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Open Access Highly Accessed Research article

Antigen-presenting genes and genomic copy number variations in the Tasmanian devil MHC

Yuanyuan Cheng1, Andrew Stuart2, Katrina Morris1, Robyn Taylor3, Hannah Siddle14, Janine Deakin5, Menna Jones6, Chris T Amemiya2 and Katherine Belov17*

Author affiliations

1 Faculty of Veterinary Science, University of Sydney, Sydney, NSW, Australia

2 Genome Resource Center, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA

3 Department of Primary Industries, Parks, Water and Environment, Prospect, TAS, Australia

4 Department of Pathology, University of Cambridge, Cambridge, UK

5 Research School of Biology, The Australian National University, Canberra, ACT, Australia

6 School of Zoology, University of Tasmania, Hobart, TAS, Australia

7 Faculty of Veterinary Science, University of Sydney, RMC Gunn B19, Sydney, NSW 2006, Australia

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Citation and License

BMC Genomics 2012, 13:87  doi:10.1186/1471-2164-13-87

Published: 12 March 2012

Abstract

Background

The Tasmanian devil (Sarcophilus harrisii) is currently under threat of extinction due to an unusual fatal contagious cancer called Devil Facial Tumour Disease (DFTD). DFTD is caused by a clonal tumour cell line that is transmitted between unrelated individuals as an allograft without triggering immune rejection due to low levels of Major Histocompatibility Complex (MHC) diversity in Tasmanian devils.

Results

Here we report the characterization of the genomic regions encompassing MHC Class I and Class II genes in the Tasmanian devil. Four genomic regions approximately 960 kb in length were assembled and annotated using BAC contigs and physically mapped to devil Chromosome 4q. 34 genes and pseudogenes were identified, including five Class I and four Class II loci. Interestingly, when two haplotypes from two individuals were compared, three genomic copy number variants with sizes ranging from 1.6 to 17 kb were observed within the classical Class I gene region. One deletion is particularly important as it turns a Class Ia gene into a pseudogene in one of the haplotypes. This deletion explains the previously observed variation in the Class I allelic number between individuals. The frequency of this deletion is highest in the northwestern devil population and lowest in southeastern areas.

Conclusions

The third sequenced marsupial MHC provides insights into the evolution of this dynamic genomic region among the diverse marsupial species. The two sequenced devil MHC haplotypes revealed three copy number variations that are likely to significantly affect immune response and suggest that future work should focus on the role of copy number variations in disease susceptibility in this species.

Keywords:
MHC; Tasmanian devil; Copy number variation; Devil facial tumour disease