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Bolivian squirrel monkey assembly and gene annotation

Assembly

The SaiBol1.0 assembly was submitted by Broad Institute on 2011/11/17 . The assembly is on the Scaffold level, consisting of 151,414 assembled into 2,686 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 38,823 while the scaffold N50 is 18,744,880.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000235385.1

Gene annotation

The black-capped squirrel monkey (Saimiri boliviensis) is a South American squirrel monkey, found in Bolivia, Brazil and Peru. This South American monkey can be found in numerous zoos (with over 80 zoos keeping them in Europe alone, the majority of them being of the Bolivian subspecies) around the world, including the Ellen Trout Zoo, London Zoo, Apenheul Primate Park, Copenhagen Zoo and Auckland Zoo.

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

AssemblySaiBol1.0, INSDC Assembly GCA_000235385.1, Nov 2011
Base Pairs2,477,147,568
Golden Path Length2,608,588,537
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedAug 2017
Genebuild releasedDec 2017
Genebuild last updated/patchedJan 2018
Database version94.1

Gene counts

Coding genes19,380
Non coding genes7,683
Small non coding genes4,146
Long non coding genes384
Misc non coding genes3,153
Pseudogenes439
Gene transcripts49,071

Other

Genscan gene predictions44,050

About this species