De novo assembly of the chimpanzee transcriptome from NextGen mRNA sequences

GigaScience

Robert B Norgren¹  Jacob D Madison¹  Mnirnal D Maudhoo¹ 

[1] Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha 68198, Nebraska, USA

关键词: Assembly;    mRNA-seq;    Transcriptome;    Chimpanzee;    Pan troglodytes;   

Others  :  1172972
DOI  :  10.1186/s13742-015-0061-x

 received in 2014-12-19, accepted in 2015-04-13,  发布年份 2015

【 摘 要 】

Background

Common chimpanzees (Pan troglodytes) and bonobos (Pan paniscus) are the species most closely related to humans. For this reason, it is especially important to have complete and accurate chimpanzee nucleotide and protein sequences to understand how humans evolved their unique capabilities. We provide transcriptome data from four untransformed cell types derived from the reference Pan troglodytes, “Clint”, to better annotate the chimpanzee genome and provide empirical validation for proposed gene models of this important species.

Findings

RNA was extracted from primary cells cultured from four tissues: skin, adipose stroma, vascular smooth muscle and skeletal muscle. These four RNA samples were sequenced on the Illumina HiSeq 2000 platform. Sequences were deposited in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA). Transcripts were assembled, annotated and deposited in the NCBI Transcriptome Shotgun Assembly (TSA) database.

Conclusions

We have provided a high quality annotation of 44,275 transcripts with full-length coding sequence (CDS). This set represented a total of 10,110 unique genes, thus providing empirical support for their existence. This dataset can be used to improve the annotation of the Pan troglodytes genome.

【 授权许可】

   
2015 Maudhoo et al.; licensee BioMed Central.

【 图 表 】

Figure 1.

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