White-tufted-ear marmoset (mCalJac1.pat.X)

White-tufted-ear 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.

Assembly

The mCalJac1.pat.X assembly was submitted by Vertebrate Genomes Project on March 2020. The assembly is on chromosome level, consisting of 1,312 contigs assembled into 353 scaffolds. From these sequences, 24 chromosomes have been built. 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 13,255,626 while the scaffold N50 is 136,971,485.

Other assemblies

Gene annotation

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.
lincRNAs were generated via RNA-seq data where no evidence of protein homology or protein domains could be found in the transcript.

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

AssemblymCalJac1.pat.X, INSDC Assembly GCA_011100555.1, Mar 2020
Base Pairs2,829,711,198
Golden Path Length2,829,711,198
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedAug 2020
Genebuild releasedDec 2020
Genebuild last updated/patchedNov 2020
Database version111.1

Gene counts

Coding genes22,078
Non coding genes16,815
Small non coding genes6,339
Long non coding genes6,272
Misc non coding genes4,204
Pseudogenes1,295
Gene transcripts71,826

Other

Genscan gene predictions105,937