The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus)

  1. Webb Miller1,10,
  2. Daniela I. Drautz1,
  3. Jan E. Janecka2,
  4. Arthur M. Lesk1,
  5. Aakrosh Ratan1,
  6. Lynn P. Tomsho1,
  7. Mike Packard1,
  8. Yeting Zhang1,
  9. Lindsay R. McClellan1,
  10. Ji Qi1,
  11. Fangqing Zhao1,
  12. M. Thomas P. Gilbert3,
  13. Love Dalén4,
  14. Juan Luis Arsuaga5,
  15. Per G.P. Ericson6,
  16. Daniel H. Huson7,
  17. Kristofer M. Helgen8,
  18. William J. Murphy2,
  19. Anders Götherström9 and
  20. Stephan C. Schuster1,10
  1. 1 Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, University Park, Pennsylvania 16802, USA;
  2. 2 Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843, USA;
  3. 3 Centre for Ancient Genetics, University of Copenhagen, DK-2100 Copenhagen, Denmark;
  4. 4 School of Biological Sciences, Royal Holloway, University of London, Egham TW20 0EX, United Kingdom;
  5. 5 Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos, c/Sinesio Delgado 4 Pabellon 14, 28029 d, Spain;
  6. 6 Department of Vertebrate Zoology, Swedish Museum of Natural History, S-10405 Stockholm, Sweden;
  7. 7 Center for Bioinformatics Tübingen, Tübingen University, Tübingen 72076, Germany;
  8. 8 Division of Mammals, National Museum of Natural History, Smithsonian Institution, Washington, D.C. 20013-7012, USA;
  9. 9 Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, S-752 36 Uppsala, Sweden

    Abstract

    We report the first two complete mitochondrial genome sequences of the thylacine (Thylacinus cynocephalus), or so-called Tasmanian tiger, extinct since 1936. The thylacine's phylogenetic position within australidelphian marsupials has long been debated, and here we provide strong support for the thylacine's basal position in Dasyuromorphia, aided by mitochondrial genome sequence that we generated from the extant numbat (Myrmecobius fasciatus). Surprisingly, both of our thylacine sequences differ by 11%–15% from putative thylacine mitochondrial genes in GenBank, with one of our samples originating from a direct offspring of the previously sequenced individual. Our data sample each mitochondrial nucleotide an average of 50 times, thereby providing the first high-fidelity reference sequence for thylacine population genetics. Our two sequences differ in only five nucleotides out of 15,452, hinting at a very low genetic diversity shortly before extinction. Despite the samples’ heavy contamination with bacterial and human DNA and their temperate storage history, we estimate that as much as one-third of the total DNA in each sample is from the thylacine. The microbial content of the two thylacine samples was subjected to metagenomic analysis, and showed striking differences between a wild-captured individual and a born-in-captivity one. This study therefore adds to the growing evidence that extensive sequencing of museum collections is both feasible and desirable, and can yield complete genomes.

    Footnotes

    • 10 Corresponding authors.

      E-mail webb{at}bx.psu.edu; fax (814) 863-6699.

      E-mail scs{at}bx.psu.edu; fax (814) 863-6699.

    • [Supplemental material is available online at www.genome.org. The sequence data from this study have been submitted to GenBank under accession nos. FJ515780–FJ515782. See also http://thylacine.psu.edu.]

    • Article published online before print. Article and publication date are available at http://www.genome.org/cgi/doi/10.1101/gr.082628.108.

      • Received June 25, 2008.
      • Accepted November 18, 2008.
    • Freely available online through the Genome Research open access option.

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