List of sequenced Deuterostomia genomes
Appearance
This list of sequenced Deuterostomia genomes contains species for which complete genome sequences have been assembled, annotated and published.
- Saccoglossus kowalevskii, Enteropneusta (2015[1])
- Ptychodera flava, Enteropneusta (2015[1])
- Acanthaster planci, starfish (2014[2])
- Apostichopus japonicus, sea cucumber (2017[3])
- Strongylocentrotus purpuratus, a sea urchin and model deuterostome (2006[4])
- Ciona intestinalis, a tunicate (2002[5])
- Ciona savignyi, a tunicate (2007[6])
- Oikopleura dioica, a larvacean (2001[7]).
Cephalochordates
[change | change source]- Branchiostoma floridae, a lancelet (2008[8])
- Petromyzon marinus, a lamprey (2009,[9] 2013[10])
- Callorhinchus milii, an elephant shark (2007[11])
- Rhincodon typus, Whale shark (2017)[12]
- Carcharodon carcharias, Great white shark ( 2018[13])
- Chiloscyllium punctatum, Brownbanded bamboo shark (2018[14])
- Scyliorhinus torazame, Cloudy catshark (2018[14])
- Order Anabantiformes
- Order Beloniformes
- Oryzias latipes, medaka (2007)[16]
- Order Centrarchiformes
- Order Characiformes
- Astyanax mexicanus, Mexican tetra (2014[18])
- Order Cichliformes
- Oreochromis niloticus, Nile tilapia (2019[19])
- Metriaclima zeb, Lake Malawi cichlid (2019[19])
- Order Clupeiformes
- Clupea harengus, Atlantic herring (2020[20])
- Coilia nasus, Japanese grenadier anchovy (2020[21])
- Sardina pilchardus, European sardine (2019[22])
- Order Coelacanthiformes
- Latimeria chalumnae, West Indian Ocean coelacanth and oldest known living lineage of Sarcopterygii (2013[23][24])
- Order Cypriniformes
- Anabarilius grahami Regan, Kanglang fish (2018[25])
- Danio rerio, a zebrafish (2007[26])
- Heterandria formosa, Least Killifish (2019[27])
- Oxygymnocypris stewartii,(2019[28])
- Megalobrama amblycephala, blunt snout bream (2017[29])
- Order Cyprinodontiformes
- Heterandria formosa, least killifish (2019[27])
- Xiphophorus maculatus, platyfish (2013[30])
- Nothobranchius furzeri, turquoise killifish (2015[31][32][33])
- Order Esociformes
- Esox lucius, northern pike (2014[34])
- Order Gadiformes
- Gadus morhua, Atlantic cod (2011[35])
- Order Gasterosteiformes
- Gasterosteus aculeatus, three-spined stickleback (2006, 2012[36])
- Order Gymnotiformes
- Order Lepisosteiformes
- Order Osmeriformes
- Protosalanx hyalocranius, clearhead icefish (2017[39])
- Order Perciformes
- Channa argus, northern snakehead (2017[40])
- Dissostichus mawsoni, Antarctic toothfish (2019[41])
- Eleginops maclovinus, Patagonian robalo (2019[41])
- Larimichthys crocea, large yellow croaker (2014[42])
- Lutjanus campechanus, Northern red snapper (2020[43])
- Parachaenichthys charcoti, Antarctic dragonfish (2017[44])
- Seriola dumerili, Greater amberjack (2017[45])
- Sillago sinica, chinese sillago (2018[46])
- Sparus aurata, gilt-head bream (2018[47])
- Order Salmoniformes
- Order Scorpaeniformes
- Order Siluriformes
- Order Tetraodontiformes
- mola mola, ocean sunfish (2016[54])
- Takifugu rubripes, a puffer fish[55] (International Fugu Genome Consortium 2002[56])
- Tetraodon nigroviridis, a puffer fish (2004[57])
- Ambystoma mexicanum, Axolotl (2018)[58]
- Xenopus tropicalis, western clawed frog (2010)[59]
- Nanorana parkeri, High Himalaya frog (2015)[60]
- Oophaga pumilio, Strawberry poison-dart frog (2018[61])
- Rana [Lithobates] catesbeiana, North American bullfrog (2017)[62]
- Rhinella marina, Cane toad (2018)[63]
- Vibrissaphora ailaonica, Mustache toad (2019)[64]
- Leptobrachium leishanense, Leishan Mustache toad (2019)[65]
- Order Crocodylia
- Alligator mississippiensis, American alligator (2012)[66]
- Alligator sinensis, Chinese alligator (2013, 2014)[67][68]
- Crocodylus porosus, salt water crocodile (2012)[66]
- Gavialis gangeticus, Indian gharial (2012)[66]
- Order Squamata
- Anolis carolinensis JBL SC #1, green anole lizard (2011[69])
- Dopasia gracilis, Burmese glass lizard, (2015)[70]
- Emydocephalus ijimae, Ijima's turtle-headed sea snake, (2019)[71]
- Eublepharis macularius, Leopard gecko (2016)[72]
- Hydrophis melanocephalus, slender-necked sea snake, (2019)[71]
- Laticauda colubrina, yellow-lipped sea krait, (2019)[71]
- Laticauda laticaudata, blue-linged sea krait, (2019)[71]
- Ophiophagus hannah, king cobra (2013)[73]
- Pantherophis guttatus, corn snake (2014)[74]
- Pogona vitticeps, Australian dragon lizard (2015)[75]
- Python molurus bivittatus, Burmese python (2013)[76]
- Salvator Merinae, tegu lizard (2018[77])
- Shinisaurus crocodilurus, Chinese crocodile lizard, (2017)[78]
- Order Testudines (Chelonii)
Birds
[change | change source]- Order Accipitriformes
- Haliaeetus albicilla, white-tailed eagle (2014[82])
- Haliaeetus leucocephalus, bald eagle (2014[82])
- Aegypius monachus, cinereous vulture (2015)
- Aquila chrysaetos, golden eagle (2018[83])
- Order Anseriformes
- Anas platyrhynchos, mallard duck (or wild duck) (2013[84])
- Order Apodiformes
- Chaetura pelagica, chimney swift (2014[82])
- Order Bucerotiformes
- Buceros rhinoceros silvestris, rhinoceros hornbill (2014[82])
- Order Caprimulgiformes
- Order Cariamiformes
- Order Cathartiformes
- Cathartes aura, turkey vulture (2014[82])
- Order Charadriiformes
- Order Ciconiiformes
- Nipponia nippon, crested ibis (2014[86])
- Order Coliiformes
- Order Columbiformes
- Columba livia, pigeon (2014[82])
- Order Coraciiformes
- Merops nubicus, carmine bee-eater (2014[82])
- Order Cuculiformes
- Cuculus canorus, common cuckoo (2014[82])
- Tauraco erythrolophus, red-crested turaco (2014[82])
- Order Eurypygiformes
- Eurypyga helias, sunbittern (2014[82])
- Order Falconiformes
- Falco cherrug, saker falcon (2013[87])
- Falco peregrinus, peregrine falcon (2013[87])
- Order Galliformes
- Arborophila rufipectus, Sichuan Partridge (2019[88])
- Gallus gallus, chicken (2004[89])
- Meleagris gallopavo, domesticated turkey (2011[90])
- Numida meleagris, helmeted guinea fowl (2019[91])
- Pavo cristatus, Indian peafowl (2018[92])
- Phasianus colchicus, Common Pheasant (2019[93])
- Syrmaticus mikado, mikado pheasant (2018[94])
- Tetrao tetrix, black grouse (2014[95])
- Order Gaviiformes
- Gavia stellata, red-throated loon (2014[82])
- Order Gruiformes
- Order Leptosomiformes
- Leptosomus discolor, cuckoo-roller (2014[82])
- Order Mesitornithiformes
- Mesitornis unicolor, brown mesite (2014[82])
- Order Opisthocomiformes
- Opisthocomus hoazin, hoatzin (2014[82])
- Order Passeriformes
- Acanthisitta chloris, rifleman (2014)[82]
- Corvus brachyrhynchos, American crow (2014[82])
- Corvus hawaiiensis, Hawaiian crow (2018[96])
- Eopsaltria australis, Eastern yellow robin (2019)[97]
- Ficedula albicollis, collared flycatcher (2012[98])
- Ficedula hypoleuca, pied flycatcher (2012[98])
- Geospiza fortis, medium ground-finch (2014[82])
- Hirundo rustica, barn swallow (2018[99])
- Lonchura striata domestica, Society finch (2018[100])
- Manacus vitellinus, golden-collared manakin (2014[82])
- Lycocorax pyrrhopterus, Paradise-crow (2019[101][102])
- Manacus vitellinus, golden-collared manakin (2014[82])
- Paradisaea rubra, red bird-of-paradise (2019[102][103])
- Pteridophora alberti, king of saxony bird-of-paradise (2019[102][104])
- Ptiloris paradiseus, paradise riflebird (2019[102][105])
- Taeniopygia guttata, zebra finch (2010[106])
- Order Pelecaniformes
- Egretta garzetta, little egret (2014[82])
- Pelecanus crispus, Dalmatian pelican (2014[82])
- Order Phaethontiformes
- Order Phoenicopteriformes
- Phoenicopterus ruber ruber, American flamingo (2014[82])
- Order Piciformes
- Order Podicipediformes
- Order Procellariiformes
- Order Pterocliformes
- Order Psittaciformes
- Amazona leucocephala, Cuban amazon (2019[107])
- Amazona ventralis, Hispaniolan amanzon (2019[107])
- Amazona vittata, Puerto Rican parrot (2012[108])
- Ara macao, Scarlet macaw (2013[109])
- Cyanoramphus malherbi, kākāriki karaka (2020[110])
- Melopsittacus undulatus, budgerigar (2014[82])
- Nestor notabilis, kea (2014[82])
- Order Struthioniformes
- Struthio camelus australis, common ostrich (2014[82])
- Order Sphenisciformes
- Aptenodytes forsteri, emperor penguin (2014[82])
- Aptenodytes patagonicus, king penguin (2019[111][112])
- Eudyptes chrysocome, Western rockhopper penguin (2019[111][113])
- Eudyptes chrysolophus chrysolophus, Macaroni penguin (2019[111][114])
- Eudyptes chrysolophus schlegeli, Royal penguin (2019[111][115])
- Eudyptes filholi, Eastern rockhopper penguin (2019[111][116])
- Eudyptes moseleyi, Northern rockhopper penguin (2019[111][117])
- Eudyptes pachyrhynchus, Fiordland-crested penguin (2019[111][118])
- Eudyptes robustus, Snares-crested penguin (2019[111][119])
- Eudyptes sclateri, Erect-crested penguin (2019[111][120])
- Eudyptula minor albosignata, white-flippered penguin (2019[111][121])
- Eudyptula minor minor, little blue penguin (2019[111][122])
- Eudyptula novaehollandiae, fairy penguin (2019[111][123])
- Megadyptes antipodes antipodes, yellow eyed penguin or hoiho (2019[111][124])
- Pygoscelis adeliae, Adélie penguin (2014[82])
- Pygoscelis antarctica, chinstrap penguin (2019[111][125])
- Pygoscelis papua, gentoo penguin (2019[111][126])
- Spheniscus demersus, African penguin (2019[111])
- Spheniscus humboldti, Humboldt penguin (2019[111][127])
- Spheniscus magellanicus, Magellanic penguin (2019[111][128])
- Spheniscus mendiculus, Galápagos penguin (2019[111][129])
- Order Strigiformes
- Tyto alba, barn owl (2014[82])
- Strix occidentalis caurina, northern spotted owl (2017[130])
- Strix varia, Barred owl (2017[130])
- Order Suliformes
- Order Tinamiformes
- Order Trochiliformes
- Calypte anna, Anna's hummingbird (2014[82])
- Order Trogoniformes
Mammals
[change | change source]- Subclass Prototheria, Order Monotremata, Family Ornithorhynchidae
- Subclass Theria (marsupials and placental mammals)
- Infraclass Metatheria (marsupials)
- Order Didelphimorphia, Family Didelphidae (opossums)
- Monodelphis domestica, gray short-tailed opossum (2007[133])
- Order Dasyuromorphia
- Family Dasyuridae
- Family Thylacinidae
- Order Diprotodontia
- Family Macropodidae
- Macropus eugenii, tammar wallaby (2011[136])
- Family Phascolarctidae
- Phascolarctos cinereus, koala (2013 draft[137])
- Family Macropodidae
- Order Didelphimorphia, Family Didelphidae (opossums)
- Infraclass Eutheria (placental mammals)
- Order Erinaceomorpha, Family Erinaceidae
- Erinaceus europaeus, European hedgehog
- Order Eulipotyphla, Family Solenodontidae
- Order Chiroptera
- Family Megadermatidae
- Family Mormoopidae
- Family Pteropodidae
- Pteropus vampyrus, fruit bat (2012[140])
- Eidolon helvum, Old World fruit bat (2013[139])
- Family Rhinolophidae
- Family Vespertilionidae
- Myotis lucifugus, little brown bat (2010[141])
- Family Phyllostomidae
- Leptonycteris yerbabuenae, long nosed bat (2020[142])
- Leptonycteris nivalis, greater long nosed bat (2020[142])
- Musonycteris harrisoni, banana bat (2020[142])
- Artibeus jamaicensis, Jamaican fruit bat (2020[142])
- Macrotus waterhousii, Waterhouse's leaf-nosed bat (2020[142])
- Order Primates
- Family Galagidae
- Otolemur garnettii, small-eared galago, or bushbaby ([143])
- Family Cercopithecidae
- Macaca mulatta, rhesus macaque (2007[144] & Chinese rhesus macaque Macaca mulatta lasiota in 2011[145])
- Macaca fascicularis, Cynomolgus or crab-eating macaque (2011[145])
- Rhinopithecus roxellana, golden snub-nosed monkey (2019[146])
- Family Hominidae
- Subfamily Ponginae
- Pongo pygmaeus/Pongo abelii, orangutan (Borneo/Sumatra) (2011[147])
- Subfamily Homininae
- Gorilla gorilla, western gorilla (2012[148])
- Homo sapiens, modern human (draft 2001[149][150] 91%-96% complete[151])
- Homo neanderthalensis, Neanderthal (draft 2010[152])
- Pan troglodytes, chimpanzee (2005[153])
- Pan paniscus, bonobo (2012[154])
- Subfamily Ponginae
- Family Callitrichidae
- Callithrix jacchus, marmoset (2010,[155] whole genome 2014[156])
- Family Galagidae
- Order Carnivora
- Family Felidae
- Acinonyx jubatus, African cheetah (2015[157])
- Felis silvestris catus, cat (2007[158])
- Panthera leo, lion (2013[159])
- Panthera pardus, Amur leopard (2016[160])
- Panthera tigris altaica, Amur tiger (or Siberian tiger) (2013[159])
- Panthera tigris tigris, Bengal tiger (2013[159]
- Panthera uncia, snow leopard (2013[159])
- Prionailurus bengalensis, leopard cat (2016[160])
- Family Canidae
- Canis lupus familiaris, dog (2005[161])
- Canis lupus lupus, wolf (2017[162]).
- Lycaon pictus, african wild dog (2018[163])
- Family Ursidae
- Family Odobenidae
- Odobenus rosmarus, walrus (2015[169])
- Family Mustelidae
- Enhydra lutris kenyoni, sea otter (2017[170])
- Mustela erminea, stoat (2018[171])
- Mustela putorius furo, ferret (2014[172])
- Pteronura brasiliensis, giant otter (2019[173])
- Family Felidae
- Order Cetacea
- Family Delphinidae
- Tursiops truncatus, bottlenosed dolphin (2012[140])
- Balaenoptera acutorostrata, common minke whale (2014[174])
- Balaenoptera physalus, fin whale (2014[174])
- Neophocaena phocaenoides, finless porpoise (2014[174])
- Orcinus orca, killer whale (2015[169])
- Sousa Chinensis, Indo-Pacific humpback dolphin (2019[175])
- Family Monodontidae
- Delphinapterus, beluga whale (2017[176])
- Family Physeteridae
- Family Delphinidae
- Order Proboscidea, Family Elephantidae
- Elephas maximus, Asian elephant (2015[178])
- Loxodonta africana, African elephant (2009[179])
- Order Sirenia (sea cows)
- Family Trichechidae
- Order Perissodactyla (odd-toed ungulates), Family Equidae
- Equus ferus caballus, horse (2009[180] 2018[181])
- Order Artiodactyla (even-toed ungulates)
- Family Antilocapridae
- Antilocapra americana, Pronghorn (2019[182])
- Family Suidae
- Sus scrofa, pig (2012[183])
- Family Bovidae
- Ammotragus lervia, Barbary sheep (2019[182])
- Antidorcas marsupialis, Springbox (2019[182])
- Bison bonasus, European bison (2017[184])
- Bos grunniens, yak 2012 ([185])
- Bos primigenius indicus, zebu or Brahman cattle (2012[186])
- Bos primigenius taurus, cow 2009 ([187])
- Bubalus bubalis, river buffalo (2017[188])
- Capra ibex, Goats (2019[182])
- Cephalophus harveyi, Harvey's duiker (2019[182])
- Connochaetes taurinus, blue wildebeest (2019[182])
- Damaliscus lunatus, common tsessebe (2019[182])
- Gazella thomsoni, Thomson's gazelle (2019[182])
- Hippotragus niger, Sable Antelope (2019[189])
- Kobus ellipsiprymnus, Waterbuck (2019[182])
- Litocranius walleri, Gerenuk (2019[182])
- Oreotragus oreotragus, Klipspringer (2019[182])
- Oryx gazella, Gemsbok (2019[190])
- Ourebia ourebi, Oribi (2019[182])
- Ovis ammon, Argali (2019[182])
- Ovis ammon polii, marco polo sheep (2017[191])
- Nanger granti, Grant's gazelle (2019[182])
- Neotragus moschatus, Suni (2019[182])
- Neotragus pygmaeus, Royal antelope (2019[182])
- Philantomba maxwellii, Maxwell's duiker (2019[182])
- Procapra przewalskii, Przewalski's gazelle (2019[182])
- Pseudois nayaur, Bharal (2019[182])
- Raphicerus campestris, Steenbox (2019[182])
- Redunca redunca, Bohor reedbuck (2019[182])
- Syncerus caffer, African buffalo (2019[182])
- Sylvicapra grimmia, common duiker (2019[182])
- Tragelaphus, Spiral-horned bovine (2019[182])
- Tragelaphus buxtoni, Mountain nyala (2019[182])
- Tragelaphus strepsiceros, Greater kudu (2019[182])
- Tragelaphus imberbis, Lesser kudu (2019[182])
- Tragelaphus spekii, Sitatunga (2019[182])
- Tragelaphus scriptus, Bushbuck (2019[182])
- Taurotragus oryx, Common eland (2019[182])
- Family Cervidae
- Cervus albirostris, Tharold's deer (2019[182])
- Elaphurus davidianus, Père David's deer (2018[192])
- Muntiacus crinifrons, hairy-fronted muntjac (2019[182])
- Muntiacus muntjak, Indian muntjac (2019[182])
- Muntiacus reevesi, Reeves's muntjac (2019[182])
- Rangifer Tarandus, Reindeer (2017[193])
- Family Giraffidae
- Giraffa camelopardalis, Giraffe (2019[182])
- Giraffa camelopardalis tippelskirchi, Masai giraffe (2019[194])
- Okapia johnstoni, Okapi (2019[182])
- Family Moschidae
- Family Tragulidae
- Family Antilocapridae
- Order Rodentia
- Family Caviidae
- Hydrochoerus hydrochaeris, capybara (2018[196])
- Family Cricetidae
- Peromyscus leucopus, white-footed mouse (2019[197])
- Family Muridae
- Mastomys coucha, Southern multimammate mouse (2019[198])
- Mus musculus Strain: C57BL/6J, mouse (2002[199])
- Rattus norvegicus, rat (2004[200])
- Family Caviidae
- Order Lagomorpha
- Family Leporidae
- Oryctolagus cuniculus, European rabbit (2010[201][202])
- Family Leporidae
- Order Erinaceomorpha, Family Erinaceidae
- Infraclass Metatheria (marsupials)
References
[change | change source]- ↑ 1.0 1.1 Simakov O, Kawashima T, Marlétaz F, Jenkins J, Koyanagi R, Mitros T, et al. (November 2015). "Hemichordate genomes and deuterostome origins". Nature. 527 (7579): 459–65. Bibcode:2015Natur.527..459S. doi:10.1038/nature16150. PMC 4729200. PMID 26580012.
- ↑ Baughman KW, McDougall C, Cummins SF, Hall M, Degnan BM, Satoh N, Shoguchi E (December 2014). "Genomic organization of Hox and ParaHox clusters in the echinoderm, Acanthaster planci". Genesis. 52 (12): 952–8. doi:10.1002/dvg.22840. PMID 25394327. S2CID 32809575.
- ↑ Jo J, Oh J, Lee HG, Hong HH, Lee SG, Cheon S, et al. (January 2017). "Draft genome of the sea cucumber Apostichopus japonicus and genetic polymorphism among color variants". GigaScience. 6 (1): 1–6. doi:10.1093/gigascience/giw006. PMC 5437941. PMID 28369350.
- ↑ Sodergren E, Weinstock GM, Davidson EH, Cameron RA, Gibbs RA, Angerer RC, et al. (November 2006). "The genome of the sea urchin Strongylocentrotus purpuratus". Science. 314 (5801): 941–52. Bibcode:2006Sci...314..941S. doi:10.1126/science.1133609. PMC 3159423. PMID 17095691.
- ↑ Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, De Tomaso A, et al. (December 2002). "The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins". Science. 298 (5601): 2157–67. Bibcode:2002Sci...298.2157D. doi:10.1126/science.1080049. PMID 12481130. S2CID 15987281.
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- ↑ Putnam NH, Butts T, Ferrier DE, Furlong RF, Hellsten U, Kawashima T, et al. (June 2008). "The amphioxus genome and the evolution of the chordate karyotype". Nature. 453 (7198): 1064–71. Bibcode:2008Natur.453.1064P. doi:10.1038/nature06967. PMID 18563158. S2CID 4418548.
- ↑ Libants S, Carr K, Wu H, Teeter JH, Chung-Davidson YW, Zhang Z, Wilkerson C, Li W (July 2009). "The sea lamprey Petromyzon marinus genome reveals the early origin of several chemosensory receptor families in the vertebrate lineage". BMC Evolutionary Biology. 9: 180. doi:10.1186/1471-2148-9-180. PMC 2728731. PMID 19646260.
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- ↑ Venkatesh B, Kirkness EF, Loh YH, Halpern AL, Lee AP, Johnson J, et al. (April 2007). "Survey sequencing and comparative analysis of the elephant shark (Callorhinchus milii) genome". PLOS Biology. 5 (4): e101. doi:10.1371/journal.pbio.0050101. PMC 1845163. PMID 17407382.
- ↑ Read TD, Petit RA, Joseph SJ, Alam MT, Weil MR, Ahmad M, et al. (July 2017). "Draft sequencing and assembly of the genome of the world's largest fish, the whale shark: Rhincodon typus Smith 1828". BMC Genomics. 18 (1): 532. doi:10.1186/s12864-017-3926-9. PMC 5513125. PMID 28709399.
- ↑ Marra NJ, Stanhope MJ, Jue NK, Wang M, Sun Q, Pavinski Bitar P, et al. (February 2019). "White shark genome reveals ancient elasmobranch adaptations associated with wound healing and the maintenance of genome stability". Proceedings of the National Academy of Sciences of the United States of America. 116 (10): 4446–4455. doi:10.1073/pnas.1819778116. PMC 6410855. PMID 30782839.
- ↑ 14.0 14.1 Hara Y, Yamaguchi K, Onimaru K, Kadota M, Koyanagi M, Keeley SD, et al. (November 2018). "Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates". Nature Ecology & Evolution. 2 (11): 1761–1771. doi:10.1038/s41559-018-0673-5. PMID 30297745. S2CID 52944566.
- ↑ Fan G, Chan J, Ma K, Yang B, Zhang H, Yang X, et al. (November 2018). "Chromosome-level reference genome of the Siamese fighting fish Betta splendens, a model species for the study of aggression". GigaScience. 7 (11). doi:10.1093/gigascience/giy087. PMC 6251983. PMID 30010754.
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ignored (help) - ↑ 102.0 102.1 102.2 102.3 Prost S, Armstrong EE, Nylander J, Thomas GW, Suh A, Petersen B, et al. (May 2019). "Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise". GigaScience. 8 (5). doi:10.1093/gigascience/giz003. PMC 6497032. PMID 30689847.
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- ↑ Ensembl entry