Difference between revisions of "Bird CoGe"

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| PRJNA212892<br>
 
| PRJNA212892<br>
 
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=16768 Unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=16775 Masked]<br>
 
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=16768 Unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=16775 Masked]<br>
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|-
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| [http://www.ncbi.nlm.nih.gov/genome/?term=japanese+quail Coturnix japonica]
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| Japanese quail
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| PRJDB1146
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| [https://genomevolution.org/coge/GenomeInfo.pl?gid=26048 Unmasked] [ Masked]
 
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| [http://dx.doi.org/10.5524/100007 Columba livia]<br>
 
| [http://dx.doi.org/10.5524/100007 Columba livia]<br>
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==References==
 
==References==
  
[1] [http://www.sciencemag.org/content/346/6215/1308.full E. D. Jarvis, a. et, Whole genome analyses resolve the early branches in the tree of life of modern birds. Science, (2014).]<br>
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[1] [http://www.sciencemag.org/content/346/6215/1320.full E. D. Jarvis, a. et, Whole genome analyses resolve the early branches in the tree of life of modern birds. Science  (2014).]<br>
[2] [http://www.sciencemag.org/content/346/6215/1311.full.html G. Zhang, e. al., Comparative genomics reveal insights into avian genome evolution and adaption. Science in press, (2014).]<br>
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[2] [http://www.sciencemag.org/content/346/6215/1311.full.html G. Zhang, e. al., Comparative genomics reveal insights into avian genome evolution and adaption. Science  (2014).]<br>

Latest revision as of 15:19, 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:

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
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).