Red Jungle Fowl

Habitat and Domestication

The red jungle fowl (Gallus gallus) lives in thick secondary forest. In the morning or evening, the bird can be found in open areas or clearings. The red jungle fowl is native to Southern and Southeastern Asia. There are three other Gallus species, the green jungle fowl (Gallus varius), the grey jungle fowl (Gallus sonneratii) and the Ceylon or Lafayette's jungle fowl (Gallus lafayettei). The red jungle fowl is considered the progenitor of the modern chicken breeds used today in commercial agriculture. The exact time and place of domestication are unclear, and this may have occurred more than once during human history. It's believed that the modern chicken derives from birds kept by the people of the Harappan culture (2500-2100 B.C.), primarily for fighting purposes.

Biology

The female red jungle fowl plumage is generally a dull brown gold color, whereas the male is more brilliantly colored in combinations of gold, red, brown, dark maroon, orange, with a bit of metallic green and gray. The red jungle fowl can measure up to 70 centimeters in length. The red jungle fowl genome, as the first sequenced representative of the avian lineage, is in important key to better understanding species evolution, via comparison to previously sequenced mammalian and fish genomes. The chicken has been described as the premier non-mammalian vertebrate model organism and was the first genome to be sequenced of an animal that represents a significant component of the world's food supply. The chicken and birds in general have a compact genome in comparison to mammals, averaging about 1.2Gb in size, with chromosome subtypes defined as macro- and microchromosomes. The sequence suggests that the smaller size of avian genomes derives primarily from a comparative dearth of repetitive elements that can copy themselves and spread throughout a genome over the course of evolution. The chicken genome appears to retain few, if any, such repetitive elements that remain able to replicate. Interestingly, the bird sex chromosomes, named Z and W, are unlike those of mammals, in that the female (ZW) is heterogametic. Chromosomal sex determination appears to have evolved independently in the evolutionary line that led to modern birds from that which occurred in the mammalian line. The last common ancestor of birds and mammals is believed to have been a reptile that lived over 310 million years ago. Birds are now thought to be direct descendants of the dinosaurs - therefore, the chicken genome is likely the closest sequenced genome to those of the dinosaurs.

-- From the Animal Diversity Web at the University of Michigan Museum of Zoology

Sequencing Summary

The red jungle fowl genome was sequenced to 6X coverage using a female known as "RJF #256" from an inbred line (UCD 001) that serves as the reference genome. The total 6X genome sequence coverage has been assembled and is available on our web site as well as all the major genome browsers. A comprehensive BAC based physical map of ~20X coverage is also available. Ongoing sequence improvement efforts at WUGSC will act to enhance the quality of the draft assembly and this new assembly will be available soon. We are in the process of BAC based finishing of biologically interesting regions defined in the ENCODE project. Funding for the sequence characterization of the red jungle fowl genome was provided by the National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH).

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Contacts

Name	Affiliation
Wes Warren	The Genome Institute, Washington University School of Medicine
Jerry Dodgson	Microbiology and Molecular Genetics, Michigan State University
Dave Burt	Roslin Institute - Edinburgh
Martien Groenen	Animal Breeding and Genetics Group, Wageningen University
Ewan Birney	Project Ensembl - European Bioinformatics Institute

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Sequences & Maps

Assemblies

Name	Date	Description	Blast DBs
Gallus_gallus-1.0	Feb 24, 2004	6.6X draft	contigs reads.unplaced supercontigs ultracontigs chromosomes
Gallus_gallus-2.1	Oct 19, 2005	improved 6.6X draft	contigs chromosomes
Gallus_gallus-3.0	Nov 09, 2008	12x 454 pcap assembly	contigs removed_data

Sequences

Name	Date	Description	Blast DBs
Gallus_gallus	Feb 24, 2004	Fosmid ends	fosmid_ends

Maps

Name	Date	Type	Description
Gallus gallus	Mar 01, 2006	Physical	FPC

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Related Links

Sequence Data

• NCBI

Genome Browser

• NCBI
• UCSC

Others

• Avian Influenza Information (Texas A&M University)
• BBSRC ChickEST Database
• Chicken RH map (INRA)
• NetVet (Birds)
• NHGRI Chicken Genome Sequencing page
• US Poultry Genome Project

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Publications

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