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Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

De novo assembly of the chimpanzee transcriptome from NextGen mRNA sequences

Mnirnal D Maudhoo¹, Jacob D Madison¹, Robert B Norgren¹

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

|April 22, 2015

Abstract

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.

Keywords:

Assembly Chimpanzee Pan troglodytes Transcriptome mRNA-seq

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