Turkey assembly and gene annotation

Assembly

Turkey_2.01 (GCA_000146605.1) is an assembly of the domesticated turkey genome. The first sequences have been generated with the GS-Titanium platform in VBI's (Virginia Bioinformatics Institute) Core Lab. Additionally, the USDA (United States Department of Agriculture) Beltsville group provided 30x coverage with Illumina 70 bp reads. And the Salzberg group at UMD (University of Maryland) assisted with assembly and annotation of the integrated 454/Illumina/BAC end sequence data set into a "draft genome sequence". The whole composite covers 90% of the genome.

The turkey genome is composed of 33 chromosomes, assembled from 152,913 contigs. The total number of bases in the genome is 1.04Gb.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000146605.1

Gene annotation

The gene set for turkey was built using the Ensembl genebuild pipeline. Gene models are based on genewise alignments of chicken proteins as well as genetically distant proteins from other species, including most vertebrates from Uniprot. To improve the accuracy of models generated from distant species, the Genewise alignments were made to stretches of genomic sequence rather than to 'miniseqs'. The protein based gene models were then extended using turkey cDNA and EST alignments as well as chicken cDNA. Potentially missing predictions and partial gene predictions were identified by examining the human-chicken one-to-one orthologs, which were then used to build new gene models.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyTurkey_2.01, INSDC Assembly GCA_000146605.1, Sep 2010
Database version77.21
Base Pairs935,922,388
Golden Path Length

The golden path is the length of the reference assembly. It consists of the sum of all top-level sequences in the seq_region table, omitting any redundant regions such as haplotypes and PARs (pseudoautosomal regions).

1,061,817,103
Genebuild byEnsembl
Genebuild methodFull genebuild
Genebuild startedSep 2010
Genebuild releasedDec 2010
Genebuild last updated/patchedApr 2014

Gene counts

Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

14,123
Small non coding genes

Small non coding genes are usually fewer than 200 bases long. They may be transcribed but are not translated. In Ensembl, genes with the following biotypes are classed as small non coding genes: miRNA, miscRNA, rRNA, scRNA, snlRNA, snoRNA, snRNA, and also the pseudogenic form of these biotypes. The majority of the small non coding genes in Ensembl are annotated automatically by our ncRNA pipeline. Please note that tRNAs are annotated separately using tRNAscan. tRNAs are included as 'simple fetaures', not genes, because they are not annotated using aligned sequence evidence.

755
Pseudogenes

A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

124
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.17,373

Other

Genscan gene predictions31,195
Short Variants6,812