Damara mole rat assembly and gene annotation

Assembly

The DMR_v1.0 assembly was submitted by BGI on 2014/09/04 . The assembly is on the Scaffold level, consisting of 162,545 assembled into 74,730 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 44,830 while the scaffold N50 is 5,314,287 The genome assembly represented here corresponds to GenBank Assembly ID: GCA_000743615.1

The genome assembly represented here corresponds to GENBANK ASSEMBLY ID GCA_000743615.1

Gene annotation

The Damaraland mole-rat, Damara mole rat, or Damaraland blesmol (Fukomys damarensis) is a burrowing rodent found in southern Africa. Along with the smaller, less hairy, naked mole rat, it is one of only two known eusocial mammals.

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

AssemblyDMR_v1.0, INSDC Assembly GCA_000743615.1, Sep 2014
Base Pairs2,286,001,154
Golden Path Length
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedOct 2016
Genebuild releasedFeb 2017
Genebuild last updated/patchedFeb 2017
Database version90.1

Gene counts

BAC end flags15,575
FP size2,722
protein_coding_NOVEL12,017
fpc clone836
protein_coding_PREDICTED257
protein_coding_KNOWN41,667

About this species