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 Ostorhinchus aureus Vermilingua Dascyllus aruanus Hypanus americanus Lethrinus atkinsoni Coryphaenoides acrolepis 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 Rattus rattus Panthera onca 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 Testudo kleinmanni Rhinecanthus aculeatus Macaca Xiphias gladius Cheilodipterus quinquelineatus Sus scrofa domesticus Nothobranchius furzeri Buteo buteo Saccoglossus kowalevskii Myoxocephalus octodecemspinosus Camelus ferus Glyptocephalus cynoglossus Bathymaster signatus Perdix perdix Mustela putorius Danio rerio Kobus Capromys pilorides Casuarius casuarius Penaeus Esox lucius Amazona Ostrea edulis 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 Scandentia Gadus morhua Gymnothorax moringa Phloeomys Buteo Chaetodon lineolatus Varecia Parupeneus spilurus Haliaeetus leucocephalus Rhinoptera bonasus Pomacentrus coelestis Pollachius virens Oxycheilinus digramma Riftia pachyptila Tapirus Buteo lagopus Phoenicopteriformes Carcharias taurus Theloderma Sebastes borealis Strongylocentrotus purpuratus Pelecanus crispus Phocidae Shinisaurus crocodilurus Patiria miniata Uromastyx 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 Hippoglossoides elassodon Antidorcas Histrio histrio Stichopus chloronotus Pelecanus Loweina terminata Rollulus Capra aegagrus Leptoptilos crumenifer Cirrhilabrus lineatus Lampropeltis Falco peregrinus Acanthurus triostegus Cuora mouhotii Centropomus robalito Plegadis falcinellus 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 Testudinidae Equus zebra Cervidae Trachemys scripta scripta Loligo vulgaris Atherinomorus vaigiensis Mustelus canis Charadriidae Agapornis canus Sebastes hopkinsi Natrix tessellata Strix uralensis Acomys Eurypygidae Theropithecus gelada Heterocephalus Lemur Bos Leiocephalus Petauridae Macaca silenus Lutjanus mahogoni Upupa epops Trioceros jacksonii Monacanthidae Calyptocephallela gayi Heloderma Ara ararauna Melopsittacus Astrochelys radiata Tockus flavirostris Python regius Lepas anatifera Photoblepharon palpebratum Balearica pavonina Copsychus malabaricus Geopelia placida Strigiformes Cyanoliseus patagonus Nectariniidae Amblyglyphidodon leucogaster Agapornis Equus asinus asinus Caiman yacare Apodemus sylvaticus Trachyphonus erythrocephalus Paracirrhites forsteri Ciconiidae Vicugna pacos Cyprinus carpio Meles meles Yangochiroptera Vicugna Astur gentilis Mustelidae Gypaetus Osteoglossum bicirrhosum Oxycercichthys veliferus Pseudomonacanthus peroni Ailurus fulgens Folivora Strix aluco Cyanoloxia brissonii Tiliqua scincoides Scolopsis bilineata Sufflamen chrysopterum Boltenia ovifera Apostichopus parvimensis Mungos mungo Cyclura Sebastes constellatus Macropodidae Coturnix delegorguei Falco tinnunculus Vidua paradisaea Eliomys quercinus Macropus Dinemellia Paroedura picta Giraffa giraffa Clupea harengus Anoplopoma fimbria Pseudanthias Clavelina picta Rhea americana Tayassuidae Scincidae Acinonyx Saimiriinae Pseudobalistes fuscus Cantherhines pardalis Nanger dama Fistularia commersonii Ecsenius Loweina rara Bubalus Echinarachnius parma Morone saxatilis Amazona agilis Sauromalus Paracanthurus hepatus Macroscelidea Malacochersus Sebastes norvegicus Leontocebus fuscicollis Grus japonensis Compsanthias ventralis Mya arenaria Sebastes mystinus Pytilia melba Cryptacanthodes maculatus Ara Halichoeres trimaculatus Crotalus Coliiformes Mustela Labroides bicolor Ammotragus Laemanctus Pycnonotus barbatus Trachemys scripta elegans Ophioderma panamensis Terrapene Lethenteron camtschaticum Podothecus accipenserinus Cercopithecus Gadus chalcogrammus Merops bullockoides Abronia anzuetoi Coris caudimacula Coturnix coturnix Crocodylia Chloropsis Geoemyda spengleri Centropristis striata 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 Accipiter nisus Ursus arctos 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 Athene noctua Salmo trutta Pitta moluccensis Geronticus eremita Ptilinopus pulchellus Ariopsis felis Leptailurus Yinpterochiroptera Boselaphus tragocamelus Hemilepidotus jordani Sphoeroides maculatus Halocynthia pyriformis Erethizon Cricetus Paralichthys dentatus Thyonella gemmata Lamprotornis chalcurus Ambystoma Vipera berus Erythrura Antilope Lepus timidus Ostorhinchus moluccensis Bodianus diana Hippotragus equinus Embiotoca jacksoni Passer domesticus Cynomys Hemitripterus americanus Cacatua alba Lynx lynx Caviidae Sebastolobus alascanus Musophaga Milvus milvus Psammomys obesus Eunectes Jacanidae Leptoclinus maculatus Salmo salar Styela montereyensis Capromyidae Branchiostoma floridae Papio Gallicolumba Aquila heliaca Petaurus breviceps Connochaetes Callocephalon fimbriatum Parus major Ophiopteris papillosa Canis lupus familiaris Macaca sylvanus Lyrurus tetrix Scophthalmus aquosus Cygnus cygnus Colobus guereza Molgula citrina Callithrix jacchus Cyclopsitta diophthalma Pisaster giganteus Euplectes Spheniscus humboldti Chloris chloris Chiroxiphia pareola Sebastes ovalis Pristigenys alta Polychrus marmoratus Canis lupus Puma concolor Scopus umbretta Platax teira Octopus vulgaris Chelydra serpentina Ciconia ciconia Dolichotis Bothriechis schlegelii Alitta succinea Cynictis 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 Pithecia pithecia Homarus americanus Testudo hermanni Nardoa novaecaledoniae Ploceus cucullatus Astrochelys yniphora Acryllium vulturinum Tamias Aptenodytes patagonicus Tringa totanus Sebastes atrovirens Ovis orientalis Struthio camelus Suricata Mimus polyglottos Phodopus campbelli Tockus alboterminatus Dendrocygna viduata Rhinocerotidae Lagostomus maximus Duttaphrynus melanostictus Varanus Cheilopogon californicus Tiliqua rugosa Ardea Naja Saguinus oedipus Sturnus vulgaris Circus cyaneus Sarcophilus Elephas maximus indicus Alectis ciliaris Holothuria cinerascens 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 Nymphicus hollandicus Centropyge heraldi Zamenis longissimus Ciona intestinalis Chamaeleonidae Gallus gallus Muntiacus Leucoraja ocellata Corvus corone Cucumaria frondosa Lophius piscatorius Panthera leo Lepus europaeus 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 Anthropoides paradiseus Panthera tigris Lutra lutra Coronella austriaca Phascolarctos cinereus Holothuria Cephalopholis miniata Spinus spinus Elops affinis Equus

PROVIDER: GSE195869 | GEO | 2022/06/18

REPOSITORIES: GEO