TY - JOUR
T1 - Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil)
AU - Miller, Webb
AU - Hayes, Vanessa M.
AU - Ratan, Aakrosh
AU - Petersen, Desiree C.
AU - Wittekindt, Nicola E.
AU - Miller, Jason
AU - Walenz, Brian
AU - Knight, James
AU - Qi, Ji
AU - Zhao, Fangqing
AU - Wang, Qingyu
AU - Bedoya-Reina, Oscar C.
AU - Katiyar, Neerja
AU - Tomsho, Lynn P.
AU - Kasson, Lindsay Mc Clellan
AU - Hardie, Rae Anne
AU - Woodbridge, Paula
AU - Tindall, Elizabeth A.
AU - Bertelsen, Mads Frost
AU - Dixon, Dale
AU - Pyecroft, Stephen
AU - Helgen, Kristofer M.
AU - Lesk, Arthur M.
AU - Pringle, Thomas H.
AU - Patterson, Nick
AU - Zhang, Yu
AU - Kreiss, Alexandre
AU - Woods, Gregory M.
AU - Jones, Menna E.
AU - Schuster, Stephan C.
PY - 2011/7/26
Y1 - 2011/7/26
N2 - 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.
AB - 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.
KW - Ancient DNA
KW - Population genetics
KW - Selective breeding
KW - Semiconductor sequencing
KW - Wildlife conservation
UR - http://www.scopus.com/inward/record.url?scp=79961044560&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=79961044560&partnerID=8YFLogxK
U2 - 10.1073/pnas.1102838108
DO - 10.1073/pnas.1102838108
M3 - Article
C2 - 21709235
AN - SCOPUS:79961044560
SN - 0027-8424
VL - 108
SP - 12348
EP - 12353
JO - Proceedings of the National Academy of Sciences of the United States of America
JF - Proceedings of the National Academy of Sciences of the United States of America
IS - 30
ER -
