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Crab-eating macaque assembly and gene annotation

Assembly

The Macaca_fascicularis_5.0 assembly was submitted by Washington University (WashU) on 2013/06/12 . The assembly is on the Chromosome level, consisting of 87,764 assembled into 7,625 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 86,040 while the scaffold N50 is 88,649,475.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000364345.1

Gene annotation

The crab-eating macaque (Macaca fascicularis), also known as the long-tailed macaque, is a cercopithecine primate native to Southeast Asia. It is referred to as the cynomolgus monkey in laboratories. It has a long history alongside humans; they have been alternately seen as agricultural pests, sacred animals in some temples, and more recently, the subject of medical experiments. The crab-eating macaque lives in matrilineal social groups with a female dominance hierarchy, and male members leave the group when they reach puberty. They are opportunistic omnivores and have been documented using tools to obtain food in Thailand and Myanmar. The crab-eating macaque is a known invasive species and a threat to biodiversity in several locations, including Hong Kong and western New Guinea. The significant overlap in macaque and human living space has resulted in greater habitat loss, synanthropic living, and inter- and intraspecies conflicts over resources.

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

AssemblyMacaca_fascicularis_5.0, INSDC Assembly GCA_000364345.1, Jun 2013
Base Pairs2,803,866,698
Golden Path Length2,946,843,737
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedAug 2017
Genebuild releasedDec 2017
Genebuild last updated/patchedJan 2018
Database version94.5

Gene counts

Coding genes21,584
Non coding genes7,438
Small non coding genes4,660
Long non coding genes738
Misc non coding genes2,040
Pseudogenes302
Gene transcripts54,368

Other

Genscan gene predictions46,957

About this species