Naked mole-rat male assembly and gene annotation

Assembly

The HetGla_1.0 assembly was submitted by Beijing Genomics Institute on 2011/10/14 . The assembly is on the Scaffold level, consisting of 273,991 assembled into 39,267 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 21,750 while the scaffold N50 is 1,603,177 The genome assembly represented here corresponds to GenBank Assembly ID: GCA_000230445.1

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000230445.1

Gene annotation

The naked mole-rat (Heterocephalus glaber), also known as the sand puppy or desert mole rat, is a burrowing rodent closely related to the blesmols, native to parts of East Africa, and is the only species currently classified in the genus Heterocephalus. The genus is classified as being in the family Bathyergidae or in its own family, Heterocephalidae. The naked mole-rat, the Damaraland mole-rat, and Mechow's mole-rat are eusocial mammals, the highest classification of sociality. It has a highly unusual set of physical traits that enable it to thrive in an otherwise harsh underground environment; it is the only mammalian thermoconformer, almost entirely ectothermic (cold-blooded) in how it regulates body temperature.

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

AssemblyHetGla_1.0, INSDC Assembly GCA_000230445.1, Oct 2011
Base Pairs2,430,064,805
Golden Path Length2,643,978,223
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedNov 2016
Genebuild releasedJul 2017
Genebuild last updated/patchedJul 2017
Database version90.1

Gene counts

Coding genes20,742
Non coding genes11,446
Small non coding genes3,009
Long non coding genes7,598
Misc non coding genes839
Pseudogenes559
Gene transcripts41,841

Other

Genscan gene predictions58,005

About this species