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 |
Genome Links |
|---|---|---|---|
| Acanthisitta chloris |
Rifleman |
PRJNA212877 |
Unmasked Masked |
| Anas platyrhynchos |
Peking Duck |
PRJNA46621 |
Unmasked Masked |
| Antrostomus carolinensis |
Chuck-will's-widow |
PRJNA212888 |
N/A |
| Apaloderma vittatum |
Bar-tailed Trogon |
PRJNA212878 |
Unmasked Masked |
| Aptenodytes forsteri |
Emperor Penguin |
PRJNA235982 |
N/A |
| Balearica regulorum |
Grey crowned-crane |
PRJNA212879 |
Unmasked Masked |
| Buceros rhinoceros |
Rhinoceros Hornbill |
PRJNA212887 |
Unmasked Masked |
| Calypte anna |
Anna's Hummingbird |
PRJNA212866 |
Unmasked Masked |
| Caprimulgus carolinensis |
Nightjar |
N/A |
Unmasked Masked |
| Cariama cristata |
Red-legged Seriema |
PRJNA212889 |
Unmasked Masked |
| Cathartes aura |
Turkey Vulture |
PRJNA212890 |
N/A |
| Chaetura pelagica |
Chimney Swift |
PRJNA210808 |
Unmasked Masked |
| Charadrius vociferus |
Killdeer |
PRJNA212867 |
Unmasked Masked |
| Chlamydotis macqueenii |
MacQueen's Bustard |
PRJNA212891 |
Unmasked Masked |
| Colius striatus |
Speckled Mousebird |
PRJNA212892 |
Unmasked Masked |
| Coturnix japonica | Japanese quail | PRJDB1146 | Unmasked [ Masked] |
| Columba livia |
Pigeon |
PRJNA167554 |
Unmasked Masked |
| Corvus brachyrhynchos |
American Crow |
PRJNA212869 |
Unmasked Masked |
| Cuculus canorus |
Common Cuckoo |
PRJNA212870 |
N/A |
| Egretta garzetta |
Little Egret |
PRJNA232959 |
Unmasked Masked |
| Eurypyga helias |
Sunbittern |
PRJNA212893 |
Unmasked Masked |
| Falco peregrinus |
Peregrine Falcon |
PRJNA159791 |
Unmasked Masked |
| Fulmarus glacialis |
Northern Fulmar |
PRJNA212894 |
Unmasked Masked |
| Gallus gallus |
Chicken |
PRJNA13342 |
Unmasked Masked |
| Gavia stellata |
Red-throated Loon |
PRJNA212895 |
Unmasked Masked |
| Geospiza fortis |
Medium Ground-finch |
PRJNA156703 |
Unmasked Masked |
| Haliaeetus albicilla |
White-tailed Eagle |
PRJNA212896 |
Unmasked Masked |
| Haliaeetus leucocephalus |
Bald Eagle |
PRJNA237821 |
N/A |
| Leptosomus discolor |
Cuckoo-roller |
PRJNA212897 |
Unmasked Masked |
| Manacus vitellinus |
Golden-collared Manakin |
PRJNA212872 |
Unmasked Masked |
| Meleagris gallopavo |
Turkey |
PRJNA42129 |
Unmasked Masked |
| Melopsittacus undulatus |
Budgerigar |
PRJEB1588 |
Unmasked Masked |
| Merops nubicus |
Carmine Bee-eater |
PRJNA212898 |
Unmasked Masked |
| Mesitornis unicolor |
Brown Mesite |
PRJNA212899 |
Unmasked Masked |
| Nestor notabilis |
Kea |
PRJNA212900 |
Unmasked Masked |
| Nipponia nippon |
Crested ibis |
PRJNA232572 |
Unmasked Masked |
| Ophisthocomus hoazin |
Hoatzin |
PRJNA212873 |
Unmasked Masked |
| Pelecanus crispus |
Dalmatian Pelican |
PRJNA212901 |
Unmasked Masked |
| Phaethon lepturus |
White-tailed Tropicbird |
PRJNA212902 |
Unmasked Masked |
| Phalacrocorax carbo |
Great Cormorant |
PRJNA212903 |
Unmasked Masked |
| Phoenicopterus ruber |
Caribbean Flamingo |
PRJNA212904 |
Unmasked Masked |
| Picoides pubescens |
Downy Woodpecker |
PRJNA212874 |
Unmasked Masked |
| Podiceps cristatus |
Great Crested Grebe |
PRJNA212905 |
Unmasked Masked |
| Pterocles gutturalis |
Yellow-throated Sandgrouse |
PRJNA212906 |
Unmasked Masked |
| Pygoscelis adeliae |
Adelie Penguin |
PRJNA235983 |
Unmasked Masked |
| Struthio camelus |
Common Ostrich |
PRJNA212875 |
Unmasked Masked |
| Taeniopygia guttata |
Zebra Finch |
PRJNA17289 |
Unmasked Masked |
| Tauraco erythrolophus |
Red-crested Turaco |
PRJNA212908 |
Unmasked Masked |
| Tinamus guttatus |
White-throated Tinamou |
PRJNA212876 |
Unmasked Masked |
| Tyto alba |
Barn Owl |
PRJNA212909 |
Unmasked Masked |
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 (2014).
[2] G. Zhang, e. al., Comparative genomics reveal insights into avian genome evolution and adaption. Science (2014).
