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

GigaScience

Robert B Norgren⁴  Jeffrey A French³  Etsuko N Moriyama²  Austin C Lubker⁴  Robert M Gibbs⁴  Julien S Gradnigo²  Dongren Ren¹  Mnirnal D Maudhoo⁴ 

[1] Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang 330045, China;School of Biological Sciences & Center for Plant Science Innovation, University of Nebraska-Lincoln, 403 Manter Hall, Lincoln, Nebraska 68588-0118, USA;Callitrichid Research Center, Department of Psychology, University of Nebraska, Omaha, USA;Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA

关键词: Assembly;    mRNA-seq;    Transcriptome;    Common marmoset;    Callithrix jacchus;   

Others  :  1118588
DOI  :  10.1186/2047-217X-3-14

 received in 2014-08-15, accepted in 2014-09-04,  发布年份 2014

【 摘 要 】

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.

【 授权许可】

   
2014 Maudhoo et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

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