1. Transcriptome reconstruction and annotation of cynomolgus and African green monkey
- Author
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Oliver Elliott, Elyse R. Nagle, Gustavo Palacios, Albert Lee, Guo-Yun Yu, Travis K. Warren, Raul Rabadan, Jeffrey R. Kugelman, and Hossein Khiabanian
- Subjects
FOS: Computer and information sciences ,Bioinformatics ,Annotation ,RNA-Seq ,Genomics ,Computational biology ,Genome browser ,Biology ,Genome ,Transcriptome ,Cynomolgus macaque ,Database ,Chlorocebus aethiops ,Genetics ,Animals ,Comparative Genomic Hybridization ,Sequence Analysis, RNA ,Gene Expression Profiling ,High-Throughput Nucleotide Sequencing ,Molecular Sequence Annotation ,Exons ,African green monkey ,Macaca fascicularis ,FOS: Biological sciences ,African Green Monkey ,DNA microarray ,RNA-seq ,Biotechnology ,Research Article - Abstract
Background Non-human primates (NHPs) and humans share major biological mechanisms, functions, and responses due to their close evolutionary relationship and, as such, provide ideal animal models to study human diseases. RNA expression in NHPs provides specific signatures that are informative of disease mechanisms and therapeutic modes of action. Unlike the human transcriptome, the transcriptomes of major NHP animal models are yet to be comprehensively annotated. Results In this manuscript, employing deep RNA sequencing of seven tissue samples, we characterize the transcriptomes of two commonly used NHP animal models: Cynomolgus macaque (Macaca fascicularis) and African green monkey (Chlorocebus aethiops). We present the Multi-Species Annotation (MSA) pipeline that leverages well-annotated primate species and annotates 99.8% of reconstructed transcripts. We elucidate tissue-specific expression profiles and report 13 experimentally validated novel transcripts in these NHP animal models. Conclusion We report comprehensively annotated transcriptomes of two non-human primates, which we have made publically available on a customized UCSC Genome Browser interface. The MSA pipeline is also freely available. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-846) contains supplementary material, which is available to authorized users.
- Published
- 2014