The Gallus_gallus-5.0 assembly of the chicken genome was released in December 2015 by the International Chicken Genome Consortium. It consists of 34 chromosomes, 1 linkage group and 15,411 unplaced scaffolds.
The genome assembly represented here corresponds to GenBank Assembly ID GCA_000002315.3
Gallus_gallus-5.0 was annotated using a standard Ensembl genebuild pipeline, incorporating RNASeq data (PRJEB12891) and PacBio long read data (PRJEB13248, PRJEB13246) provided by the Roslin Institute. The annotation process is described in the document below.
PacBio long read data set
Two tissue samples were sequenced using the PacBio long read sequencing technology, embryo and brain. Both sets were used to add UTR to gene models and as input source for our lincRNA discovery pipeline. The embryo set was sequenced using 5' and 3' capping, therefore all the sequences were considered as full length cDNAs and incorporated into the gene models.
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. 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:
|Tissue||Number of gene models|
|Left optic lobe||7616|
General information about this species can be found in Wikipedia.
|Assembly||Gallus_gallus-5.0, INSDC Assembly GCA_000002315.3, Dec 2015|
|Golden Path Length||1,230,258,557|
|Annotation method||Full genebuild|
|Genebuild started||Jun 2016|
|Genebuild released||Oct 2016|
|Genebuild last updated/patched||Dec 2016|
|Non coding genes||6,492|
|Small non coding genes||1,705|
|Long non coding genes||4,643|
|Misc non coding genes||144|
|Genscan gene predictions||50,996|