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The immune gene repertoire of an important viral reservoir, the Australian black flying fox

Anthony T Papenfuss12, Michelle L Baker34*, Zhi-Ping Feng15, Mary Tachedjian3, Gary Crameri3, Chris Cowled3, Justin Ng3, Vijaya Janardhana3, Hume E Field67 and Lin-Fa Wang36*

Author Affiliations

1 Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC, 3052, Australia

2 Department of Mathematics and Statistics, University of Melbourne, Melbourne, VIC, 3010, Australia

3 CSIRO Livestock Industries, Australian Animal Health Laboratory, PO Bag 24, Geelong, VIC, 3220, Australia

4 Center for Evolutionary and Theoretical Immunology, Department of Biology, The University of New Mexico, Albuquerque, NM, 87131, USA

5 Department of Medical Biology, University of Melbourne, Melbourne, VIC, 3010, Australia

6 Australian Biosecurity Cooperative Research Centre for Emerging Infectious Diseases, Brisbane, Australia

7 Queensland Primary Industries and Fisheries, Biosecurity Queensland, Brisbane, Australia

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BMC Genomics 2012, 13:261  doi:10.1186/1471-2164-13-261

Published: 20 June 2012



Bats are the natural reservoir host for a range of emerging and re-emerging viruses, including SARS-like coronaviruses, Ebola viruses, henipaviruses and Rabies viruses. However, the mechanisms responsible for the control of viral replication in bats are not understood and there is little information available on any aspect of antiviral immunity in bats. Massively parallel sequencing of the bat transcriptome provides the opportunity for rapid gene discovery. Although the genomes of one megabat and one microbat have now been sequenced to low coverage, no transcriptomic datasets have been reported from any bat species. In this study, we describe the immune transcriptome of the Australian flying fox, Pteropus alecto, providing an important resource for identification of genes involved in a range of activities including antiviral immunity.


Towards understanding the adaptations that have allowed bats to coexist with viruses, we have de novo assembled transcriptome sequence from immune tissues and stimulated cells from P. alecto. We identified about 18,600 genes involved in a broad range of activities with the most highly expressed genes involved in cell growth and maintenance, enzyme activity, cellular components and metabolism and energy pathways. 3.5% of the bat transcribed genes corresponded to immune genes and a total of about 500 immune genes were identified, providing an overview of both innate and adaptive immunity. A small proportion of transcripts found no match with annotated sequences in any of the public databases and may represent bat-specific transcripts.


This study represents the first reported bat transcriptome dataset and provides a survey of expressed bat genes that complement existing bat genomic data. In addition, these data provide insight into genes relevant to the antiviral responses of bats, and form a basis for examining the roles of these molecules in immune response to viral infection.