Difference between revisions of "Bird CoGe"

Latest revision as of 16:19, 27 July 2015

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:

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 (2014).
[2] G. Zhang, e. al., Comparative genomics reveal insights into avian genome evolution and adaption. Science (2014).