Journal
IMMUNOGENETICS
Volume 67, Issue 5-6, Pages 305-321Publisher
SPRINGER
DOI: 10.1007/s00251-015-0833-6
Keywords
Major histocompatibility complex; Toll-like receptor; RIG-I-like receptor; Koala retrovirus; Spleen; Buffy coat
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Funding
- Purdue University Faculty Scholar program (JAD)
- National Science Foundation Graduate Research Fellowship Program [DGE-1333468]
- San Diego Zoo and the participants of the Koala Education and Conservation Program
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The study of the koala transcriptome has the potential to advance our understanding of its immunome-immunological reaction of a given host to foreign antigens-and to help combat infectious diseases (e.g., chlamydiosis) that impede ongoing conservation efforts. We used Illumina sequencing of cDNA to characterize genes expressed in two different koala tissues of immunological importance, blood and spleen. We generated nearly 600 million raw sequence reads, and about 285 million of these were subsequently assembled and condensed into similar to 70,000 subcomponents that represent putative transcripts. We annotated similar to 16 % of these subcomponents and identified those related to infection and the immune response, including Toll-like receptors (TLRs), RIG-I-like receptors (RLRs), major histocompatibility complex (MHC) genes, and koala retrovirus (KoRV). Using phylogenetic analyses, we identified 29 koala genes in these target categories and report their concordance with currently accepted gene groups. By mapping multiple sequencing reads to transcripts, we identified 56 putative SNPs in genes of interest. The distribution of these SNPs indicates that MHC genes (34 SNPs) are more diverse than KoRV (12 SNPs), TLRs (8 SNPs), or RLRs (2 SNPs). Our sequence data also indicate that KoRV sequences are highly expressed in the transcriptome. Our efforts have produced full-length sequences for potentially important immune genes in koala, which should serve as targets for future investigations that aim to conserve koala populations.
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