugar ant	Insecta	Biosecurity	Coming soon	Contig	Ben Hoffmann
Leucochrysum albicans	Hoary sunray	Asteraceae	Conservation	Assembled	Scaffold	Alexander Schmidt-Lebuhn
Lobesia botrana	European grapevine moth	Insecta	Biosecurity	Coming soon	Scaffold	Wee Tek-Tay
Lolium rigidum	Annual grass	Poaceae	Biosecurity	Public – refseq	Chromosome	Alexandre Fournier-Level
Lycium ferocissimum	African boxthorn	Solanaceae	Biosecurity	Assembled	Chromosome	Kumaran Nagalingam
Maccullochella macquariensis	Trout cod	Actinopterygii	Conservation	Coming soon	Contig	AGI Team
Maccullochella peelii peelii	Murray cod	Actinopterygii	Environment	Coming soon	Contig	AGI Team
Macquaria ambigua	Golden perch	Actinopterygii	Environment	Coming soon	Contig	AGI Team
Macquaria australasica	Macquarie perch	Actinopterygii	Conservation	Coming soon	Contig	AGI Team
Melanotaenia fluviatilis	Murray river rainbowfish	Actinopterygii	Environment	Coming soon	Contig	AGI Team
Melanotaenia splendida tatei	Desert rainbowfish	Actinopterygii	Environment	Coming soon	Contig	AGI Team
Misgurnus anguillicaudatus	Oriental weatherloach	Actinopterygii	Environment	Coming soon	Contig	AGI Team
Mogurnda adspersa	Southern purple-spotted gudgeon	Actinopterygii	Conservation	Coming soon	Contig	AGI Team
Monomorium liliuokalanii	Liliuokalani ant	Insecta	Biosecurity	Coming soon	Contig	Ben Hoffmann
Monoplex parthenopeus	Giant triton	Gastropoda	Environment	Coming soon	Scaffold	Cherie Motti
Mordacia mordax	Short headed lamprey	Hyperoartia	Environment	Coming soon	Contig	AGI Team
Mordacia praecox	Non-parasitic lamprey	Hyperoartia	Environment	Coming soon	Contig	AGI Team
Musca vetustissima	Australian bush fly	Insecta	Environment	Data generation	Scaffold	Juan David Lobarton
Myzus persicae	Green peach aphid	Insecta	Agriculture	Coming soon	Contig	AGI Team
Nannoperca australis	Southern pygmy perch	Actinopterygii	Conservation	Coming soon	Contig	AGI Team
Nannoperca obscura	Yarra pygmy perch	Actinopterygii	Conservation	Coming soon	Contig	AGI Team
Nannoperca oxleyana	Oxleyan pygmy perch	Actinopterygii	Conservation	Coming soon	Contig	AGI Team
Nematalosa erebi	Bony herring	Actinopterygii	Environment	Coming soon	Contig	AGI Team
Neosilurus hyrtlii	Hyrtl’s tandan	Actinopterygii	Environment	Coming soon	Contig	AGI Team
Nysius vinitor	Rutherglen Bug	Insecta	Agriculture	Coming soon	Scaffold	James Hereward
Oncorhynchus mykiss	Rainbow trout	Actinopterygii	Environment	Coming soon	Contig	AGI Team
Onthophagus vacca	Dung beetle	Insecta	Agriculture	Coming soon	Scaffold	Matt Morgan
Oryctes rhinoceros	Coconut rhinoceros beetle	Insecta	Biosecurity	Coming soon	Scaffold	Wee Tek-Tay
Oryctolagus cuniculus	European rabbit	Mammalia	Biosecurity	Coming soon	Contig	Tanja Strive
Paratya australiensis	Freshwater shrimp	Malacostraca	Ecotoxicology	Coming soon	Chromosome	Anu Kumar
Pediculus humanus capitis	Head louse	Insecta	Health	Coming soon	Contig	AGI Team
Perca fluviatilis	European perch	Actinopterygii	Environment	Coming soon	Contig	AGI Team
Pezoporus wallicus	Eastern Ground Parrot	Aves	Conservation	Coming soon	Chromosome	Leo Joseph
Pheidole megacephala	African big-headed ant	Insecta	Biosecurity	Coming soon	Contig	Ben Hoffmann
Phenacoccus solenopsis	Cotton mealybug	Insecta	Agriculture	Coming soon	Contig	Jamie Hopkinson
Philypnodon grandiceps	Flathead gudgeon	Actinopterygii	Environment	Coming soon	Contig	AGI Team
Philypnodon macrostomus	Dwarf flathead gudgeon	Actinopterygii	Environment	Coming soon	Contig	AGI Team
Phoracantha sp Male	Longicorn Beetle	Insecta	Conservation	Coming soon	Scaffold	Matthew Brookhouse
Pocillopora verrucosa	Cauliflower coral	Hexacorallia	Environment	Coming soon	Scaffold	UQ/AIMS
Prototroctes maraena	Australian grayling	Actinopterygii	Conservation	Coming soon	Contig	AGI Team
Pseudaphritis urvillii	Congolli	Actinopterygii	Conservation	Coming soon	Contig	AGI Team
Raphanus raphanistrum	Wild radish	Brassicaceae	Biosecurity	Assembled	Chromosome	Kumaran Nagalingam
Rattus rattus	House rat	Mammalia	Biosecurity	Coming soon	Chromosome	AGI Team
Retropinna semoni	Australian smelt	Actinopterygii	Environment	Coming soon	Contig	AGI Team
Rhinella marina	Canetoad	Amphibia	Biosecurity	Coming soon	Scaffold	Lee Rollins
Saccostrea cucullata	Oyster	Bivalvia	Environment	Data generation	Scaffold	Sharon Hook
Saccostrea echinate	Oyster	Bivalvia	Environment	Data generation	Scaffold	Sharon Hook
Saccostrea glomerata	Sydney rock oyster	Bivalvia	Environment	Data generation	Scaffold	Sharon Hook
Salmo trutta	Brown trout	Actinopterygii	Environment	Coming soon	Contig	AGI Team
Schistorhinotermes sp.	Termite	Insecta	Circular economy	Coming soon	Scaffold	Gene Wijffels
Solenopsis geminata	Tropical fire ant	Insecta	Biosecurity	Coming soon	Contig	Ben Hoffmann
Spodoptera frugiperda	Fall armyworm	Insecta	Biosecurity	Public – refseq	Chromosome	AGI Team
Spodoptera litura	Tobacco cutworm	Insecta	Agriculture	Coming soon	Scaffold	AGI Team
Stylophora pistillata	Hood coral	Insecta	Conservation	Coming soon	Scaffold	UQ/AIMS
Sus scrofa	Feral pig	Mammalia	Biosecurity	Coming soon	Contig	AGI Team
Tandanus tandanus	Eel-tailed catfish	Actinopterygii	Conservation	Coming soon	Contig	AGI Team
Tasmannia lanceolata	Tasmanian pepperberry	Winteraceae	Conservation	Coming soon	Scaffold	Alexandre Fournier-Level
Tenebrio molitor	Mealworm	Insecta	Circular economy	Coming soon	Scaffold	Gene Wijffels
Tetramorium caldarium	Ant	Insecta	Biosecurity	Coming soon	Contig	Ben Hoffmann
Thelymitra variegata	Queen of Sheba	Orchidaceae	Conservation	Data generation	Scaffold	Katharina Schulte
Tineola bisselliella	Common clothes moth	Insecta	Circular economy	Coming soon	Scaffold	AGI Team
Tripteroides apicotriangulatus	Mosquito	Insecta	Health	Coming soon	Contig	AGI Team
Tripteroides atripes	Mosquito	Insecta	Health	Coming soon	Contig	AGI Team
Tripteroides punctolateralis	Mosquito	Insecta	Health	Coming soon	Contig	AGI Team
Trogoderma granarium	Khapra beetle	Insecta	Biosecurity	Coming soon	Scaffold	AGI Team
Verrallina lineata	Mosquito	Insecta	Health	Coming soon	Contig	AGI Team
Vulpes vulpes	Red fox	Mammalia	Biosecurity	Coming soon	Contig	AGI Team
Ylistrum balloti	Ballot’s saucer scallop	Bivalvia	Environment	Data generation	Scaffold	Sharon Hook
Zophobas morio	Superworm larvae	Insecta	Circular economy	Data generation	Scaffold	Chris Rinke

Updated on 11 Nov 2022 by Gunjan Pandey