Marmoset assembly and gene annotation

Assembly

The ASM275486v1 assembly was submitted by the Broad Institute on 2017/11/06. The assembly is on the scaffold level, consisting of 88,439 contigs assembled into 39,944 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 155,284 while the scaffold N50 is 129,239,660 The genome assembly represented here corresponds to GenBank Assembly ID: GCA_002754865.1

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000004665.1

Other assemblies

Gene annotation

Most marmosets are about 20 centimetres (8 in) long. Relative to other monkeys, they show some apparently primitive features: they have claws rather than nails, and tactile hairs on their wrists. They lack wisdom teeth, and their brain layout seems to be relatively primitive. Their body temperature is unusually variable, changing by up to 4 °C (7 °F) in a day. Marmosets are native to South America and have been found in Bolivia, Brazil, Colombia, Ecuador, Paraguay, and Peru. They have also been spotted in Central America and Mexico.

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

AssemblyC_jacchus3.2.1, INSDC Assembly GCA_000004665.1, Jan 2010
Base Pairs2,759,289,125
Golden Path Length2,914,958,544
Annotation methodFull genebuild
Genebuild startedFeb 2010
Genebuild releasedMay 2010
Genebuild last updated/patchedFeb 2014
Database version93.321

Gene counts

Coding genes20,978
Pseudogenes2,345
Gene transcripts55,116

Other

Genscan gene predictions53,363

About this species