The avian phylogenomic project data.

Dataset type: Genomic
Data released on May 16, 2014

Zhang G; Li B; Li C; Gilbert MTP; Jarvis ED; The Avian Genome Consortium ; Wang J (2014): The avian phylogenomic project data. GigaScience Database.


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.
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.
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.
Please see the README file for a more complete description of the files that can be downloaded here.
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.

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

Additional details

Read the peer-reviewed publication(s):

Zhang, G., Li, B., Li, C., Gilbert, M. T. P., Jarvis, E. D., & Wang, J. (2014). Comparative genomic data of the Avian Phylogenomics Project. GigaScience, 3(1). doi:10.1186/2047-217x-3-26
Zhang, G., Li, C., Li, Q., Li, B., Larkin, D. M., Lee, C., … Meredith, R. W. (2014). Comparative genomics reveals insights into avian genome evolution and adaptation. Science, 346(6215), 1311–1320. doi:10.1126/science.1251385
Jarvis, E. D., Mirarab, S., Aberer, A. J., Li, B., Houde, P., Li, C., … Howard, J. T. (2014). Whole-genome analyses resolve early branches in the tree of life of modern birds. Science, 346(6215), 1320–1331. doi:10.1126/science.1253451


Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Chicken (Red jungle fowl)9031ChickenGallus gallus Source material identifiers:Hillier et al 2004 Nat...
Estimated genome size:1.3
Funding source:NIH
Wild turkey9103TurkeyTurkey Source material identifiers:Dalloul et al 2010 Plo...
Estimated genome size:1.4
Funding source:Roche 454/Univ Minnesota/Utah Univ/...
Zebra finch59729ZebrafinchZebrafinch Source material identifiers:Warren et al 2010 Natu...
Estimated genome size:1.25
Funding source:NIH
Displaying 1-3 of 3 Sample(s).

File NameSample IDData TypeFile FormatSizeRelease Date 
OtherUNKNOWN7.3 MB2014-02-07
Mixed archiveTAR16.52 GB2014-02-07
SoftwareTAR3.74 KB2014-06-24
SoftwareTAR970.81 KB2014-06-24
Chicken (Red jungle fowl)Coding sequenceFASTA7.16 MB2014-02-07
Chicken (Red jungle fowl)Sequence assemblyFASTA309.54 MB2014-02-07
Chicken (Red jungle fowl)AnnotationGFF1.66 MB2014-02-07
Chicken (Red jungle fowl)Protein sequenceFASTA4.63 MB2014-02-07
Chicken (Red jungle fowl)Repeat sequenceUNKNOWN12.13 MB2014-02-07
SoftwareTAR35.54 KB2014-06-24
Displaying 1-10 of 28 File(s).
Date Action
October 14, 2015 File 48birds_ortholog.list updated
October 14, 2015 File 48birds_ortholog.list updated
October 26, 2015 File bird_phylogenomics_data.tar.gz updated
October 28, 2015 File dNdS_analyses.tar.gz updated
October 28, 2015 File Gallus_gallus.cds.gz updated
October 28, 2015 File bird_phylogenomics_data.tar.gz updated
October 28, 2015 File bird_phylogenomics_data.tar.gz updated
October 28, 2015 File 48birds_ortholog.list updated
October 29, 2015 File Gallus_gallus.cds.gz updated
October 29, 2015 File Meleagris_gallopavo.cds.gz updated
October 29, 2015 File bird_phylogenomics_data.tar.gz updated
October 29, 2015 File Gallus_gallus.pep.gz updated
November 2, 2015 File Gallus_gallus.fa.gz updated
November 2, 2015 File Gallus_gallus.gff.gz updated
November 2, 2015 File Gallus_gallus.pep.gz updated
November 5, 2015 File dNdS_analyses.tar.gz updated
November 5, 2015 File 48birds_ortholog.list updated