Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences.
Mikkelsen TS., Wakefield MJ., Aken B., Amemiya CT., Chang JL., Duke S., Garber M., Gentles AJ., Goodstadt L., Heger A., Jurka J., Kamal M., Mauceli E., Searle SM., Sharpe T., Baker ML., Batzer MA., Benos PV., Belov K., Clamp M., Cook A., Cuff J., Das R., Davidow L., Deakin JE., Fazzari MJ., Glass JL., Grabherr M., Greally JM., Gu W., Hore TA., Huttley GA., Kleber M., Jirtle RL., Koina E., Lee JT., Mahony S., Marra MA., Miller RD., Nicholls RD., Oda M., Papenfuss AT., Parra ZE., Pollock DD., Ray DA., Schein JE., Speed TP., Thompson K., VandeBerg JL., Wade CM., Walker JA., Waters PD., Webber C., Weidman JR., Xie X., Zody MC., Broad Institute Genome Sequencing Platform None., Broad Institute Whole Genome Assembly Team None., Graves JA., Ponting CP., Breen M., Samollow PB., Lander ES., Lindblad-Toh K.
We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in protein-coding genes seems to be relatively rare, with lineage-specific differences being largely due to diversification and rapid turnover in gene families involved in environmental interactions. In contrast, about 20% of eutherian conserved non-coding elements (CNEs) are recent inventions that postdate the divergence of Eutheria and Metatheria. A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation.