DOI: 10.5524/101000
title: The avian phylogenomic project data.

description: 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 Beijing duck, have been published during the development of this project.
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The data posted here include the full genome assemblies of 45 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 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.
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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. 
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Please see the README file for a more complete description of the files that can be downloaded here.<br>
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 for those who wish to retrieve the complete set.<br>
<br>Adelie Penguin - <em>Pygoscelis adeliae</em> - PYGAD - doi:10.5524/100006
<br>American Crow - <em>Corvus brachyrhynchos</em> - CORBR - doi:10.5524/101008
<br>American Flamingo - <em>Phoenicopterus ruber ruber</em> - PHORU - doi:10.5524/101035
<br>Anna's Hummingbird - <em>Calypte anna</em> - CALAN - doi:10.5524/101004
<br>Beijing Duck (Mallard) - <em>Anas platyrhynchos</em> - ANAPL - doi:10.5524/101001
<br>Bald Eagle - <em>Haliaeetus leucocephalus</em> - HALLE - doi:10.5524/101040
<br>Barn Owl - <em>Tyto alba</em> - TYTAL - doi:10.5524/101039
<br>Bar-tailed Trogon - <em>Apaloderma vittatum</em> - APAVI - doi:10.5524/101016
<br>Brown Mesite - <em>Mesitornis unicolor</em> - MESUN - doi:10.5524/101030
<br>Budgerigar - <em>Melopsittacus undulatus</em> - MELUN - doi:10.5524/100059
<br>Carmine Bee-eater - <em>Merops nubicus</em> - MERNU - doi:10.5524/101029
<br>Chicken - <em>Gallus gallus</em> - GALGA - Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
<br>Chimney Swift - <em>Chaetura pelagica</em> - CHAPE - doi:10.5524/101005
<br>Chuck-will's-widow - <em>Antrostomus carolinensis</em> - ANTCA - doi:10.5524/101019
<br>Common Cuckoo - <em>Cuculus canorus</em> - CUCCA - doi:10.5524/101009
<br>Common Ostrich - <em>Struthio camelus australis</em> - STRCA - doi:10.5524/101013
<br>Crested Ibis - <em>Nipponia nippon</em> - NIPNI - doi:10.5524/101003
<br>Cuckoo-roller - <em>Leptosomus discolor</em> - LEPDI - doi:10.5524/101028
<br>Dalmatian Pelican - <em>Pelecanus crispus </em> - PELCR - doi:10.5524/101032
<br>Downy Woodpecker - <em>Picoides pubescens</em> - PICPU - doi:10.5524/101012
<br>Emperor Penguin - <em>Aptenodytes forsteri</em> - APTFO - doi:10.5524/100005
<br>Golden-collared Manakin - <em>Manacus vitellinus</em> - MANVI - doi:10.5524/101010
<br>Great Cormorant - <em>Phalacrocorax carbo</em> - PHACA - doi:10.5524/101034
<br>Great-crested Grebe - <em>Podiceps cristatus</em> - PODCR - doi:10.5524/101036
<br>Grey-crowned Crane - <em>Balearica regulorum gibbericeps</em> - BALRE - doi:10.5524/101017
<br>Hoatzin - <em>Opisthocomus hoazin</em> - OPHHO - doi:10.5524/101011
<br>Kea - <em>Nestor notabilis </em> - NESNO - doi:10.5524/101031
<br>Killdeer - <em>Charadrius vociferus </em> - CHAVO - doi:10.5524/101007
<br>Little Egret - <em>Egretta garzetta</em> - EGRGA - doi:10.5524/101002
<br>MacQueen's Bustard - <em>Chlamydotis macqueenii </em> - CHLMA - doi:10.5524/101022
<br>Medium Ground-finch - <em>Geospiza fortis</em> - GEOFO - doi:10.5524/100040
<br>Northern Fulmar - <em>Fulmarus glacialis</em> - FULGL - doi:10.5524/101025
<br>Peregrine Falcon - <em>Falco peregrinus</em> - FALPE - doi:10.5524/101006
<br>Pigeon - <em>Columba livia</em> - COLLI - doi:10.5524/100007
<br>Red-crested Turaco - <em>Tauraco erythrolophus</em> - TAUER - doi:10.5524/101038
<br>Red-legged Seriema - <em>Cariama cristata</em> - CARCR - doi:10.5524/101020
<br>Red-throated Loon - <em>Gavia stellata</em> - GAVST - doi:10.5524/101026
<br>Rhinoceros Hornbill - <em>Buceros rhinoceros silvestris</em> - BUCRH - doi:10.5524/101018
<br>Rifleman - <em>Acanthisitta chloris</em> - ACACH - doi:10.5524/101015
<br>Speckled Mousebird - <em>Colius striatus</em> - COLST - doi:10.5524/101023
<br>Sunbittern - <em>Eurypyga helias</em> - EURHE - doi:10.5524/101024
<br>Turkey - <em>Meleagris gallopavo</em> - MELGA - Multi-Platform Next-Generation Sequencing of the Domestic Turkey (<em>Meleagris gallopavo</em>): Genome Assembly and Analysis
<br>Turkey Vulture - <em>Cathartes aura</em> - CATAU - doi:10.5524/101021
<br>White-tailed Eagle - <em>Haliaeetus albicilla</em> - HALAL - doi:10.5524/101027
<br>White-tailed Tropicbird - <em>Phaethon lepturus</em> - PHALE - doi:10.5524/101033
<br>White-throated Tinamou - <em>Tinamus guttatus</em> - TINGU - doi:10.5524/101014
<br>Yellow-throated Sandgrouse - <em>Pterocles gutturalis</em> - PTEGU - doi:10.5524/101037
<br>Zebra Finch - <em>Taeniopygia guttata</em> - TAEGU - The genome of a songbird