Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

T.S. Mikkelsen, 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 & 215 others 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, M. Kleber, 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. Wade, J.A. Walker, P.D. Waters, C. Webber, J.R. Weidman, X. Xie, M.C. Zody, J. Baldwin, A. Abdouelleil, J. Abdulkadir, A. Abebe, B. Abera, J. Abreu, St.C. Acer, L. Aftuck, A. Alexander, P. An, E. Anderson, S. Anderson, H. Arachi, M. Azer, P. Bachantsang, A. Barry, T. Bayul, A. Berlin, D. Bessette, T. Bloom, J. Blye, L. Boguslavskiy, C. Bonnet, B. Boukhgalter, I. Bourzgui, A. Brown, P. Cahill, S. Channer, Y. Cheshatsang, L. Chuda, M. Citroen, A. Collymore, P. Cooke, M. Costello, K. D'Aco, R. Daza, G. De Haan, S. DeGray, C. DeMaso, N. Dhargay, K. Dooley, E. Dooley, M. Doricent, P. Dorje, K. Dorjee, A. Dupes, R. Elong, J. Falk, A. Farina, S. Faro, D. Ferguson, S. Fisher, C.D. Foley, A. Franke, D. Friedrich, L. Gadbois, G. Gearin, C.R. Gearin, G. Giannoukos, T. Goode, J. Graham, E. Grandbois, S. Grewal, K. Gyaltsen, N. Hafez, B. Hagos, J. Hall, C. Henson, A. Hollinger, T. Honan, M.D. Huard, L. Hughes, B. Hurhula, M.E. Husby, A. Kamat, B. Kanga, S. Kashin, D. Khazanovich, P. Kisner, K. Lance, M. Lara, W. Lee, N. Lennon, F. Letendre, R. LeVine, A. Lipovsky, X. Liu, J. Liu, S. Liu, T. Lokyitsang, Y. Lokyitsang, R. Lubonja, A. Lui, P. MacDonald, V. Magnisalis, K. Maru, C. Matthews, W. McCusker, S. McDonough, T. Mehta, J. Meldrim, L. Meneus, O. Mihai, A. Mihalev, T. Mihova, R. Mittelman, V. Mlenga, A. Montmayeur, L. Mulrain, A. Navidi, J. Naylor, T. Negash, T. Nguyen, N. Nguyen, R. Nicol, C. Norbu, N. Norbu, N. Novod, B. O'Neill, S. Osman, E. Markiewicz, O.L. Oyono, C. Patti, P. Phunkhang, F. Pierre, M. Priest, S. Raghuraman, F. Rege, R. Reyes, C. Rise, P. Rogov, K. Ross, E. Ryan, S. Settipalli, T. Shea, N. Sherpa, L. Shi, D. Shih, T. Sparrow, J. Spaulding, J. Stalker, N. Stange-Thomann, S. Stavropoulos, C. Stone, C. Strader, S. Tesfaye, T. Thomson, Y. Thoulutsang, D. Thoulutsang, K. Topham, I. Topping, T. Tsamla, H. Vassiliev, A. Vo, T. Wangchuk, T. Wangdi, M. Weiand, J. Wilkinson, A. Wilson, S. Yadav, G. Young, Q. Yu, L. Zembek, D. Zhong, A. Zimmer, Z. Zwirko, D.B. Jaffe, P. Alvarez, W. Brockman, J. Butler, C. Chin, S. Gnerre, I. MacCallum, J.A.M. Graves, C.P. Ponting, M. Breen, P.B. Samollow, E.S. Lander, K. Lindblad-Toh

    Research output: Contribution to journalArticle

    490 Citations (Scopus)

    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. ©2007 Nature Publishing Group.
    Original languageUndefined
    Pages (from-to)167-177
    Number of pages11
    JournalNature
    Volume447
    Issue number7141
    DOIs
    Publication statusPublished - 2007

    Cite this

    Mikkelsen, T. S., Wakefield, M. J., Aken, B., Amemiya, C. T., Chang, J. L., Duke, S., ... Lindblad-Toh, K. (2007). Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature, 447(7141), 167-177. https://doi.org/10.1038/nature05805
    Mikkelsen, T.S. ; Wakefield, M.J. ; Aken, B. ; Amemiya, C.T. ; Chang, J.L. ; Duke, S. ; Garber, M. ; Gentles, A.J. ; Goodstadt, L. ; Heger, A. ; Jurka, J. ; Kamal, M. ; Mauceli, E. ; Searle, S.M.J. ; Sharpe, T. ; Baker, M.L. ; Batzer, M.A. ; Benos, P.V. ; Belov, K. ; Clamp, M. ; Cook, A. ; Cuff, J. ; Das, R. ; Davidow, L. ; Deakin, J.E. ; Fazzari, M.J. ; Glass, J.L. ; Grabherr, M. ; Greally, J.M. ; Gu, W. ; Hore, T.A. ; Huttley, G.A. ; Kleber, M. ; Jirtle, R.L. ; Koina, E. ; Lee, J.T. ; Mahony, S. ; Marra, M.A. ; Miller, R.D. ; Nicholls, R.D. ; Oda, M. ; Papenfuss, A.T. ; Parra, Z.E. ; Pollock, D.D. ; Ray, D.A. ; Schein, J.E. ; Speed, T.P. ; Thompson, K. ; VandeBerg, J.L. ; Wade, C.M. ; Walker, J.A. ; Waters, P.D. ; Webber, C. ; Weidman, J.R. ; Xie, X. ; Zody, M.C. ; Baldwin, J. ; Abdouelleil, A. ; Abdulkadir, J. ; Abebe, A. ; Abera, B. ; Abreu, J. ; Acer, St.C. ; Aftuck, L. ; Alexander, A. ; An, P. ; Anderson, E. ; Anderson, S. ; Arachi, H. ; Azer, M. ; Bachantsang, P. ; Barry, A. ; Bayul, T. ; Berlin, A. ; Bessette, D. ; Bloom, T. ; Blye, J. ; Boguslavskiy, L. ; Bonnet, C. ; Boukhgalter, B. ; Bourzgui, I. ; Brown, A. ; Cahill, P. ; Channer, S. ; Cheshatsang, Y. ; Chuda, L. ; Citroen, M. ; Collymore, A. ; Cooke, P. ; Costello, M. ; D'Aco, K. ; Daza, R. ; De Haan, G. ; DeGray, S. ; DeMaso, C. ; Dhargay, N. ; Dooley, K. ; Dooley, E. ; Doricent, M. ; Dorje, P. ; Dorjee, K. ; Dupes, A. ; Elong, R. ; Falk, J. ; Farina, A. ; Faro, S. ; Ferguson, D. ; Fisher, S. ; Foley, C.D. ; Franke, A. ; Friedrich, D. ; Gadbois, L. ; Gearin, G. ; Gearin, C.R. ; Giannoukos, G. ; Goode, T. ; Graham, J. ; Grandbois, E. ; Grewal, S. ; Gyaltsen, K. ; Hafez, N. ; Hagos, B. ; Hall, J. ; Henson, C. ; Hollinger, A. ; Honan, T. ; Huard, M.D. ; Hughes, L. ; Hurhula, B. ; Husby, M.E. ; Kamat, A. ; Kanga, B. ; Kashin, S. ; Khazanovich, D. ; Kisner, P. ; Lance, K. ; Lara, M. ; Lee, W. ; Lennon, N. ; Letendre, F. ; LeVine, R. ; Lipovsky, A. ; Liu, X. ; Liu, J. ; Liu, S. ; Lokyitsang, T. ; Lokyitsang, Y. ; Lubonja, R. ; Lui, A. ; MacDonald, P. ; Magnisalis, V. ; Maru, K. ; Matthews, C. ; McCusker, W. ; McDonough, S. ; Mehta, T. ; Meldrim, J. ; Meneus, L. ; Mihai, O. ; Mihalev, A. ; Mihova, T. ; Mittelman, R. ; Mlenga, V. ; Montmayeur, A. ; Mulrain, L. ; Navidi, A. ; Naylor, J. ; Negash, T. ; Nguyen, T. ; Nguyen, N. ; Nicol, R. ; Norbu, C. ; Norbu, N. ; Novod, N. ; O'Neill, B. ; Osman, S. ; Markiewicz, E. ; Oyono, O.L. ; Patti, C. ; Phunkhang, P. ; Pierre, F. ; Priest, M. ; Raghuraman, S. ; Rege, F. ; Reyes, R. ; Rise, C. ; Rogov, P. ; Ross, K. ; Ryan, E. ; Settipalli, S. ; Shea, T. ; Sherpa, N. ; Shi, L. ; Shih, D. ; Sparrow, T. ; Spaulding, J. ; Stalker, J. ; Stange-Thomann, N. ; Stavropoulos, S. ; Stone, C. ; Strader, C. ; Tesfaye, S. ; Thomson, T. ; Thoulutsang, Y. ; Thoulutsang, D. ; Topham, K. ; Topping, I. ; Tsamla, T. ; Vassiliev, H. ; Vo, A. ; Wangchuk, T. ; Wangdi, T. ; Weiand, M. ; Wilkinson, J. ; Wilson, A. ; Yadav, S. ; Young, G. ; Yu, Q. ; Zembek, L. ; Zhong, D. ; Zimmer, A. ; Zwirko, Z. ; Jaffe, D.B. ; Alvarez, P. ; Brockman, W. ; Butler, J. ; Chin, C. ; Gnerre, S. ; MacCallum, I. ; Graves, J.A.M. ; Ponting, C.P. ; Breen, M. ; Samollow, P.B. ; Lander, E.S. ; Lindblad-Toh, K. / Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. In: Nature. 2007 ; Vol. 447, No. 7141. pp. 167-177.
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    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. {\circledC}2007 Nature Publishing Group.",
    author = "T.S. Mikkelsen and M.J. Wakefield and B. Aken and C.T. Amemiya and J.L. Chang and S. Duke and M. Garber and A.J. Gentles and L. Goodstadt and A. Heger and J. Jurka and M. Kamal and E. Mauceli and S.M.J. Searle and T. Sharpe and M.L. Baker and M.A. Batzer and P.V. Benos and K. Belov and M. Clamp and A. Cook and J. Cuff and R. Das and L. Davidow and J.E. Deakin and M.J. Fazzari and J.L. Glass and M. Grabherr and J.M. Greally and W. Gu and T.A. Hore and G.A. Huttley and M. Kleber and R.L. Jirtle and E. Koina and J.T. Lee and S. Mahony and M.A. Marra and R.D. Miller and R.D. Nicholls and M. Oda and A.T. Papenfuss and Z.E. Parra and D.D. Pollock and D.A. Ray and J.E. Schein and T.P. Speed and K. Thompson and J.L. VandeBerg and C.M. Wade and J.A. Walker and P.D. Waters and C. Webber and J.R. Weidman and X. Xie and M.C. Zody and J. Baldwin and A. Abdouelleil and J. Abdulkadir and A. Abebe and B. Abera and J. Abreu and St.C. Acer and L. Aftuck and A. Alexander and P. An and E. Anderson and S. Anderson and H. Arachi and M. Azer and P. Bachantsang and A. Barry and T. Bayul and A. Berlin and D. Bessette and T. Bloom and J. Blye and L. Boguslavskiy and C. Bonnet and B. Boukhgalter and I. Bourzgui and A. Brown and P. Cahill and S. Channer and Y. Cheshatsang and L. Chuda and M. Citroen and A. Collymore and P. Cooke and M. Costello and K. D'Aco and R. Daza and {De Haan}, G. and S. DeGray and C. DeMaso and N. Dhargay and K. Dooley and E. Dooley and M. Doricent and P. Dorje and K. Dorjee and A. Dupes and R. Elong and J. Falk and A. Farina and S. Faro and D. Ferguson and S. Fisher and C.D. Foley and A. Franke and D. Friedrich and L. Gadbois and G. Gearin and C.R. Gearin and G. Giannoukos and T. Goode and J. Graham and E. Grandbois and S. Grewal and K. Gyaltsen and N. Hafez and B. Hagos and J. Hall and C. Henson and A. Hollinger and T. Honan and M.D. Huard and L. Hughes and B. Hurhula and M.E. Husby and A. Kamat and B. Kanga and S. Kashin and D. Khazanovich and P. Kisner and K. Lance and M. Lara and W. Lee and N. Lennon and F. Letendre and R. LeVine and A. Lipovsky and X. Liu and J. Liu and S. Liu and T. Lokyitsang and Y. Lokyitsang and R. Lubonja and A. Lui and P. MacDonald and V. Magnisalis and K. Maru and C. Matthews and W. McCusker and S. McDonough and T. Mehta and J. Meldrim and L. Meneus and O. Mihai and A. Mihalev and T. Mihova and R. Mittelman and V. Mlenga and A. Montmayeur and L. Mulrain and A. Navidi and J. Naylor and T. Negash and T. Nguyen and N. Nguyen and R. Nicol and C. Norbu and N. Norbu and N. Novod and B. O'Neill and S. Osman and E. Markiewicz and O.L. Oyono and C. Patti and P. Phunkhang and F. Pierre and M. Priest and S. Raghuraman and F. Rege and R. Reyes and C. Rise and P. Rogov and K. Ross and E. Ryan and S. Settipalli and T. Shea and N. Sherpa and L. Shi and D. Shih and T. Sparrow and J. Spaulding and J. Stalker and N. Stange-Thomann and S. Stavropoulos and C. Stone and C. Strader and S. Tesfaye and T. Thomson and Y. Thoulutsang and D. Thoulutsang and K. Topham and I. Topping and T. Tsamla and H. Vassiliev and A. Vo and T. Wangchuk and T. Wangdi and M. Weiand and J. Wilkinson and A. Wilson and S. Yadav and G. Young and Q. Yu and L. Zembek and D. Zhong and A. Zimmer and Z. Zwirko and D.B. Jaffe and P. Alvarez and W. Brockman and J. Butler and C. Chin and S. Gnerre and I. MacCallum and J.A.M. Graves and C.P. Ponting and M. Breen and P.B. Samollow and E.S. Lander and K. Lindblad-Toh",
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    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, 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, Baldwin, J, Abdouelleil, A, Abdulkadir, J, Abebe, A, Abera, B, Abreu, J, Acer, SC, Aftuck, L, Alexander, A, An, P, Anderson, E, Anderson, S, Arachi, H, Azer, M, Bachantsang, P, Barry, A, Bayul, T, Berlin, A, Bessette, D, Bloom, T, Blye, J, Boguslavskiy, L, Bonnet, C, Boukhgalter, B, Bourzgui, I, Brown, A, Cahill, P, Channer, S, Cheshatsang, Y, Chuda, L, Citroen, M, Collymore, A, Cooke, P, Costello, M, D'Aco, K, Daza, R, De Haan, G, DeGray, S, DeMaso, C, Dhargay, N, Dooley, K, Dooley, E, Doricent, M, Dorje, P, Dorjee, K, Dupes, A, Elong, R, Falk, J, Farina, A, Faro, S, Ferguson, D, Fisher, S, Foley, CD, Franke, A, Friedrich, D, Gadbois, L, Gearin, G, Gearin, CR, Giannoukos, G, Goode, T, Graham, J, Grandbois, E, Grewal, S, Gyaltsen, K, Hafez, N, Hagos, B, Hall, J, Henson, C, Hollinger, A, Honan, T, Huard, MD, Hughes, L, Hurhula, B, Husby, ME, Kamat, A, Kanga, B, Kashin, S, Khazanovich, D, Kisner, P, Lance, K, Lara, M, Lee, W, Lennon, N, Letendre, F, LeVine, R, Lipovsky, A, Liu, X, Liu, J, Liu, S, Lokyitsang, T, Lokyitsang, Y, Lubonja, R, Lui, A, MacDonald, P, Magnisalis, V, Maru, K, Matthews, C, McCusker, W, McDonough, S, Mehta, T, Meldrim, J, Meneus, L, Mihai, O, Mihalev, A, Mihova, T, Mittelman, R, Mlenga, V, Montmayeur, A, Mulrain, L, Navidi, A, Naylor, J, Negash, T, Nguyen, T, Nguyen, N, Nicol, R, Norbu, C, Norbu, N, Novod, N, O'Neill, B, Osman, S, Markiewicz, E, Oyono, OL, Patti, C, Phunkhang, P, Pierre, F, Priest, M, Raghuraman, S, Rege, F, Reyes, R, Rise, C, Rogov, P, Ross, K, Ryan, E, Settipalli, S, Shea, T, Sherpa, N, Shi, L, Shih, D, Sparrow, T, Spaulding, J, Stalker, J, Stange-Thomann, N, Stavropoulos, S, Stone, C, Strader, C, Tesfaye, S, Thomson, T, Thoulutsang, Y, Thoulutsang, D, Topham, K, Topping, I, Tsamla, T, Vassiliev, H, Vo, A, Wangchuk, T, Wangdi, T, Weiand, M, Wilkinson, J, Wilson, A, Yadav, S, Young, G, Yu, Q, Zembek, L, Zhong, D, Zimmer, A, Zwirko, Z, Jaffe, DB, Alvarez, P, Brockman, W, Butler, J, Chin, C, Gnerre, S, MacCallum, I, Graves, JAM, Ponting, CP, Breen, M, Samollow, PB, Lander, ES & Lindblad-Toh, K 2007, 'Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences', Nature, vol. 447, no. 7141, pp. 167-177. https://doi.org/10.1038/nature05805

    Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. / Mikkelsen, T.S.; Wakefield, M.J.; Aken, B.; Amemiya, C.T.; Chang, J.L.; Duke, S.; Garber, M.; Gentles, A.J.; Goodstadt, L.; Heger, A.; Jurka, J.; Kamal, M.; Mauceli, E.; Searle, S.M.J.; Sharpe, T.; Baker, M.L.; Batzer, M.A.; Benos, P.V.; Belov, K.; Clamp, M.; Cook, A.; Cuff, J.; Das, R.; Davidow, L.; Deakin, J.E.; Fazzari, M.J.; Glass, J.L.; Grabherr, M.; Greally, J.M.; Gu, W.; Hore, T.A.; Huttley, G.A.; Kleber, M.; Jirtle, R.L.; Koina, E.; Lee, J.T.; Mahony, S.; Marra, M.A.; Miller, R.D.; Nicholls, R.D.; Oda, M.; Papenfuss, A.T.; Parra, Z.E.; Pollock, D.D.; Ray, D.A.; Schein, J.E.; Speed, T.P.; Thompson, K.; VandeBerg, J.L.; Wade, C.M.; Walker, J.A.; Waters, P.D.; Webber, C.; Weidman, J.R.; Xie, X.; Zody, M.C.; Baldwin, J.; Abdouelleil, A.; Abdulkadir, J.; Abebe, A.; Abera, B.; Abreu, J.; Acer, St.C.; Aftuck, L.; Alexander, A.; An, P.; Anderson, E.; Anderson, S.; Arachi, H.; Azer, M.; Bachantsang, P.; Barry, A.; Bayul, T.; Berlin, A.; Bessette, D.; Bloom, T.; Blye, J.; Boguslavskiy, L.; Bonnet, C.; Boukhgalter, B.; Bourzgui, I.; Brown, A.; Cahill, P.; Channer, S.; Cheshatsang, Y.; Chuda, L.; Citroen, M.; Collymore, A.; Cooke, P.; Costello, M.; D'Aco, K.; Daza, R.; De Haan, G.; DeGray, S.; DeMaso, C.; Dhargay, N.; Dooley, K.; Dooley, E.; Doricent, M.; Dorje, P.; Dorjee, K.; Dupes, A.; Elong, R.; Falk, J.; Farina, A.; Faro, S.; Ferguson, D.; Fisher, S.; Foley, C.D.; Franke, A.; Friedrich, D.; Gadbois, L.; Gearin, G.; Gearin, C.R.; Giannoukos, G.; Goode, T.; Graham, J.; Grandbois, E.; Grewal, S.; Gyaltsen, K.; Hafez, N.; Hagos, B.; Hall, J.; Henson, C.; Hollinger, A.; Honan, T.; Huard, M.D.; Hughes, L.; Hurhula, B.; Husby, M.E.; Kamat, A.; Kanga, B.; Kashin, S.; Khazanovich, D.; Kisner, P.; Lance, K.; Lara, M.; Lee, W.; Lennon, N.; Letendre, F.; LeVine, R.; Lipovsky, A.; Liu, X.; Liu, J.; Liu, S.; Lokyitsang, T.; Lokyitsang, Y.; Lubonja, R.; Lui, A.; MacDonald, P.; Magnisalis, V.; Maru, K.; Matthews, C.; McCusker, W.; McDonough, S.; Mehta, T.; Meldrim, J.; Meneus, L.; Mihai, O.; Mihalev, A.; Mihova, T.; Mittelman, R.; Mlenga, V.; Montmayeur, A.; Mulrain, L.; Navidi, A.; Naylor, J.; Negash, T.; Nguyen, T.; Nguyen, N.; Nicol, R.; Norbu, C.; Norbu, N.; Novod, N.; O'Neill, B.; Osman, S.; Markiewicz, E.; Oyono, O.L.; Patti, C.; Phunkhang, P.; Pierre, F.; Priest, M.; Raghuraman, S.; Rege, F.; Reyes, R.; Rise, C.; Rogov, P.; Ross, K.; Ryan, E.; Settipalli, S.; Shea, T.; Sherpa, N.; Shi, L.; Shih, D.; Sparrow, T.; Spaulding, J.; Stalker, J.; Stange-Thomann, N.; Stavropoulos, S.; Stone, C.; Strader, C.; Tesfaye, S.; Thomson, T.; Thoulutsang, Y.; Thoulutsang, D.; Topham, K.; Topping, I.; Tsamla, T.; Vassiliev, H.; Vo, A.; Wangchuk, T.; Wangdi, T.; Weiand, M.; Wilkinson, J.; Wilson, A.; Yadav, S.; Young, G.; Yu, Q.; Zembek, L.; Zhong, D.; Zimmer, A.; Zwirko, Z.; Jaffe, D.B.; Alvarez, P.; Brockman, W.; Butler, J.; Chin, C.; Gnerre, S.; MacCallum, I.; Graves, J.A.M.; Ponting, C.P.; Breen, M.; Samollow, P.B.; Lander, E.S.; Lindblad-Toh, K.

    In: Nature, Vol. 447, No. 7141, 2007, p. 167-177.

    Research output: Contribution to journalArticle

    TY - JOUR

    T1 - Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

    AU - Mikkelsen, T.S.

    AU - Wakefield, M.J.

    AU - Aken, B.

    AU - Amemiya, C.T.

    AU - Chang, J.L.

    AU - Duke, S.

    AU - Garber, M.

    AU - Gentles, A.J.

    AU - Goodstadt, L.

    AU - Heger, A.

    AU - Jurka, J.

    AU - Kamal, M.

    AU - Mauceli, E.

    AU - Searle, S.M.J.

    AU - Sharpe, T.

    AU - Baker, M.L.

    AU - Batzer, M.A.

    AU - Benos, P.V.

    AU - Belov, K.

    AU - Clamp, M.

    AU - Cook, A.

    AU - Cuff, J.

    AU - Das, R.

    AU - Davidow, L.

    AU - Deakin, J.E.

    AU - Fazzari, M.J.

    AU - Glass, J.L.

    AU - Grabherr, M.

    AU - Greally, J.M.

    AU - Gu, W.

    AU - Hore, T.A.

    AU - Huttley, G.A.

    AU - Kleber, M.

    AU - Jirtle, R.L.

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    N1 - cited By 453

    PY - 2007

    Y1 - 2007

    N2 - 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. ©2007 Nature Publishing Group.

    AB - 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. ©2007 Nature Publishing Group.

    U2 - 10.1038/nature05805

    DO - 10.1038/nature05805

    M3 - Article

    VL - 447

    SP - 167

    EP - 177

    JO - Nature: New biology

    JF - Nature: New biology

    SN - 0028-0836

    IS - 7141

    ER -

    Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S et al. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature. 2007;447(7141):167-177. https://doi.org/10.1038/nature05805