Transcriptome reconstruction and annotation of cynomolgus and African green monkey

BMC Genomics

Raul Rabadan²  Gustavo Palacios³  Travis Warren⁴  Guo-Yun Yu¹  Elyse Nagle¹  Oliver Elliott²  Jeffrey Kugelman¹  Hossein Khiabanian²  Albert Lee² 

[1] Genomics Division, the U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA;Department of Systems Biology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA;National Center for Biodefense and Infectious Disease, George Mason University, Manassas, VA 20110, USA;Molecular and Translational Sciences Divisions, the U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA

关键词: Database;    Annotation;    Genomics;    Transcriptome;    RNA-seq;    Chlorocebus aethiops;    African green monkey;    Macaca fascicularis;    Cynomolgus macaque;   

Others  :  1139157
DOI  :  10.1186/1471-2164-15-846

 received in 2014-04-17, accepted in 2014-09-25,  发布年份 2014

【 摘 要 】

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.

【 授权许可】

   
2014 Lee et al.; licensee BioMed Central Ltd.

【 图 表 】

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