Chicken assembly and gene annotation

The red junglefowl (Gallus gallus) is a tropical member of the family Phasianidae. It is the primary progenitor of the domestic chicken (though genetic evidence strongly suggests some past hybridisation with the grey junglefowl, as well). The red junglefowl was first domesticated at least 5000 years ago in Asia. Since then, it has spread around the world, and the domestic form is kept globally as a very productive food source of both meat and eggs.

Assembly

The Gallus_gallus-4.0 assembly of the chicken genome was produced in November 2011 by the International Chicken Genome Consortium. It consists of 31 chromosomes, 2 linkage groups and 14,093 unplaced scaffolds.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000002315.2

Other assemblies

Gene annotation

Gallus_gallus-4.0 was annotated using a standard Ensembl genebuild pipeline, incorporating RNASeq data provided by a number of sources. The annotation process is described in the document below.

RNASeq data set

In addition to the main set, we have predicted gene models for each tissue type using the RNA-Seq pipeline. We did a BLASTp of these models against UniProt proteins of vertabrate species with protein existence level 1 and 2 in order to confirm the open reading frame (ORF). The best BLAST hit is displayed as a transcript supporting evidence. 5139 gene models were made exclusively from RNASeq data. The data was also used to add UTR to gene models.

The tissue-specific sets of transcript models built using our RNAseq pipeline are as follows:

TissueNumber of gene models
embryo13326
merged16915
heart10710
testes14600
macrophage11339
unspecified11324
somites11350
df1_fibroblast9266
kidney10688
breast9161
cerebellum10591
brain10890

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyGalgal4, INSDC Assembly GCA_000002315.2, Nov 2011
Base Pairs1,072,544,763
Golden Path Length1,046,932,099
Annotation methodFull genebuild
Genebuild startedDec 2011
Genebuild releasedApr 2013
Genebuild last updated/patchedDec 2013
Database version95.4

Gene counts

Coding genes15,508
Pseudogenes42
Gene transcripts17,954

Other

Genscan gene predictions40,572
Short Variants9,456,218

About this species