Journal Article

Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil)

Lesk, Arthur M, Petersen, Desiree C, Zhang, Yu, Kreiss, Alexandre, Katiyar, Neerja, Woodbridge, Paula, Hayes, Vanessa M, Bedoya-Reina, Oscar C, Pringle, Thomas H, Kasson, Lindsay McClellan, Wittekindt, Nicola E, Helgen, Kristofer M, Jones, Menna E, Qi, Ji, Woods, Gregory M, Walenz, Brian, Tomsho, Lynn P, Hardie, Rae-Anne, Dixon, Dale, Wang, Qingyu, Zhao, Fangqing, Bertelsen, Mads Frost, Miller, Jason, Schuster, Stephan C, Tindall, Elizabeth A, Ratan, Aakrosh, Knight, James, Pyecroft, Stephen, Patterson, Nick, Miller, Webb

2011

Overview

The Tasmanian devil (Sarcophilus harrisii) is threatened with extinction because of a contagious cancer known as Devil Facial Tumor Disease. The inability to mount an immune response and to reject these tumors might be caused by a lack of genetic diversity within a dwindling population. Here we report a whole-genome analysis of two animals originating from extreme northwest and southeast Tasmania, the maximal geographic spread, together with the genome from a tumor taken from one of them. A 3.3-Gb de novo assembly of the sequence data from two complementary next-generation sequencing platforms was used to identify 1 million polymorphic genomic positions, roughly one-quarter of the number observed between two genetically distant human genomes. Analysis of 14 complete mitochondrial genomes from current and museum specimens, as well as mitochondrial and nuclear SNP markers in 175 animals, suggests that the observed low genetic diversity in today's population preceded the Devil Facial Tumor Disease disease outbreak by at least 100 y. Using a genetically characterized breeding stock based on the genome sequence will enable preservation of the extant genetic diversity in future Tasmanian devil populations.

• Publisher: National Academy of Sciences,National Acad Sciences
• Subject: Animal populations / Animals / Biological Sciences / Breeding / breeding stock / Cancer / disease outbreaks / DNA / DNA, Mitochondrial - genetics / DNA, Neoplasm - genetics / Extinction / Extinction, Biological / Facial Neoplasms - genetics / Facial Neoplasms - veterinary / Genetic diversity / Genetic Variation / Genetics, Population / Genome, Mitochondrial / Genomes / Genomics / high-throughput nucleotide sequencing / Humans / Immune response / Marsupialia - genetics / Marsupials / Metatheria / Mitochondria / mitochondrial genome / Models, Molecular / Molecular Sequence Data / Neoplasm Proteins - chemistry / Neoplasm Proteins - genetics / neoplasms / Neoplasms - genetics / Neoplasms - veterinary / Nucleotide sequence / nucleotide sequences / Phylogeny / Polymorphism, Single Nucleotide / Population structure / Preservation / Sequencing / Single-nucleotide polymorphism / Species diversity / Species extinction / Tasmania / Time Factors / Tumors