Marmoset assembly and gene annotation

The common marmoset (Callithrix jacchus) is a New World monkey. It originally lived on the northeastern coast of Brazil, but has spread southwards, becoming an invasive species in its non-native regions. It is used as model organisms in areas of research such as teratology, periodontal disease, reproduction, immunology, endocrinology, obesity and aging, and was the first New World monkey to have its genome sequenced.


Callithrix jacchus-3.2.1 (GCA_000004665.1) is a draft assembly of the common marmoset genome. This assembly is used by UCSC to create their calJac3 database. It was sequenced to 6X coverage using a female marmoset (animal id #186/17066) DNA source kindly provided by Dr. Suzette Tardif, of the Southwestern National Primate Research Center (San Antonio, Texas). The DNA source for the CHORI-259 BAC library was male and the full brother of the female used for whole genome shotgun sequencing (#186/17066). The combined sequence reads were assembled using the PCAP software (Genome Res. 13(9):2164-70 2003) and filtered for all known non-marmoset sequence contaminants.

The new Callithrix jacchus-3.2.1 assembly spans 2.75Gb with 2.62Gb ordered and oriented along 24 chromosomes. Chromosomes were not available in Callithrix jacchus-3.2 (released in Ensembl 56 and Ensembl 57), which was composed of scaffolds and contigs only.

The N50 length is defined as the scaffold (or contig) length N for which 50% of the genome lies in scaffolds (or contigs) of the N50 size or longer. The Callithrix jacchus-3.2.1 assembly is made up of a total of 73,756 scaffolds with an N50 scaffold length of over 6.4Mb. Scaffolds placed on chromosomes have been annotated as described below.

The sequence assembly was provided by The Genome Center, Washington University School of Medicineand the Human Genome Center, Baylor College of Medicine.

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

Other assemblies

Gene annotation

The gene set for marmoset was built using the Ensembl gene annotation pipeline. Species-specific resources for marmoset are relatively limited and therefore sequences from other primates, especially human, were also used as supporting evidence for coding transcript models. In addition to the coding transcript models, non-coding RNAs and pseudogenes were annotated. Marmoset cDNAs and ESTs and human cDNAs were mapped to the genome using Exonerate.

More information

General information about this species can be found in Wikipedia.



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 version95.321

Gene counts

Coding genes20,978
Gene transcripts55,116


Genscan gene predictions53,363

About this species