Research from the Batzer lab featured on the cover of Nature
In the 10 May 2007 issue of the journal Nature, the genome sequence of the first marsupial (pouched mammal) is revealed. The Batzer laboratory recently took part in this multi-institutional effort spearheaded by the Broad Institute of MIT and Harvard University to sequence the complete genome of the gray, short-tailed opossum, Monodelphis domestica.
Kangaroos of Australia and the North American opossum, which is abundant in Louisiana, typically come to mind when we think of marsupials. However, Monodelphis domestica, a South American opossum, was chosen for genome sequencing because it is the predominant laboratory-bred research marsupial in the world and therefore represents an important model organism for comparative genomics.
COVER: The South American Opossum (Image: Larry Wadsworth, Media Resources Texas A&M University)
Marsupials diverged from a common ancestor with placental mammals, a group including humans, approximately 180 million years ago. Marsupials and placental mammals are more closely related to one another than to any other vertebrate model species such as birds, amphibians or fish, yet marsupials are also genetically distinct from all current mammalian biomedical research models. This makes the marsupial an integral part of evolutionary and biomedical studies. Studies in the opossum will help identify genome features common to all mammals versus the evolution of distinctly human differences in gene regulation, expression and function, particularly those related to reproduction in placental versus non-placental mammals. The research from Mark Batzer’s group focused primarily on the analysis of the mobile element composition within the opossum genome. They found that mobile elements make up about 52 percent of the opossum genome, compared to only about 50 percent in primate genomes, and have distinct compositional differences as well. In addition, they report an ancient transposable element that appears to have been recruited to a specific biological function perhaps in regulating gene expression. These findings are reported in a companion paper published in Genome Research, online 10 May 2007. Mobile elements are commonly utilized for population genetic studies since they represent “identical by descent” markers of evolution. The genetic diversity and ancestral population structure of recently active mobile elements in diverse opossum populations is the topic of a second companion paper to be published in an upcoming issue of the journal Gene.
Mikkelsen, T.S., M. J. Wakefield, B. Aken, C. T. Amemiya, J. L. Chang, S. Duke, M. Garber, A. J. Gentles, L. Goodstadt, A. Heger, J. Jurka, M. Kamal, E. Mauceli, S. M. J. Searle, T. Sharpe, M. L. Baker, M. A. Batzer, P. V. Benos, K. Belov, M. Clamp, A. Cook, J. Cuff, R. Das, L. Davidow, J. E. Deakin, M. J. Fazzari, J. L. Glass, M. Grabherr, J. M. Greally, W. Gu, T. A. Hore, G. A. Huttley, R. L. Jirtle, E. Koina, J. T. Lee, S. Mahony, M. A. Marra, R. D. Miller, R. D. Nicholls, M. Oda, A. T. Papenfuss, Z. E. Parra, D. D. Pollock, D. A. Ray, J. E. Schein, T. P. Speed, K. Thompson, J. L. VandeBerg, C. M. Wade1, J. A. Walker, P. D. Waters, C. Webber, J. R. Weidman, X. Xie, M. C. Zody, Broad Institute Genome Sequencing Platform, Broad Institute Whole Genome Assembly Team, J. A. Marshall Graves, C. P. Ponting, M. Breen, P. B. Samollow, E. S. Lander and K. Lindblad-Toh (2007) Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 447: 167-178. [cover article]
Gentles, A. J., M. J. Wakefield, O. Kohany, W. Gu, M. A. Batzer, D. D. Pollock and J. Jurka (2007) Evolutionary dynamics and biological impact of transposable elements in the short-tailed opossum Monodelphis domestica. Genome Research.
Gu, W. *, D. A. Ray*, J. A. Walker, E. Barnes, A. J. Gentles, P. B. Samollow, J. Jurka, D. D. Pollock‡ and M. A. Batzer‡ (2007) SINEs, evolution and genomic structure in the opossum. Gene 396: 46-58.
* These authors contributed equally to this work. ‡ These authors are equal senior authors.
Link to Nature
http://www.nature.com/nature/journal/v447/n7141/index.html
Link to the Batzer lab