Degu assembly and gene annotation

The common degu (Octodon degus) is a small caviomorph rodent endemic to the Chilean matorral ecoregion of central Chile. Common degus are in the parvorder Caviomorpha of the infraorder Hystricognathi, along with the chinchilla and guinea pig.

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.

Gene annotation

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.

• Detailed information on rodent clade genebuild (PDF)

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.