Comparative analysis of genome-scale, base-resolution DNA methylation profiles across 580 animal species

ABSTRACT: We mapped DNA methylation in 580 animal species (535 vertebrates, 45 invertebrates), resulting in 2443 genome-scale, base-resolution DNA methylation profiles of primary tissue samples from various organs. Reference-genome independent analysis of this comprehensive dataset defined a “genomic code” of DNA methylation, which allowed us to predict global and locus-specific DNA methylation from the DNA sequence within and across species. This code appears broadly conserved throughout vertebrate evolution, with two major transitions – once in the first vertebrates and again with the emergence of reptiles. Beyond the central role of species-specific DNA sequence composition, our dataset identified the tissue type and the individual as two main sources of DNA methylation variability within species. Tissue type was the dominant factor in fish, birds, and mammals, while in invertebrates, reptiles, and amphibians both factors were similarly strong. Cross-species comparisons focusing on heart and liver tissues supported a highly conserved role of DNA methylation for tissue type and identity and cross-mapping based promoter methylation analysis revealed divergence at specific genes. In summary, this study establishes a large resource of vertebrate and invertebrate DNA methylomes, it showcases the power of reference-free epigenome analysis in species for which no reference genomes are available, and it contributes an epigenetic perspective to the study of vertebrate evolution.

ORGANISM(S): Rhacophorus reinwardtii Sebastes chrysomelas Pongo Chaetodon lunula Saguinus mystax Potamochoerus porcus Agapornis taranta Vipera ammodytes Haliaeetus albicilla Fromia indica Coccothraustes Ophiothrix spiculata Glyptocephalus zachirus Oryctolagus cuniculus Hippoglossoides platessoides Coracias cyanogaster Ovis aries Stenotomus chrysops Python molurus Dascyllus aruanus Ostorhinchus aureus Vermilingua Hypanus americanus Coryphaenoides acrolepis Lethrinus atkinsoni Leucoraja erinaceus Procyon lotor Tockus deckeni Tragelaphus angasii Urophycis tenuis Pomatomus saltator Salvelinus alpinus Lumpenus lampretaeformis Geochelone Tetrao urogallus Axis axis Fromia Prionotus carolinus Phyllopteryx taeniolatus Columbidae Neurergus Macroscelides proboscideus Cervus elaphus Ecteinascidia turbinata Pleoticus muelleri Saguinus Pisaster brevispinus Phalacrocorax carbo Oxylebius pictus Lytechinus variegatus Heleophrynidae Picus viridis Ambystoma mexicanum Tetrastes bonasia Cricetomyinae Ctenochaetus striatus Merops apiaster Rhyticeros narcondami Notamacropus rufogriseus Bycanistes bucinator Hemitragus Cornufer guentheri Sciurus vulgaris Acanthosaura Panthera onca Rattus rattus Nasua Pleurogrammus monopterygius Varanus gouldii Parapercis xanthozona Vanellus armatus Ptilinopus Canis lupus lycaon Tockus nasutus Choerodon fasciatus Emydidae Polypedates otilophus Hystricidae Garrulus glandarius Furcifer pardalis Cervus nippon Iguanidae Neoniphon sammara Kobus leche Papio hamadryas Sebastes miniatus Myzopsetta ferruginea Rhinecanthus aculeatus Testudo kleinmanni Macaca Xiphias gladius Cheilodipterus quinquelineatus Sus scrofa domesticus Nothobranchius furzeri Buteo buteo Saccoglossus kowalevskii Myoxocephalus octodecemspinosus Camelus ferus Glyptocephalus cynoglossus Bathymaster signatus Perdix perdix Danio rerio Mustela putorius Kobus Capromys pilorides Penaeus Casuarius casuarius Esox lucius Ostrea edulis Amazona Vulpes vulpes Aonyx cinereus Semicossyphus pulcher Lonchura oryzivora Marmota Recurvirostra avosetta Chamaeleo calyptratus Corvus corax Felis silvestris Apodemus flavicollis Ammodytes hexapterus Boltenia echinata Euplectes orix Gadus morhua Scandentia Gymnothorax moringa Phloeomys Buteo Chaetodon lineolatus Varecia Parupeneus spilurus Haliaeetus leucocephalus Rhinoptera bonasus Pomacentrus coelestis Pollachius virens Oxycheilinus digramma Buteo lagopus Tapirus Phoenicopteriformes Carcharias taurus Theloderma Sebastes borealis Strongylocentrotus purpuratus Pelecanus crispus Shinisaurus crocodilurus Phocidae Uromastyx Patiria miniata Hypselecara coryphaenoides Correlophus ciliatus Squalus acanthias Chrysopelea Rhabdamia gracilis Cricetinae Zenopsis conchifer Spermophilus Rhinogobiops nicholsii Chromis punctipinnis Psarisomus dalhousiae Rattus norvegicus Negaprion brevirostris Batoidea Philomachus Saguinus imperator Leontopithecus chrysomelas Ursus Canis aureus Camelus dromedarius Diodon hystrix Salvelinus umbla Lissemys punctata Ascidiella aspersa Trachemys Ostorhinchus rueppellii Thunnus albacares Sebastes paucispinis Uraeginthus bengalus Leontopithecus Dromaius novaehollandiae Histrio histrio Hippoglossoides elassodon Antidorcas Stichopus chloronotus Pelecanus Loweina terminata Capra aegagrus Leptoptilos crumenifer Rollulus Cirrhilabrus lineatus Lampropeltis Falco peregrinus Acanthurus triostegus Cuora mouhotii Plegadis falcinellus Centropomus robalito Felis catus Eudyptes chrysocome Spatula querquedula Tragelaphus spekii Rangifer tarandus Dolichotis patagonum Agapornis lilianae Coracias garrulus Uromastyx ocellata Bison bonasus Pterocaesio marri Botryllus schlosseri Ducula bicolor Erpeton Sylvia atricapilla Cyclura cornuta Cirrhilabrus roseafascia Psittacus Cervidae Testudinidae Equus zebra Trachemys scripta scripta Atherinomorus vaigiensis Loligo vulgaris Mustelus canis Accipiter gentilis Charadriidae Agapornis canus Sebastes hopkinsi Natrix tessellata Strix uralensis Acomys Eurypygidae Heterocephalus Theropithecus gelada Lemur Bos Leiocephalus Petauridae Macaca silenus Lutjanus mahogoni Upupa epops Monacanthidae Calyptocephallela gayi Trioceros jacksonii Heloderma Ara ararauna Melopsittacus Astrochelys radiata Tockus flavirostris Python regius Lepas anatifera Photoblepharon palpebratum Balearica pavonina Geopelia placida Copsychus malabaricus Strigiformes Cyanoliseus patagonus Nectariniidae Amblyglyphidodon leucogaster Agapornis Equus asinus asinus Caiman yacare Apodemus sylvaticus Paracirrhites forsteri Trachyphonus erythrocephalus Ciconiidae Vicugna pacos Cyprinus carpio Meles meles Yangochiroptera Vicugna Mustelidae Gypaetus Osteoglossum bicirrhosum Oxycercichthys veliferus Pseudomonacanthus peroni Ailurus fulgens Folivora Strix aluco Cyanoloxia brissonii Tiliqua scincoides Scolopsis bilineata Boltenia ovifera Sufflamen chrysopterum Apostichopus parvimensis Mungos mungo Cyclura Sebastes constellatus Macropodidae Coturnix delegorguei Falco tinnunculus Vidua paradisaea Eliomys quercinus Macropus Paroedura picta Dinemellia Giraffa giraffa Clupea harengus Anoplopoma fimbria Pseudanthias Clavelina picta Rhea americana Tayassuidae Acinonyx Scincidae Saimiriinae Pseudobalistes fuscus Cantherhines pardalis Nanger dama Fistularia commersonii Ecsenius Bubalus Loweina rara Echinarachnius parma Morone saxatilis Amazona agilis Sauromalus Paracanthurus hepatus Macroscelidea Malacochersus Sebastes norvegicus Leontocebus fuscicollis Grus japonensis Sebastes mystinus Cryptacanthodes maculatus Pytilia melba Pseudanthias ventralis Halichoeres trimaculatus Ara Crotalus Coliiformes Mustela Labroides bicolor Ammotragus Laemanctus Pycnonotus barbatus Ophioderma panamensis Trachemys scripta elegans Terrapene Lethenteron camtschaticum Podothecus accipenserinus Cercopithecus Gadus chalcogrammus Merops bullockoides Abronia anzuetoi Coris caudimacula Coturnix coturnix Crocodylia Chloropsis Centropristis striata Geoemyda spengleri Pogona barbata Callorhinchus milii Hydrochoerus hydrochaeris Magallana gigas Triglops scepticus Pachyuromys Cebinae Doryteuthis pealeii Tamiops Onuxodon fowleri Phasianus colchicus Cariamidae Capreolus capreolus Galeocerdo cuvier Cygnus melancoryphus Ursus arctos Accipiter nisus Hoplobatrachus tigerinus Sus scrofa Holothuria atra Taurotragus Graptemys Pythonidae Mus musculus Hippotragus Glis glis Tinca tinca Otaria Anas platyrhynchos Sebastes caurinus Musophagidae Agapornis personatus Varanus exanthematicus Capricornis Corucia zebrata Lepidopsetta polyxystra Scyliorhinus retifer Panthera pardus Strongylocentrotus droebachiensis Oplurus Illex illecebrosus Jaculus Brachylophus Caloenas nicobarica Hippoglossina oblonga Corvus frugilegus Ammodytes dubius Salmo trutta Athene noctua Geronticus eremita Pitta moluccensis Ariopsis felis Ptilinopus pulchellus Leptailurus Yinpterochiroptera Boselaphus tragocamelus Hemilepidotus jordani Sphoeroides maculatus Halocynthia pyriformis Erethizon Cricetus Paralichthys dentatus Lamprotornis chalcurus Thyonella gemmata Riftia pachyptila Ambystoma Vipera berus Erythrura Lepus timidus Antilope Ostorhinchus moluccensis Hippotragus equinus Bodianus diana Embiotoca jacksoni Passer domesticus Cynomys Cacatua alba Hemitripterus americanus Lynx lynx Mya arenaria Caviidae Sebastolobus alascanus Musophaga Milvus milvus Psammomys obesus Eunectes Jacanidae Leptoclinus maculatus Salmo salar Styela montereyensis Capromyidae Branchiostoma floridae Papio Gallicolumba Aquila heliaca Connochaetes Petaurus breviceps Parus major Callocephalon fimbriatum Ophiopteris papillosa Canis lupus familiaris Lyrurus tetrix Macaca sylvanus Scophthalmus aquosus Colobus guereza Cygnus cygnus Molgula citrina Callithrix jacchus Cyclopsitta diophthalma Pisaster giganteus Euplectes Spheniscus humboldti Chloris chloris Chiroxiphia pareola Pristigenys alta Sebastes ovalis Polychrus marmoratus Canis lupus Puma concolor Scopus umbretta Octopus vulgaris Platax teira Chelydra serpentina Ciconia ciconia Dolichotis Bothriechis schlegelii Cynictis Alitta succinea Capra Boa constrictor Castoridae Haemulon flavolineatum Ambystoma andersoni Erinaceidae Lama glama Serinus Columba livia Gallus Zosteropidae Lutjanus quinquelineatus Myocastor coypus Cuora mccordi Colobus polykomos Irena puella Martes foina Homarus americanus Pithecia pithecia Testudo hermanni Nardoa novaecaledoniae Ploceus cucullatus Astrochelys yniphora Acryllium vulturinum Tamias Tringa totanus Aptenodytes patagonicus Sebastes atrovirens Ovis orientalis Struthio camelus Suricata Mimus polyglottos Phodopus campbelli Tockus alboterminatus Dendrocygna viduata Rhinocerotidae Duttaphrynus melanostictus Lagostomus maximus Varanus Cheilopogon californicus Tiliqua rugosa Ardea Naja Saguinus oedipus Sarcophilus Sturnus vulgaris Circus cyaneus Holothuria cinerascens Elephas maximus indicus Alectis ciliaris Nyctereutes Chauna torquata Dracaena guianensis Notamacropus parma Falco cherrug Tragulus javanicus Mullus surmuletus Incilius alvarius Pteropus Probosciger aterrimus Cynoscion regalis Gekkonidae Dama dama Hemisphaeriodon Loriculus galgulus Zamenis longissimus Nymphicus hollandicus Centropyge heraldi Ciona intestinalis Chamaeleonidae Gallus gallus Muntiacus Leucoraja ocellata Corvus corone Cucumaria frondosa Lophius piscatorius Lepus europaeus Panthera leo Cyclopterus lumpus Carollia perspicillata Tupaia Dasypodidae Asio otus Zaprora silenus Aplonis panayensis Rupicapra rupicapra Sebastes semicinctus Bubo bubo Amandava subflava Aotidae Xenagama wilmsi Zoarces americanus Coris gaimard Corvus Circus aeruginosus Panthera tigris Anthropoides paradiseus Lutra lutra Coronella austriaca Phascolarctos cinereus Cephalopholis miniata Holothuria Spinus spinus Elops affinis Equus

PROVIDER: GSE195869 | GEO | 2022/06/18

REPOSITORIES: GEO