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, SMJ; 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, WJ; 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, XH; Zody, MC; Graves, JAM; Ponting, CP; Breen, M; Samollow, PB; Lander, ES; Lindblad-Toh, K

Author(s): 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, SMJ; 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, WJ; 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, XH; Zody, MC; Graves, JAM; Ponting, CP; Breen, M; Samollow, PB; Lander, ES; Lindblad-Toh, K;
Details: Publication Year 2007-05-10,Volume 447,Issue #7141,Page 167-177
Journal Title: NATURE
Publication Type: Journal Article
Abstract: 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.
Publisher: NATURE PUBLISHING GROUP
Keywords: X-CHROMOSOME INACTIVATION; SHORT-TAILED OPOSSUM; RECOMBINATION RATES; TRANSPOSABLE ELEMENTS; VERTEBRATE EVOLUTION; REGULATORY NETWORKS; MAMMALIAN EVOLUTION; MOBILE ELEMENTS; GENE DESERTS; MOUSE
Research Division(s): Bioinformatics
Publisher's Version: https://doi.org/10.1038/nature05805
Open Access at Publisher's Site: http://www.nature.com/nature/journal/v447/n7141/full/nature05805.html

Creation Date: 2007-05-10 12:00:00