The avian phylogenomic project data
The evolutionary relationship of modern birds is one of the most challenging questions in systematic biology and has been debated for centuries. We proposed to rebuild the avian phylogenetic tree by using whole genome data, thus we have collected genomes of 48 bird species, representing 36 orders of...
| Main Authors: | , , , , , , |
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| Format: | Dataset |
| Language: | English |
| Published: |
GigaScience Database
2014
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| Subjects: | |
| Online Access: | https://dx.doi.org/10.5524/101000 http://gigadb.org/dataset/101000 |
| Summary: | The evolutionary relationship of modern birds is one of the most challenging questions in systematic biology and has been debated for centuries. We proposed to rebuild the avian phylogenetic tree by using whole genome data, thus we have collected genomes of 48 bird species, representing 36 orders of bird class. The chicken, zebrafinch, and turkey genomes, which were sequenced in Sanger method, were collected from public domain. Another three genomes, pigeon, peregrine falcon, and duck, have been published during the development of this project. The data posted here include the full genome assemblies of 42 bird species, the repeat and gene annotation produced by our new pipeline, 8295 1:1 syntenic orthologous genes, and the whole genome alignment data for all bird species. The detailed information of the published genomes can be accessed from their own publications. The 42 genomes first released here were sequenced and assembled with NGS technology in whole genome shotgun strategy. Using an homology-based method, we annotated 13000~17000 protein-coding genes in each avian genome. So far as we known, the avian phylogenomic project is the biggest comparative genomics project to date. The unprecedented genomic data presented here will contribute to the downstream analyses in many fields, including phylogenetics, comparative genomics, neurology, development biology, etc. Below are listed the links to all the individual species data used in this study. In addition, the entire dataset has been compressed into a single archive file bird_phylogenomics_data.tar.gz for those who wish to retrieve the complete set. Adelie Penguin - Pygoscelis adeliae - PYGAD - http://dx.doi.org/10.5524/100006 doi:10.5524/100006 American Crow - Corvus brachyrhynchos - CORBR - http://dx.doi.org/10.5524/101008 doi:10.5524/101008 American Flamingo - Phoenicopterus ruber ruber - PHORU - http://dx.doi.org/10.5524/101035 doi:10.5524/101035 Anna's Hummingbird - Calypte anna - CALAN - http://dx.doi.org/10.5524/101004>doi:10.5524/101004 Bald Eagle - Haliaeetus leucocephalus - HALLE - https://www.ebi.ac.uk/ena/data/view/SRS561389 SRA sample: SRS561389 Barn Owl - Tyto alba - TYTAL - http://dx.doi.org/10.5524/101039 doi:10.5524/101039 Bar-tailed Trogon - Apaloderma vittatum - APAVI - http://dx.doi.org/10.5524/101016 doi:10.5524/101016 Brown Mesite - Mesitornis unicolor - MESUN - http://dx.doi.org/10.5524/101030 doi:10.5524/101030 Budgerigar - Melopsittacus undulatus - MELUN - http://dx.doi.org/10.5524/100059 doi:10.5524/100059 Carmine Bee-eater - Merops nubicus - MERNU - http://dx.doi.org/10.5524/101029 doi:10.5524/101029 Chicken - Gallus gallus - GALGA - http://www.nature.com/nature/journal/v432/n7018/full/nature03154.html Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution Chimney Swift - Chaetura pelagica - CHAPE - http://dx.doi.org/10.5524/101005 doi:10.5524/101005 Chuck-will's-widow - Antrostomus carolinensis - ANTCA - http://dx.doi.org/10.5524/101019 doi:10.5524/101019 Common Cuckoo - Cuculus canorus - CUCCA - http://dx.doi.org/10.5524/101009 doi:10.5524/101009 Common Ostrich - Struthio camelus australis - STRCA - http://dx.doi.org/10.5524/101013 doi:10.5524/101013 Crested Ibis - Nipponia nippon - NIPNI - http://dx.doi.org/10.5524/101003 doi:10.5524/101003 Cuckoo-roller - Leptosomus discolor - LEPDI - http://dx.doi.org/10.5524/101028 doi:10.5524/101028 Dalmatian Pelican - Pelecanus crispus - PELCR - http://dx.doi.org/10.5524/101032 doi:10.5524/101032 Downy Woodpecker - Picoides pubescens - PICPU - http://dx.doi.org/10.5524/101012 doi:10.5524/101012 Emperor Penguin - Aptenodytes forsteri - APTFO - http://dx.doi.org/10.5524/100005 doi:10.5524/100005 Golden-collared Manakin - Manacus vitellinus - MANVI - http://dx.doi.org/10.5524/101010 doi:10.5524/101010 Great Cormorant - Phalacrocorax carbo - PHACA - http://dx.doi.org/10.5524/101034 doi:10.5524/101034 Great-crested Grebe - Podiceps cristatus - PODCR - http://dx.doi.org/10.5524/101036 doi:10.5524/101036 Grey-crowned Crane - Balearica regulorum gibbericeps - BALRE - http://dx.doi.org/10.5524/101017 doi:10.5524/101017 Hoatzin - Opisthocomus hoazin - OPHHO - http://dx.doi.org/10.5524/101011 doi:10.5524/101011 Kea - Nestor notabilis - NESNO - http://dx.doi.org/10.5524/101031 doi:10.5524/101031 Killdeer - Charadrius vociferus - CHAVO - http://dx.doi.org/10.5524/101007 doi:10.5524/101007 Little Egret - Egretta garzetta - EGRGA - http://dx.doi.org/10.5524/101002 doi:10.5524/101002 MacQueen's Bustard - Chlamydotis macqueenii - CHLMA - http://dx.doi.org/10.5524/101022 doi:10.5524/101022 Mallard - Anas platyrhynchos - ANAPL - http://dx.doi.org/10.5524/101001 doi:10.5524/101001 Medium Ground-finch - Geospiza fortis - GEOFO - http://dx.doi.org/10.5524/100040 doi:10.5524/100040 Northern Fulmar - Fulmarus glacialis - FULGL - http://dx.doi.org/10.5524/101025 doi:10.5524/101025 Peregrine Falcon - Falco peregrinus - FALPE - http://dx.doi.org/10.5524/101006 doi:10.5524/101006 Pigeon - Columba livia - COLLI - http://dx.doi.org/10.5524/100007 doi:10.5524/100007 Red-crested Turaco - Tauraco erythrolophus - TAUER - http://dx.doi.org/10.5524/101038 doi:10.5524/101038 Red-legged Seriema - Cariama cristata - CARCR - http://dx.doi.org/10.5524/101020 doi:10.5524/101020 Red-throated Loon - Gavia stellata - GAVST - http://dx.doi.org/10.5524/101026 doi:10.5524/101026 Rhinoceros Hornbill - Buceros rhinoceros silvestris - BUCRH - http://dx.doi.org/10.5524/101018 doi:10.5524/101018 Rifleman - Acanthisitta chloris - ACACH - http://dx.doi.org/10.5524/101015 doi:10.5524/101015 Speckled Mousebird - Colius striatus - COLST - http://dx.doi.org/10.5524/101023 doi:10.5524/101023 Sunbittern - Eurypyga helias - EURHE - http://dx.doi.org/10.5524/101024 doi:10.5524/101024 Turkey - Meleagris gallopavo - MELGA - http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000475 Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis Turkey Vulture - Cathartes aura - CATAU - http://dx.doi.org/10.5524/101021 doi:10.5524/101021 White-tailed Eagle - Haliaeetus albicilla - HALAL - http://dx.doi.org/10.5524/101027 doi:10.5524/101027 White-tailed Tropicbird - Phaethon lepturus - PHALE - http://dx.doi.org/10.5524/101033 doi:10.5524/101033 White-throated Tinamou - Tinamus guttatus - TINGU - http://dx.doi.org/10.5524/101014 doi:10.5524/101014 Yellow-throated Sandgrouse - Pterocles gutturalis - PTEGU - http://dx.doi.org/10.5524/101037 doi:10.5524/101037 Zebra Finch - Taeniopygia guttata - TAEGU - http://www.nature.com/nature/journal/v464/n7289/full/nature08819.html The genome of a songbird |
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