De novo transcriptome reconstruction and annotation of the Egyptian rousette bat

BMC Genomics

Research Article

Brian R. Amman¹  Jonathan S. Towner¹  Megan E.B. Jones¹  Albert K. Lee²  Raul Rabadan²  Oliver Elliott³  Hossein Khiabanian³  Elyse R. Nagle⁴  Kirsten A. Kulcsar⁴  Mariano Sanchez-Lockhart⁴  Gustavo Palacios⁵ 

[1] Centers for Disease Control and Prevention, Viral Special Pathogens Branch, 1600 Clifton Rd. NE, 30333, Atlanta, USA;Department of Biomedical Informatics, Columbia University College of Physicians and Surgeons, 1130 St. Nicholas Ave, New York, USA;Department of Systems Biology, Columbia University College of Physicians and Surgeons, 1130 St. Nicholas Ave, New York, USA;Department of Systems Biology, Columbia University College of Physicians and Surgeons, 1130 St. Nicholas Ave, New York, USA;United States Army Medical Research Institute for Infectious Disease, Center for Genome Sciences, 1425 Porter St, 21702, Ft Detrick, USA;United States Army Medical Research Institute for Infectious Disease, Center for Genome Sciences, 1425 Porter St, 21702, Ft Detrick, USA;National Center for Biodefense and Infectious Disease, George Mason University, 20110, Manassas, USA;

关键词: RNA-seq;    Transcriptome;    Genomics;    Annotation;    Database;   

DOI  :  10.1186/s12864-015-2124-x

 received in 2015-08-06, accepted in 2015-10-22,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundThe Egyptian Rousette bat (Rousettus aegyptiacus), a common fruit bat species found throughout Africa and the Middle East, was recently identified as a natural reservoir host of Marburg virus. With Ebola virus, Marburg virus is a member of the family Filoviridae that causes severe hemorrhagic fever disease in humans and nonhuman primates, but results in little to no pathological consequences in bats. Understanding host-pathogen interactions within reservoir host species and how it differs from hosts that experience severe disease is an important aspect of evaluating viral pathogenesis and developing novel therapeutics and methods of prevention.ResultsProgress in studying bat reservoir host responses to virus infection is hampered by the lack of host-specific reagents required for immunological studies. In order to establish a basis for the design of reagents, we sequenced, assembled, and annotated the R. aegyptiacus transcriptome. We performed de novo transcriptome assembly using deep RNA sequencing data from 11 distinct tissues from one male and one female bat. We observed high similarity between this transcriptome and those available from other bat species. Gene expression analysis demonstrated clustering of expression profiles by tissue, where we also identified enrichment of tissue-specific gene ontology terms. In addition, we identified and experimentally validated the expression of novel coding transcripts that may be specific to this species.ConclusionWe comprehensively characterized the R. aegyptiacus transcriptome de novo. This transcriptome will be an important resource for understanding bat immunology, physiology, disease pathogenesis, and virus transmission.

【 授权许可】

CC BY   
© Lee et al. 2015