Bird CoGe

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About the Project

CoGe is providing support for the Avian Phylogenomics Initiative. This group has sequenced genomes of over 50 avian species, including one species belonging to each major order. The goals of the project are to:

1) Perform phylogenomic analyses to decipher avian phylogeny;
2) Identify genetic changes as signatures of convergent selection, including in vocal learning species;
3) Sequence genomes of avian species that provide scientific value to the community, are national symbols, or endangered; and
4) Provide a public resource for scientist.

The project is partnered with other initiatives such as the Genome 10K (G10K) group to sequencing 10,000 vertebrate species in 10 years, a Copenhagen phylogenome group to decipher avian phylogeny, and the Beijing Genome Institute (BGI) to also decipher avian phylogeny and provide genomic resources. The project is coordinated by Erich Jarvis (Duke), Tom Gilbert (Copenhagen), and Goujie Zhang (BGI).

For select publications from this project, see References.

Available Resources

Genomes sequences for the following species are available, either as part of this project, or from other avian genome projects:

Table 1. Genomes used in the avian phylogenomics project. Listed are the scientific species name, English name, BioProject ID in the NCBI database for each genome (http://www.ncbi.nlm.nih.gov/bioproject), and GigaScience deposited genome sequences and raw reads. Full details are in references [1] and [2].
Species
English Name
BioProject ID
GigaScience
Acanthisitta chloris
Rifleman
PRJNA212877
http://dx.doi.org/10.5524/101015
Anas platyrhynchos
Peking Duck
PRJNA46621
http://dx.doi.org/10.5524/101001
Antrostomus carolinensis
Chuck-will's-widow
PRJNA212888
http://dx.doi.org/10.5524/101019
Apaloderma vittatum Bar-tailed Trogon
Bar-tailed Trogon
PRJNA212878
http://dx.doi.org/10.5524/101016
Aptenodytes forsteri
Emperor Penguin
PRJNA235982
http://dx.doi.org/10.5524/100005
Balearica regulorum
Grey crowned-crane
PRJNA212879
http://dx.doi.org/10.5524/101017
Buceros rhinoceros
Rhinoceros Hornbill
PRJNA212887
http://dx.doi.org/10.5524/101018
Calypte anna
Anna's Hummingbird
PRJNA212866
http://dx.doi.org/10.5524/101004
Cariama cristata
Red-legged Seriema
PRJNA212889
http://dx.doi.org/10.5524/101020
Cathartes aura
Turkey Vulture
PRJNA212890
http://dx.doi.org/10.5524/101021
Chaetura pelagica
Chimney Swift
PRJNA210808
http://dx.doi.org/10.5524/101005
Charadrius vociferus
Killdeer
PRJNA212867
http://dx.doi.org/10.5524/101007
Chlamydotis macqueenii
MacQueen's Bustard
PRJNA212891
http://dx.doi.org/10.5524/101022
Colius striatus
Speckled Mousebird
PRJNA212892
http://dx.doi.org/10.5524/101023
Columba livia
Pigeon
PRJNA167554
http://dx.doi.org/10.5524/100007
Corvus brachyrhynchos
American Crow
PRJNA212869
http://dx.doi.org/10.5524/101008
Cuculus canorus
Common Cuckoo
PRJNA212870
http://dx.doi.org/10.5524/101009
Egretta garzetta
Little Egret
PRJNA232959
http://dx.doi.org/10.5524/101002
Eurypyga helias
Sunbittern
PRJNA212893
http://dx.doi.org/10.5524/101024
Falco peregrinus
Peregrine Falcon
PRJNA159791
http://dx.doi.org/10.5524/101006
Fulmarus glacialis
Northern Fulmar
PRJNA212894
http://dx.doi.org/10.5524/101025
Gallus gallus
Chicken
PRJNA13342
N.A.
Gavia stellata
Red-throated Loon
PRJNA212895
http://dx.doi.org/10.5524/101026
Geospiza fortis
Medium Ground-finch
PRJNA156703
http://dx.doi.org/10.5524/100040
Haliaeetus albicilla
White-tailed Eagle
PRJNA212896
http://dx.doi.org/10.5524/101027
Haliaeetus leucocephalus
Bald Eagle
PRJNA237821
http://dx.doi.org/10.5524/101040
Leptosomus discolor
Cuckoo-roller
PRJNA212897
http://dx.doi.org/10.5524/101028
Manacus vitellinus
Golden-collared Manakin
PRJNA212872
http://dx.doi.org/10.5524/101010
Meleagris gallopavo
Turkey
PRJNA42129
N.A.
Melopsittacus undulatus
Budgerigar
PRJEB1588
http://dx.doi.org/10.5524/100059
Merops nubicus
Carmine Bee-eater
PRJNA212898
http://dx.doi.org/10.5524/101029
Mesitornis unicolor
Brown Mesite
PRJNA212899
http://dx.doi.org/10.5524/101030
Nestor notabilis
Kea
PRJNA212900
http://dx.doi.org/10.5524/101031
Nipponia nippon
Crested ibis
PRJNA232572
http://dx.doi.org/10.5524/101003
Ophisthocomus hoazin
Hoatzin
PRJNA212873
http://dx.doi.org/10.5524/101011
Pelecanus crispus
Dalmatian Pelican
PRJNA212901
http://dx.doi.org/10.5524/101032
Phaethon lepturus
White-tailed Tropicbird
PRJNA212902
http://dx.doi.org/10.5524/101033
Phalacrocorax carbo
Great Cormorant
PRJNA212903
http://dx.doi.org/10.5524/101034
Phoenicopterus ruber
American Flamingo
PRJNA212904
http://dx.doi.org/10.5524/101035
Picoides pubescens
Downy Woodpecker
PRJNA212874
http://dx.doi.org/10.5524/101012
Podiceps cristatus
Great Crested Grebe
PRJNA212905
http://dx.doi.org/10.5524/101036
Pterocles gutturalis
Yellow-throated Sandgrouse
PRJNA212906
http://dx.doi.org/10.5524/101037
Pygoscelis adeliae
Adelie Penguin
PRJNA235983
http://dx.doi.org/10.5524/100006
Struthio camelus
Common Ostrich
PRJNA212875
http://dx.doi.org/10.5524/101013
Taeniopygia guttata
Zebra Finch
PRJNA17289
N.A.
Tauraco erythrolophus
Red-crested Turaco
PRJNA212908
http://dx.doi.org/10.5524/101038
Tinamus guttatus
White-throated Tinamou
PRJNA212876
http://dx.doi.org/10.5524/101014
Tyto alba
Barn Owl
PRJNA212909
http://dx.doi.org/10.5524/101039


Using the Resources on CoGe

The Comparative Genomics (CoGe) browser is designed to make it easy to find and compare genomic sequences, including multiple species and multiple versions of genomes. There is no single, linear workflow through the system. Instead, CoGe's tools allow you to access the system to find sequences of interest, and "hub" points to take you from one part of the system to another. This allows for ideas to be generated while working CoGe, and be able to quickly branch out to investigate any number of interesting phenomena you find.

The bird genomes are publicly available through CoGe, and are organized into notebooks.

CoGe's web-tools have several applications for initiating an analysis:

  • OrganismView: Search and get an overview of an organism and its genomic information
  • CoGeBlast: Blast against any number of organisms using CoGe's Blast interface (supports Blast, and BlastZ).
  • FeatView: Search for genomic features by name or description
  • SynMap: Generate syntenic dotplots of any two genomes
  • GEvo: Compare multiple genomic regions using a variety of sequence comparison algorithms for high-resolution analysis to quickly identify patterns of genome evolution

More information on getting started, including tutoials on how to use CoGe tools, is here: https://genomevolution.org/wiki/index.php/New_to_CoGe

Useful Links

  • Birdbase - A database of avian genes and genomes.
  • AgBase - A curated resource for functional analysis of agricultural plant and animal gene products, including Gene Ontology annotations.
  • Chicken Gene Nomenclature Consortium (CGNC) - Providing standardized gene nomenclature for chicken genes.

Related Resources

  • Croc CoGe - Crocodile genomes from the Croc Genome Project

References

[1] E. D. Jarvis, a. et, Whole genome analyses resolve the early branches in the tree of life of modern birds. Science in press, (2014).
[2] G. Zhang, e. al., Comparative genomics reveal insights into avian genome evolution and adaption. Science in press, (2014).