View source for Tasmanian devil genome sequenced

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<p><a href="http://www.pnas.org/content/early/2011/06/23/1102838108">http://www.pnas.org/content/early/2011/06/23/1102838108</a></p>
<h1 id="article-title-1">Genetic diversity and population structure of the endangered marsupial <em>Sarcophilus harrisii</em> (Tasmanian devil)</h1>
<div class="contributors">
<ol class="contributor-list" id="contrib-group-1">
    <li class="contributor" id="contrib-1"><span class="name"><a class="name-search" href="http://www.pnas.org/search?author1=Webb+Miller&amp;sortspec=date&amp;submit=Submit">Webb Miller</a></span><a class="xref-aff" id="xref-aff-1-1" href="http://www.pnas.org/content/early/2011/06/23/1102838108#aff-1"><sup><font size="2">a</font></sup></a><span class="xref-sep">,</span><a class="xref-fn" id="xref-fn-3-1" href="http://www.pnas.org/content/early/2011/06/23/1102838108#fn-3"><sup><font size="2">1</font></sup></a>,</li>
    <li class="contributor" id="contrib-2"><span class="name"><a class="name-search" href="http://www.pnas.org/search?author1=Vanessa+M.+Hayes&amp;sortspec=date&amp;submit=Submit">Vanessa M. Hayes</a></span><a class="xref-aff" id="xref-aff-2-1" href="http://www.pnas.org/content/early/2011/06/23/1102838108#aff-2"><sup><font size="2">b</font></sup></a><span class="xref-sep">,</span><a class="xref-aff" id="xref-aff-3-1" href="http://www.pnas.org/content/early/2011/06/23/1102838108#aff-3"><sup><font size="2">c</font></sup></a><span class="xref-sep">,</span><a class="xref-fn" id="xref-fn-3-2" href="http://www.pnas.org/content/early/2011/06/23/1102838108#fn-3"><sup><font size="2">1</font></sup></a><span class="xref-sep">,</span><a class="xref-corresp" id="xref-corresp-1-1" href="http://www.pnas.org/content/early/2011/06/23/1102838108#corresp-1"><sup><font size="2">2</font></sup></a>,</li>
    <li class="contributor" id="contrib-3"><span class="name"><a class="name-search" href="http://www.pnas.org/search?author1=Aakrosh+Ratan&amp;sortspec=date&amp;submit=Submit">Aakrosh Ratan</a></span><a class="xref-aff" id="xref-aff-1-2" href="http://www.pnas.org/content/early/2011/06/23/1102838108#aff-1"><sup><font size="2">a</font></sup></a>,</li>
    <li class="contributor" id="contrib-4"><span class="name"><a class="name-search" href="http://www.pnas.org/search?author1=Desiree+C.+Petersen&amp;sortspec=date&amp;submit=Submit">Desiree C. Petersen</a></span><a class="xref-aff" id="xref-aff-2-2" href="http://www.pnas.org/content/early/2011/06/23/1102838108#aff-2"><sup><font size="2">b</font></sup></a><span class="xref-sep">,</span><a class="xref-aff" id="xref-aff-3-2" href="http://www.pnas.org/content/early/2011/06/23/1102838108#aff-3"><sup><font size="2">c</font></sup></a>,</li>
    <li class="contributor" id="contrib-5"><span class="name"><a class="name-search" href="http://www.pnas.org/search?author1=Nicola+E.+Wittekindt&amp;sortspec=date&amp;submit=Submit">Nicola E. Wittekindt</a></span><a class="xref-aff" id="xref-aff-1-3" href="http://www.pnas.org/content/early/2011/06/23/1102838108#aff-1"><sup><font size="2">a</font></sup></a>,</li>
    <li class="contributor" id="contrib-6"><span class="name"><a class="name-search" href="http://www.pnas.org/search?author1=Jason+Miller&amp;sortspec=date&amp;submit=Submit">Jason Miller</a></span><a class="xref-aff" id="xref-aff-3-3" href="http://www.pnas.org/content/early/2011/06/23/1102838108#aff-3"><sup><font size="2">c</font></sup></a>,</li>
    <li class="contributor" id="contrib-7"><span class="name"><a class="name-search" href="http://www.pnas.org/search?author1=Brian+Walenz&amp;sortspec=date&amp;submit=Submit">Brian Walenz</a></span><a class="xref-aff" id="xref-aff-3-4" href="http://www.pnas.org/content/early/2011/06/23/1102838108#aff-3"><sup><font size="2">c</font></sup></a>,</li>
    <li class="contributor" id="contrib-8"><span class="name"><a class="name-search" href="http://www.pnas.org/search?author1=James+Knight&amp;sortspec=date&amp;submit=Submit">James Knight</a></span><a class="xref-aff" id="xref-aff-4-1" href="http://www.pnas.org/content/early/2011/06/23/1102838108#aff-4"><sup><font size="2">d</font></sup></a>,</li>
    <li class="contributor" id="contrib-9"><span class="name"><a class="name-search" href="http://www.pnas.org/search?author1=Ji+Qi&amp;sortspec=date&amp;submit=Submit">Ji Qi</a></span><a class="xref-aff" id="xref-aff-1-4" href="http://www.pnas.org/content/early/2011/06/23/1102838108#aff-1"><sup><font size="2">a</font></sup></a>,</li>
    <li class="contributor" id="contrib-10"><span class="name"><a class="name-search" href="http://www.pnas.org/search?author1=Fangqing+Zhao&amp;sortspec=date&amp;submit=Submit">Fangqing Zhao</a></span><a class="xref-aff" id="xref-aff-1-5" href="http://www.pnas.org/content/early/2011/06/23/1102838108#aff-1"><sup><font size="2">a</font></sup></a>,</li>
    <li class="contributor" id="contrib-11"><span class="name"><a class="name-search" href="http://www.pnas.org/search?author1=Qingyu+Wang&amp;sortspec=date&amp;submit=Submit">Qingyu Wang</a></span><a class="xref-aff" id="xref-aff-1-6" href="http://www.pnas.org/content/early/2011/06/23/1102838108#aff-1"><sup><font size="2">a</font></sup></a>,</li>
    <li class="contributor" id="contrib-12"><span class="name"><a class="name-search" href="http://www.pnas.org/search?author1=Oscar+C.++Bedoya-Reina&amp;sortspec=date&amp;submit=Submit">Oscar C.  Bedoya-Reina</a></span><a class="xref-aff" id="xref-aff-1-7" href="http://www.pnas.org/content/early/2011/06/23/1102838108#aff-1"><sup><font size="2">a</font></sup></a>,</li>
    <li class="contributor" id="contrib-13"><span class="name"><a class="name-search" href="http://www.pnas.org/search?author1=Neerja+Katiyar&amp;sortspec=date&amp;submit=Submit">Neerja Katiyar</a></span><a class="xref-aff" id="xref-aff-1-8" href="http://www.pnas.org/content/early/2011/06/23/1102838108#aff-1"><sup><font size="2">a</font></sup></a>,</li>
    <li class="contributor" id="contrib-14"><span class="name"><a class="name-search" href="http://www.pnas.org/search?author1=Lynn+P.+Tomsho&amp;sortspec=date&amp;submit=Submit">Lynn P. Tomsho</a></span><a class="xref-aff" id="xref-aff-1-9" href="http://www.pnas.org/content/early/2011/06/23/1102838108#aff-1"><sup><font size="2">a</font></sup></a>,</li>
    <li class="contributor" id="contrib-15"><span class="name"><a class="name-search" href="http://www.pnas.org/search?author1=Lindsay+McClellan+Kasson&amp;sortspec=date&amp;submit=Submit">Lindsay McClellan Kasson</a></span><a class="xref-aff" id="xref-aff-1-10" href="http://www.pnas.org/content/early/2011/06/23/1102838108#aff-1"><sup><font size="2">a</font></sup></a>,</li>
    <li class="contributor" id="contrib-16"><span class="name"><a class="name-search" href="http://www.pnas.org/search?author1=Rae-Anne+Hardie&amp;sortspec=date&amp;submit=Submit">Rae-Anne Hardie</a></span><a class="xref-aff" id="xref-aff-2-3" href="http://www.pnas.org/content/early/2011/06/23/1102838108#aff-2"><sup><font size="2">b</font></sup></a>,</li>
    <li class="contributor" id="contrib-17"><span class="name"><a class="name-search" href="http://www.pnas.org/search?author1=Paula+Woodbridge&amp;sortspec=date&amp;submit=Submit">Paula Woodbridge</a></span><a class="xref-aff" id="xref-aff-2-4" href="http://www.pnas.org/content/early/2011/06/23/1102838108#aff-2"><sup><font size="2">b</font></sup></a>,</li>
    <li class="contributor" id="contrib-18"><span class="name"><a class="name-search" href="http://www.pnas.org/search?author1=Elizabeth+A.+Tindall&amp;sortspec=date&amp;submit=Submit">Elizabeth A. Tindall</a></span><a class="xref-aff" id="xref-aff-2-5" href="http://www.pnas.org/content/early/2011/06/23/1102838108#aff-2"><sup><font size="2">b</font></sup></a>,</li>
    <li class="contributor" id="contrib-19"><span class="name"><a class="name-search" href="http://www.pnas.org/search?author1=Mads+Frost+Bertelsen&amp;sortspec=date&amp;submit=Submit">Mads Frost Bertelsen</a></span><a class="xref-aff" id="xref-aff-5-1" href="http://www.pnas.org/content/early/2011/06/23/1102838108#aff-5"><sup><font size="2">e</font></sup></a>,</li>
    <li class="contributor" id="contrib-20"><span class="name"><a class="name-search" href="http://www.pnas.org/search?author1=Dale+Dixon&amp;sortspec=date&amp;submit=Submit">Dale Dixon</a></span><a class="xref-aff" id="xref-aff-6-1" href="http://www.pnas.org/content/early/2011/06/23/1102838108#aff-6"><sup><font size="2">f</font></sup></a>,</li>
    <li class="contributor" id="contrib-21"><span class="name"><a class="name-search" href="http://www.pnas.org/search?author1=Stephen+Pyecroft&amp;sortspec=date&amp;submit=Submit">Stephen Pyecroft</a></span><a class="xref-aff" id="xref-aff-7-1" href="http://www.pnas.org/content/early/2011/06/23/1102838108#aff-7"><sup><font size="2">g</font></sup></a>,</li>
    <li class="contributor" id="contrib-22"><span class="name"><a class="name-search" href="http://www.pnas.org/search?author1=Kristofer+M.+Helgen&amp;sortspec=date&amp;submit=Submit">Kristofer M. Helgen</a></span><a class="xref-aff" id="xref-aff-8-1" href="http://www.pnas.org/content/early/2011/06/23/1102838108#aff-8"><sup><font size="2">h</font></sup></a>,</li>
    <li class="contributor" id="contrib-23"><span class="name"><a class="name-search" href="http://www.pnas.org/search?author1=Arthur+M.+Lesk&amp;sortspec=date&amp;submit=Submit">Arthur M. Lesk</a></span><a class="xref-aff" id="xref-aff-1-11" href="http://www.pnas.org/content/early/2011/06/23/1102838108#aff-1"><sup><font size="2">a</font></sup></a>,</li>
    <li class="contributor" id="contrib-24"><span class="name"><a class="name-search" href="http://www.pnas.org/search?author1=Thomas+H.+Pringle&amp;sortspec=date&amp;submit=Submit">Thomas H. Pringle</a></span><a class="xref-aff" id="xref-aff-9-1" href="http://www.pnas.org/content/early/2011/06/23/1102838108#aff-9"><sup><font size="2">i</font></sup></a>,</li>
    <li class="contributor" id="contrib-25"><span class="name"><a class="name-search" href="http://www.pnas.org/search?author1=Nick+Patterson&amp;sortspec=date&amp;submit=Submit">Nick Patterson</a></span><a class="xref-aff" id="xref-aff-10-1" href="http://www.pnas.org/content/early/2011/06/23/1102838108#aff-10"><sup><font size="2">j</font></sup></a>,</li>
    <li class="contributor" id="contrib-26"><span class="name"><a class="name-search" href="http://www.pnas.org/search?author1=Yu+Zhang&amp;sortspec=date&amp;submit=Submit">Yu Zhang</a></span><a class="xref-aff" id="xref-aff-1-12" href="http://www.pnas.org/content/early/2011/06/23/1102838108#aff-1"><sup><font size="2">a</font></sup></a>,</li>
    <li class="contributor" id="contrib-27"><span class="name"><a class="name-search" href="http://www.pnas.org/search?author1=Alexandre+Kreiss&amp;sortspec=date&amp;submit=Submit">Alexandre Kreiss</a></span><a class="xref-aff" id="xref-aff-11-1" href="http://www.pnas.org/content/early/2011/06/23/1102838108#aff-11"><sup><font size="2">k</font></sup></a>,</li>
    <li class="contributor" id="contrib-28"><span class="name"><a class="name-search" href="http://www.pnas.org/search?author1=Gregory+M.+Woods&amp;sortspec=date&amp;submit=Submit">Gregory M. Woods</a></span><a class="xref-aff" id="xref-aff-11-2" href="http://www.pnas.org/content/early/2011/06/23/1102838108#aff-11"><sup><font size="2">k</font></sup></a><span class="xref-sep">,</span><a class="xref-aff" id="xref-aff-12-1" href="http://www.pnas.org/content/early/2011/06/23/1102838108#aff-12"><sup><font size="2">l</font></sup></a>,</li>
    <li class="contributor" id="contrib-29"><span class="name"><a class="name-search" href="http://www.pnas.org/search?author1=Menna+E.+Jones&amp;sortspec=date&amp;submit=Submit">Menna E. Jones</a></span><a class="xref-aff" id="xref-aff-11-3" href="http://www.pnas.org/content/early/2011/06/23/1102838108#aff-11"><sup><font size="2">k</font></sup></a>, and</li>
    <li class="last" id="contrib-30"><span class="name"><a class="name-search" href="http://www.pnas.org/search?author1=Stephan+C.+Schuster&amp;sortspec=date&amp;submit=Submit">Stephan C. Schuster</a></span><a class="xref-aff" id="xref-aff-1-13" href="http://www.pnas.org/content/early/2011/06/23/1102838108#aff-1"><sup><font size="2">a</font></sup></a><span class="xref-sep">,</span><a class="xref-aff" id="xref-fn-3-3" href="http://www.pnas.org/content/early/2011/06/23/1102838108#fn-3"><sup><font size="2">1</font></sup></a><span class="xref-sep">,</span><a class="xref-corresp" id="xref-corresp-1-2" href="http://www.pnas.org/content/early/2011/06/23/1102838108#corresp-1"><sup><font size="2">2</font></sup></a></li>
</ol>
<p class="affiliation-list-reveal"><a class="view-more" href="http://www.pnas.org/content/early/2011/06/23/1102838108#">+</a> Author Affiliations</p>
<ol class="affiliation-list hideaffil">
    <li class="aff"><a id="aff-1" name="aff-1"></a>
    <address><sup><font size="2">a</font></sup>Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, University Park, PA 16802;</address>
    </li>
    <li class="aff"><a id="aff-2" name="aff-2"></a>
    <address><sup><font size="2">b</font></sup>Children's Cancer Institute Australia and University of New South Wales, Lowy Cancer Research Centre, Randwick, NSW 2031,                           Australia;</address>
    </li>
    <li class="aff"><a id="aff-3" name="aff-3"></a>
    <address><sup><font size="2">c</font></sup>The J. Craig Venter Institute, Rockville, MD 20850;</address>
    </li>
    <li class="aff"><a id="aff-4" name="aff-4"></a>
    <address><sup><font size="2">d</font></sup>454 Life Sciences, Branford, CT 06405;</address>
    </li>
    <li class="aff"><a id="aff-5" name="aff-5"></a>
    <address><sup><font size="2">e</font></sup>Center for Zoo and Wild Animal Health, Copenhagen Zoo, 2000 Frederiksberg, Denmark;</address>
    </li>
    <li class="aff"><a id="aff-6" name="aff-6"></a>
    <address><sup><font size="2">f</font></sup>Museum and Art Gallery of the Northern Territory, Darwin 0801, Australia;</address>
    </li>
    <li class="aff"><a id="aff-7" name="aff-7"></a>
    <address><sup><font size="2">g</font></sup>Department of Primary Industries and Water, Mt. Pleasant Animal Health Laboratories, Kings Meadows, Tasmania 7249, Australia;</address>
    </li>
    <li class="aff"><a id="aff-8" name="aff-8"></a>
    <address><sup><font size="2">h</font></sup>National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012;</address>
    </li>
    <li class="aff"><a id="aff-9" name="aff-9"></a>
    <address><sup><font size="2">i</font></sup>The Sperling Foundation, Eugene, OR 97405;</address>
    </li>
    <li class="aff"><a id="aff-10" name="aff-10"></a>
    <address><sup><font size="2">j</font></sup>Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge Center, Cambridge, MA 02142;</address>
    </li>
    <li class="aff"><a id="aff-11" name="aff-11"></a>
    <address><sup><font size="2">k</font></sup>University of Tasmania, Hobart, TAS 7001, Australia; and</address>
    </li>
    <li class="aff"><a id="aff-12" name="aff-12"></a>
    <address><sup><font size="2">l</font></sup>Immunology, Menzies Research Institute, Hobart, Tasmania 7000, Australia</address>
    </li>
</ol>
<ol class="fn-track">
    <li class="fn-edited-by" id="fn-1">
    <p id="p-1">Edited<a class="xref-fn" id="xref-fn-6-1" href="http://www.pnas.org/content/early/2011/06/23/1102838108#fn-6">*</a> by Luis Herrera Estrella, Center for Research and Advanced Studies, Irapuato, Mexico, and approved May 23, 2011 (received                           for review February 24, 2011)</p>
    </li>
</ol>
</div>
<div class="section abstract" id="abstract-1">
<h2>Abstract</h2>
<p id="p-4">The Tasmanian devil (<em>Sarcophilus harrisii</em>) 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.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</p>
</div>