Degu assembly and gene annotation

Assembly

The OctDeg1.0 assembly was submitted by Broad Institute on 2012/05/01 . The assembly is on the Scaffold level, consisting of 259,905 assembled into 7,135 scaffolds. The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 length for the contigs is 19,847 while the scaffold N50 is 12,091,372 The genome assembly represented here corresponds to GenBank Assembly ID: GCA_000260255.1

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000260255.1

Gene annotation

The common degu (Octodon degus, /ˈdeɪɡuː/) is a small caviomorph rodent endemic to the Chilean matorral ecoregion of central Chile. The name "degu" on its own indicates either the genus Octodon or, more usually, O. degus. Common degus are in the parvorder Caviomorpha of the infraorder Hystricognathi, along with the chinchilla and guinea pig. The word degu comes from the Mapudungun dewü (mouse, rat).

The gene annotation process was carried out using a combination of protein-to-genome alignments, annotation mapping from a suitable reference species and RNA-seq alignments (where RNA-seq data with appropriate meta data were publicly available). For each candidate gene region, a selection process was applied to choose the most appropriate set of transcripts based on evolutionary distance, experimental evidence for the source data and quality of the alignments. Small ncRNAs were obtained using a combination of BLAST and Infernal/RNAfold. Pseudogenes were calculated by looking at genes with a large percentage of non-biological introns (introns of <10bp), where the gene was covered in repeats, or where the gene was single exon and evidence of a functional multi-exon paralog was found elsewhere in the genome. lincRNAs were generated via RNA-seq data where no evidence of protein homology or protein domains could be found in the transcript.

In accordance with the Fort Lauderdale Agreement , please check the publication status of the genome/assembly before publishing any genome-wide analyses using these data.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyOctDeg1.0, INSDC Assembly GCA_000260255.1, May 2012
Base Pairs2,526,244,269
Golden Path Length2,995,872,505
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedNov 2016
Genebuild releasedJul 2017
Genebuild last updated/patchedJul 2017
Database version90.1

Gene counts

Coding genes19,982
Non coding genes5,340
Small non coding genes4,275
Long non coding genes11
Misc non coding genes1,054
Pseudogenes581
Gene transcripts32,968

Other

Genscan gene predictions73,541

About this species