Bird CoGe

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
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.

• Bird Genomes: All
• Bird Genomes: Masked
• Bird Genomes: Unmasked

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).