De novo transcriptome reconstruction and annotation of the Egyptian rousette bat

Albert K. Lee, Kirsten A. Kulcsar, Oliver Elliott, Hossein Khiabanian, Elyse R. Nagle, Megan E.B. Jones, Brian R. Amman, Mariano Sanchez-Lockhart, Jonathan S. Towner, Gustavo Palacios, Raul Rabadan

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

Background: The 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. Results: Progress 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. Conclusion: We 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.

Original languageEnglish (US)
Article number1033
JournalBMC genomics
Volume16
Issue number1
DOIs
StatePublished - Dec 7 2015

Fingerprint

Transcriptome
Marburgvirus
Virus Diseases
Filoviridae
Ebolavirus
RNA Sequence Analysis
Host-Pathogen Interactions
High-Throughput Nucleotide Sequencing
Gene Ontology
Middle East
Allergy and Immunology
Primates
Cluster Analysis
Fruit
Fever
Gene Expression

Keywords

  • Annotation
  • Database
  • Genomics
  • RNA-seq
  • Transcriptome

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Lee, A. K., Kulcsar, K. A., Elliott, O., Khiabanian, H., Nagle, E. R., Jones, M. E. B., ... Rabadan, R. (2015). De novo transcriptome reconstruction and annotation of the Egyptian rousette bat. BMC genomics, 16(1), [1033]. https://doi.org/10.1186/s12864-015-2124-x

De novo transcriptome reconstruction and annotation of the Egyptian rousette bat. / Lee, Albert K.; Kulcsar, Kirsten A.; Elliott, Oliver; Khiabanian, Hossein; Nagle, Elyse R.; Jones, Megan E.B.; Amman, Brian R.; Sanchez-Lockhart, Mariano; Towner, Jonathan S.; Palacios, Gustavo; Rabadan, Raul.

In: BMC genomics, Vol. 16, No. 1, 1033, 07.12.2015.

Research output: Contribution to journalArticle

Lee, AK, Kulcsar, KA, Elliott, O, Khiabanian, H, Nagle, ER, Jones, MEB, Amman, BR, Sanchez-Lockhart, M, Towner, JS, Palacios, G & Rabadan, R 2015, 'De novo transcriptome reconstruction and annotation of the Egyptian rousette bat', BMC genomics, vol. 16, no. 1, 1033. https://doi.org/10.1186/s12864-015-2124-x
Lee AK, Kulcsar KA, Elliott O, Khiabanian H, Nagle ER, Jones MEB et al. De novo transcriptome reconstruction and annotation of the Egyptian rousette bat. BMC genomics. 2015 Dec 7;16(1). 1033. https://doi.org/10.1186/s12864-015-2124-x
Lee, Albert K. ; Kulcsar, Kirsten A. ; Elliott, Oliver ; Khiabanian, Hossein ; Nagle, Elyse R. ; Jones, Megan E.B. ; Amman, Brian R. ; Sanchez-Lockhart, Mariano ; Towner, Jonathan S. ; Palacios, Gustavo ; Rabadan, Raul. / De novo transcriptome reconstruction and annotation of the Egyptian rousette bat. In: BMC genomics. 2015 ; Vol. 16, No. 1.
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