De novo assembly of the common marmoset transcriptome from NextGen mRNA sequences

Mnirnal D. Maudhoo, Dongren Ren, Julien S. Gradnigo, Robert M. Gibbs, Austin C. Lubker, Etsuko N. Moriyama, Jeffrey A. French, Robert B. Norgren

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Background: Nonhuman primates are important for both biomedical studies and understanding human evolution. Although research in these areas has mostly focused on Old World primates, such as the rhesus macaque, the common marmoset (Callithrix jacchus), a New World primate, offers important advantages in comparison to other primates, such as an accelerated lifespan. To conduct Next Generation expression studies or to study primate evolution, a high quality annotation of the marmoset genome is required. The availability of marmoset transcriptome data from five tissues, including both raw sequences and assembled transcripts, will aid in the annotation of the newly released marmoset assembly.Findings: RNA was extracted from five tissues: skeletal muscle, bladder and hippocampus from a male common marmoset, and cerebral cortex and cerebellum from a female common marmoset. All five RNA samples were sequenced on the Illumina HiSeq 2000 platform. Sequences were deposited in the NCBI Sequence Read Archive. Transcripts were assembled, annotated and deposited in the NCBI Transcriptome Shotgun Assembly database.Conclusions: We have provided a high quality annotation of 51,163 transcripts with full-length coding sequence. This set represented a total of 10,833 unique genes. In addition to providing empirical support for the existence of these 10,833 genes, we also provide sequence information for 2,422 genes that were not previously identified in the Ensembl annotation of the marmoset genome.

Original languageEnglish (US)
Article number14
JournalGigaScience
Volume3
Issue number1
DOIs
StatePublished - Sep 19 2014

Fingerprint

Callithrix
Transcriptome
Genes
Messenger RNA
Primates
RNA
Tissue
Genome
Muscle
Availability
Firearms
Macaca mulatta
Cerebral Cortex
Cerebellum
Hippocampus
Skeletal Muscle
Urinary Bladder
Databases

Keywords

  • Assembly
  • Callithrix jacchus
  • Common marmoset
  • Transcriptome
  • mRNA-seq

ASJC Scopus subject areas

  • Computer Science Applications
  • Health Informatics

Cite this

De novo assembly of the common marmoset transcriptome from NextGen mRNA sequences. / Maudhoo, Mnirnal D.; Ren, Dongren; Gradnigo, Julien S.; Gibbs, Robert M.; Lubker, Austin C.; Moriyama, Etsuko N.; French, Jeffrey A.; Norgren, Robert B.

In: GigaScience, Vol. 3, No. 1, 14, 19.09.2014.

Research output: Contribution to journalArticle

Maudhoo, Mnirnal D. ; Ren, Dongren ; Gradnigo, Julien S. ; Gibbs, Robert M. ; Lubker, Austin C. ; Moriyama, Etsuko N. ; French, Jeffrey A. ; Norgren, Robert B. / De novo assembly of the common marmoset transcriptome from NextGen mRNA sequences. In: GigaScience. 2014 ; Vol. 3, No. 1.
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