Bird CoGe
Contents
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:
| Species |
English Name |
BioProject ID |
GigaScience |
|---|---|---|---|
| Acanthisitta chloris |
Rifleman |
PRJNA212877 |
|
| Anas platyrhynchos |
Peking Duck |
PRJNA46621 |
|
| Antrostomus carolinensis |
Chuck-will's-widow |
PRJNA212888 |
|
| Apaloderma vittatum |
Bar-tailed Trogon |
PRJNA212878 |
|
| Aptenodytes forsteri |
Emperor Penguin |
PRJNA235982 |
|
| Balearica regulorum |
Grey crowned-crane |
PRJNA212879 |
|
| Buceros rhinoceros |
Rhinoceros Hornbill |
PRJNA212887 |
|
| Calypte anna |
Anna's Hummingbird |
PRJNA212866 |
|
| Cariama cristata |
Red-legged Seriema |
PRJNA212889 |
|
| Cathartes aura |
Turkey Vulture |
PRJNA212890 |
|
| Chaetura pelagica |
Chimney Swift |
PRJNA210808 |
|
| Charadrius vociferus |
Killdeer |
PRJNA212867 |
|
| Chlamydotis macqueenii |
MacQueen's Bustard |
PRJNA212891 |
|
| Colius striatus |
Speckled Mousebird |
PRJNA212892 |
|
| Columba livia |
Pigeon |
PRJNA167554 |
|
| Corvus brachyrhynchos |
American Crow |
PRJNA212869 |
|
| Cuculus canorus |
Common Cuckoo |
PRJNA212870 |
|
| Egretta garzetta |
Little Egret |
PRJNA232959 |
|
| Eurypyga helias |
Sunbittern |
PRJNA212893 |
|
| Falco peregrinus |
Peregrine Falcon |
PRJNA159791 |
|
| Fulmarus glacialis |
Northern Fulmar |
PRJNA212894 |
|
| Gallus gallus |
Chicken |
PRJNA13342 |
|
| Gavia stellata |
Red-throated Loon |
PRJNA212895 |
|
| Geospiza fortis |
Medium Ground-finch |
PRJNA156703 |
|
| Haliaeetus albicilla |
White-tailed Eagle |
PRJNA212896 |
|
| Haliaeetus leucocephalus |
Bald Eagle |
PRJNA237821 |
|
| Leptosomus discolor |
Cuckoo-roller |
PRJNA212897 |
|
| Manacus vitellinus |
Golden-collared Manakin |
PRJNA212872 |
|
| Meleagris gallopavo |
Turkey |
PRJNA42129 |
|
| Melopsittacus undulatus |
Budgerigar |
PRJEB1588 |
|
| Merops nubicus |
Carmine Bee-eater |
PRJNA212898 |
|
| Mesitornis unicolor |
Brown Mesite |
PRJNA212899 |
|
| Nestor notabilis |
Kea |
PRJNA212900 |
|
| Nipponia nippon |
Crested ibis |
PRJNA232572 |
|
| Ophisthocomus hoazin |
Hoatzin |
PRJNA212873 |
|
| Pelecanus crispus |
Dalmatian Pelican |
PRJNA212901 |
|
| Phaethon lepturus |
White-tailed Tropicbird |
PRJNA212902 |
|
| Phalacrocorax carbo |
Great Cormorant |
PRJNA212903 |
|
| Phoenicopterus ruber |
American Flamingo |
PRJNA212904 |
|
| Picoides pubescens |
Downy Woodpecker |
PRJNA212874 |
|
| Podiceps cristatus |
Great Crested Grebe |
PRJNA212905 |
|
| Pterocles gutturalis |
Yellow-throated Sandgrouse |
PRJNA212906 |
|
| Pygoscelis adeliae |
Adelie Penguin |
PRJNA235983 |
|
| Struthio camelus |
Common Ostrich |
PRJNA212875 |
|
| Taeniopygia guttata |
Zebra Finch |
PRJNA17289 |
|
| Tauraco erythrolophus |
Red-crested Turaco |
PRJNA212908 |
|
| Tinamus guttatus |
White-throated Tinamou |
PRJNA212876 |
|
| Tyto alba |
Barn Owl |
PRJNA212909 |
|
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.
- CoGe Bird Genomes Notebook - CoGe Notebook containing all masked and unmasked Croc genomes, for easy access to comparative genome analyses.
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).
