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Coquerel's sifaka assembly and gene annotation

Assembly

The Pcoq_1.0 assembly was submitted by Baylor College of Medicine on 2015/03/23 . The assembly is on the Scaffold level, consisting of 299,070 assembled into 22,539 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 28,129 while the scaffold N50 is 5,604,909.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000956105.1

Gene annotation

The Coquerel's sifaka (Propithecus coquereli) is a diurnal, medium-sized lemur of the sifaka genus Propithecus. It is native to Madagascar. The Coquerel's sifaka was once considered to be a subspecies of the Verreaux's sifaka, but was eventually granted full species level.

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.

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

AssemblyPcoq_1.0, INSDC Assembly GCA_000956105.1, Mar 2015
Base Pairs2,083,764,538
Golden Path Length2,798,152,141
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedAug 2017
Genebuild releasedDec 2017
Genebuild last updated/patchedDec 2017
Database version94.1

Gene counts

Coding genes17,925
Non coding genes5,294
Small non coding genes3,245
Long non coding genes7
Misc non coding genes2,042
Pseudogenes416
Gene transcripts37,912

Other

Genscan gene predictions48,580

About this species