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

Tarjei S. Mikkelsen; Matthew J. Wakefield; Bronwen Aken; Chris T. Amemiya; Jean L. Chang; Shannon Duke; Manuel Garber; Andrew J. Gentles; Leo Goodstadt; Andreas Heger; Jerzy Jurka; Michael Kamal; Evan Mauceli; Stephen M.J. Searle; Ted Sharpe; Michelle L. Baker; Mark A. Batzer; Panayiotis V. Benos; Katherine Belov; Michele Clamp; April Cook; James Cuff; Radhika Das; Lance Davidow; Janine E. Deakin; Melissa J. Fazzari; Jacob L. Glass; Manfred Grabherr; John M. Greally; Wanjun Gu; Timothy A. Hore; Gavin A. Huttley; Michael Kleber; Randy L. Jirtle; Edda Koina; Jeannie T. Lee; Shaun Mahony; Marco A. Marra; Robert D. Miller; Robert D. Nicholls; Mayumi Oda; Anthony T. Papenfuss; Zuly E. Parra; David D. Pollock; David A. Ray; Jacqueline E. Schein; Terence P. Speed; Katherine Thompson; John L. VandeBerg; Claire M. Wade; Jerilyn A. Walker; Paul D. Waters; Caleb Webber; Jennifer R. Weidman; Xiaohui Xie; Michael C. Zody; Jennifer Baldwin; Amr Abdouelleil; Jamal Abdulkadir; Adal Abebe; Brikti Abera; Justin Abreu; St Christophe Acer; Lynne Aftuck; Allen Alexander; Peter An; Erica Anderson; Scott Anderson; Harindra Arachi; Marc Azer; Pasang Bachantsang; Andrew Barry; Tashi Bayul; Aaron Berlin; Daniel Bessette; Toby Bloom; Jason Blye; Leonid Boguslavskiy; Claude Bonnet; Boris Boukhgalter; Imane Bourzgui; Adam Brown; Patrick Cahill; Sheridon Channer; Yama Cheshatsang; Lisa Chuda; Mieke Citroen; Alville Collymore; Patrick Cooke; Maura Costello; Katie D'Aco; Riza Daza; Georgius De Haan; Stuart DeGray; Christina DeMaso; Norbu Dhargay; Kimberly Dooley; Erin Dooley; Missole Doricent; Passang Dorje; Kunsang Dorjee; Alan Dupes; Richard Elong; Jill Falk; Abderrahim Farina; Susan Faro; Diallo Ferguson; Sheila Fisher; Chelsea D. Foley; Alicia Franke; Dennis Friedrich; Loryn Gadbois; Gary Gearin; Christina R. Gearin; Georgia Giannoukos; Tina Goode; Joseph Graham; Edward Grandbois; Sharleen Grewal; Kunsang Gyaltsen; Nabil Hafez; Birhane Hagos; Jennifer Hall; Charlotte Henson; Andrew Hollinger; Tracey Honan; Monika D. Huard; Leanne Hughes; Brian Hurhula; M. Erii Husby; Asha Kamat; Ben Kanga; Seva Kashin; Dmitry Khazanovich; Peter Kisner; Krista Lance; Marcia Lara; William Lee; Niall Lennon; Frances Letendre; Rosie LeVine; Alex Lipovsky; Xiaohong Liu; Jinlei Liu; Shangtao Liu; Tashi Lokyitsang; Yeshi Lokyitsang; Rakela Lubonja; Annie Lui; Pen MacDonald; Vasilia Magnisalis; Kebede Maru; Charles Matthews; William McCusker; Susan McDonough; Teena Mehta; James Meldrim; Louis Meneus; Oana Mihai; Atanas Mihalev; Tanya Mihova; Rachel Mittelman; Valentine Mlenga; Anna Montmayeur; Leonidas Mulrain; Adam Navidi; Jerome Naylor; Tamrat Negash; Thu Nguyen; Nga Nguyen; Robert Nicol; Choe Norbu; Nyima Norbu; Nathaniel Novod; Barry O'Neill; Sahal Osman; Eva Markiewicz; Otero L. Oyono; Christopher Patti; Pema Phunkhang; Fritz Pierre; Margaret Priest; Sujaa Raghuraman; Filip Rege; Rebecca Reyes; Cecil Rise; Peter Rogov; Keenan Ross; Elizabeth Ryan; Sampath Settipalli; Terry Shea; Ngawang Sherpa; Lu Shi; Diana Shih; Todd Sparrow; Jessica Spaulding; John Stalker; Nicole Stange-Thomann; Sharon Stavropoulos; Catherine Stone; Christopher Strader; Senait Tesfaye; Talene Thomson; Yama Thoulutsang; Dawa Thoulutsang; Kerri Topham; Ira Topping; Tsamla Tsamla; Helen Vassiliev; Andy Vo; Tsering Wangchuk; Tsering Wangdi; Michael Weiand; Jane Wilkinson; Adam Wilson; Shailendra Yadav; Geneva Young; Qing Yu; Lisa Zembek; Danni Zhong; Andrew Zimmer; Zac Zwirko; David B. Jaffe; Pablo Alvarez; Will Brockman; Jonathan Butler; Chee Whye Chin; Sante Gnerre; Iain MacCallum; Jennifer A.Marshall Graves; Chris P. Ponting; Matthew Breen; Paul B. Samollow; Eric S. Lander; Kerstin Lindblad-Toh

doi:10.1038/nature05805

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

Tarjei S. Mikkelsen, Matthew J. Wakefield, Bronwen Aken, Chris T. Amemiya, Jean L. Chang, Shannon Duke, Manuel Garber, Andrew J. Gentles, Leo Goodstadt, Andreas Heger, Jerzy Jurka, Michael Kamal, Evan Mauceli, Stephen M.J. Searle, Ted Sharpe, Michelle L. Baker, Mark A. Batzer, Panayiotis V. Benos, Katherine Belov, Michele ClampApril Cook, James Cuff, Radhika Das, Lance Davidow, Janine E. Deakin, Melissa J. Fazzari, Jacob L. Glass, Manfred Grabherr, John M. Greally, Wanjun Gu, Timothy A. Hore, Gavin A. Huttley, Michael Kleber, Randy L. Jirtle, Edda Koina, Jeannie T. Lee, Shaun Mahony, Marco A. Marra, Robert D. Miller, Robert D. Nicholls, Mayumi Oda, Anthony T. Papenfuss, Zuly E. Parra, David D. Pollock, David A. Ray, Jacqueline E. Schein, Terence P. Speed, Katherine Thompson, John L. VandeBerg, Claire M. Wade, Jerilyn A. Walker, Paul D. Waters, Caleb Webber, Jennifer R. Weidman, Xiaohui Xie, Michael C. Zody, Jennifer Baldwin, Amr Abdouelleil, Jamal Abdulkadir, Adal Abebe, Brikti Abera, Justin Abreu, St Christophe Acer, Lynne Aftuck, Allen Alexander, Peter An, Erica Anderson, Scott Anderson, Harindra Arachi, Marc Azer, Pasang Bachantsang, Andrew Barry, Tashi Bayul, Aaron Berlin, Daniel Bessette, Toby Bloom, Jason Blye, Leonid Boguslavskiy, Claude Bonnet, Boris Boukhgalter, Imane Bourzgui, Adam Brown, Patrick Cahill, Sheridon Channer, Yama Cheshatsang, Lisa Chuda, Mieke Citroen, Alville Collymore, Patrick Cooke, Maura Costello, Katie D'Aco, Riza Daza, Georgius De Haan, Stuart DeGray, Christina DeMaso, Norbu Dhargay, Kimberly Dooley, Erin Dooley, Missole Doricent, Passang Dorje, Kunsang Dorjee, Alan Dupes, Richard Elong, Jill Falk, Abderrahim Farina, Susan Faro, Diallo Ferguson, Sheila Fisher, Chelsea D. Foley, Alicia Franke, Dennis Friedrich, Loryn Gadbois, Gary Gearin, Christina R. Gearin, Georgia Giannoukos, Tina Goode, Joseph Graham, Edward Grandbois, Sharleen Grewal, Kunsang Gyaltsen, Nabil Hafez, Birhane Hagos, Jennifer Hall, Charlotte Henson, Andrew Hollinger, Tracey Honan, Monika D. Huard, Leanne Hughes, Brian Hurhula, M. Erii Husby, Asha Kamat, Ben Kanga, Seva Kashin, Dmitry Khazanovich, Peter Kisner, Krista Lance, Marcia Lara, William Lee, Niall Lennon, Frances Letendre, Rosie LeVine, Alex Lipovsky, Xiaohong Liu, Jinlei Liu, Shangtao Liu, Tashi Lokyitsang, Yeshi Lokyitsang, Rakela Lubonja, Annie Lui, Pen MacDonald, Vasilia Magnisalis, Kebede Maru, Charles Matthews, William McCusker, Susan McDonough, Teena Mehta, James Meldrim, Louis Meneus, Oana Mihai, Atanas Mihalev, Tanya Mihova, Rachel Mittelman, Valentine Mlenga, Anna Montmayeur, Leonidas Mulrain, Adam Navidi, Jerome Naylor, Tamrat Negash, Thu Nguyen, Nga Nguyen, Robert Nicol, Choe Norbu, Nyima Norbu, Nathaniel Novod, Barry O'Neill, Sahal Osman, Eva Markiewicz, Otero L. Oyono, Christopher Patti, Pema Phunkhang, Fritz Pierre, Margaret Priest, Sujaa Raghuraman, Filip Rege, Rebecca Reyes, Cecil Rise, Peter Rogov, Keenan Ross, Elizabeth Ryan, Sampath Settipalli, Terry Shea, Ngawang Sherpa, Lu Shi, Diana Shih, Todd Sparrow, Jessica Spaulding, John Stalker, Nicole Stange-Thomann, Sharon Stavropoulos, Catherine Stone, Christopher Strader, Senait Tesfaye, Talene Thomson, Yama Thoulutsang, Dawa Thoulutsang, Kerri Topham, Ira Topping, Tsamla Tsamla, Helen Vassiliev, Andy Vo, Tsering Wangchuk, Tsering Wangdi, Michael Weiand, Jane Wilkinson, Adam Wilson, Shailendra Yadav, Geneva Young, Qing Yu, Lisa Zembek, Danni Zhong, Andrew Zimmer, Zac Zwirko, David B. Jaffe, Pablo Alvarez, Will Brockman, Jonathan Butler, Chee Whye Chin, Sante Gnerre, Iain MacCallum, Jennifer A.Marshall Graves, Chris P. Ponting, Matthew Breen, Paul B. Samollow, Eric S. Lander, Kerstin Lindblad-Toh

Research output: Contribution to journal › Article › peer-review

578 Scopus citations

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.

Original language	English (US)
Pages (from-to)	167-177
Number of pages	11
Journal	Nature
Volume	447
Issue number	7141
DOIs	https://doi.org/10.1038/nature05805
State	Published - May 10 2007

All Science Journal Classification (ASJC) codes

General

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10.1038/nature05805

Cite this

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., ... 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

@article{39e128f98f0d4e3088626873cf94a8b5,

title = "Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences",

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.",

author = "Mikkelsen, {Tarjei S.} and Wakefield, {Matthew J.} and Bronwen Aken and Amemiya, {Chris T.} and Chang, {Jean L.} and Shannon Duke and Manuel Garber and Gentles, {Andrew J.} and Leo Goodstadt and Andreas Heger and Jerzy Jurka and Michael Kamal and Evan Mauceli and Searle, {Stephen M.J.} and Ted Sharpe and Baker, {Michelle L.} and Batzer, {Mark A.} and Benos, {Panayiotis V.} and Katherine Belov and Michele Clamp and April Cook and James Cuff and Radhika Das and Lance Davidow and Deakin, {Janine E.} and Fazzari, {Melissa J.} and Glass, {Jacob L.} and Manfred Grabherr and Greally, {John M.} and Wanjun Gu and Hore, {Timothy A.} and Huttley, {Gavin A.} and Michael Kleber and Jirtle, {Randy L.} and Edda Koina and Lee, {Jeannie T.} and Shaun Mahony and Marra, {Marco A.} and Miller, {Robert D.} and Nicholls, {Robert D.} and Mayumi Oda and Papenfuss, {Anthony T.} and Parra, {Zuly E.} and Pollock, {David D.} and Ray, {David A.} and Schein, {Jacqueline E.} and Speed, {Terence P.} and Katherine Thompson and VandeBerg, {John L.} and Wade, {Claire M.} and Walker, {Jerilyn A.} and Waters, {Paul D.} and Caleb Webber and Weidman, {Jennifer R.} and Xiaohui Xie and Zody, {Michael C.} and Jennifer Baldwin and Amr Abdouelleil and Jamal Abdulkadir and Adal Abebe and Brikti Abera and Justin Abreu and Acer, {St Christophe} and Lynne Aftuck and Allen Alexander and Peter An and Erica Anderson and Scott Anderson and Harindra Arachi and Marc Azer and Pasang Bachantsang and Andrew Barry and Tashi Bayul and Aaron Berlin and Daniel Bessette and Toby Bloom and Jason Blye and Leonid Boguslavskiy and Claude Bonnet and Boris Boukhgalter and Imane Bourzgui and Adam Brown and Patrick Cahill and Sheridon Channer and Yama Cheshatsang and Lisa Chuda and Mieke Citroen and Alville Collymore and Patrick Cooke and Maura Costello and Katie D'Aco and Riza Daza and {De Haan}, Georgius and Stuart DeGray and Christina DeMaso and Norbu Dhargay and Kimberly Dooley and Erin Dooley and Missole Doricent and Passang Dorje and Kunsang Dorjee and Alan Dupes and Richard Elong and Jill Falk and Abderrahim Farina and Susan Faro and Diallo Ferguson and Sheila Fisher and Foley, {Chelsea D.} and Alicia Franke and Dennis Friedrich and Loryn Gadbois and Gary Gearin and Gearin, {Christina R.} and Georgia Giannoukos and Tina Goode and Joseph Graham and Edward Grandbois and Sharleen Grewal and Kunsang Gyaltsen and Nabil Hafez and Birhane Hagos and Jennifer Hall and Charlotte Henson and Andrew Hollinger and Tracey Honan and Huard, {Monika D.} and Leanne Hughes and Brian Hurhula and Husby, {M. Erii} and Asha Kamat and Ben Kanga and Seva Kashin and Dmitry Khazanovich and Peter Kisner and Krista Lance and Marcia Lara and William Lee and Niall Lennon and Frances Letendre and Rosie LeVine and Alex Lipovsky and Xiaohong Liu and Jinlei Liu and Shangtao Liu and Tashi Lokyitsang and Yeshi Lokyitsang and Rakela Lubonja and Annie Lui and Pen MacDonald and Vasilia Magnisalis and Kebede Maru and Charles Matthews and William McCusker and Susan McDonough and Teena Mehta and James Meldrim and Louis Meneus and Oana Mihai and Atanas Mihalev and Tanya Mihova and Rachel Mittelman and Valentine Mlenga and Anna Montmayeur and Leonidas Mulrain and Adam Navidi and Jerome Naylor and Tamrat Negash and Thu Nguyen and Nga Nguyen and Robert Nicol and Choe Norbu and Nyima Norbu and Nathaniel Novod and Barry O'Neill and Sahal Osman and Eva Markiewicz and Oyono, {Otero L.} and Christopher Patti and Pema Phunkhang and Fritz Pierre and Margaret Priest and Sujaa Raghuraman and Filip Rege and Rebecca Reyes and Cecil Rise and Peter Rogov and Keenan Ross and Elizabeth Ryan and Sampath Settipalli and Terry Shea and Ngawang Sherpa and Lu Shi and Diana Shih and Todd Sparrow and Jessica Spaulding and John Stalker and Nicole Stange-Thomann and Sharon Stavropoulos and Catherine Stone and Christopher Strader and Senait Tesfaye and Talene Thomson and Yama Thoulutsang and Dawa Thoulutsang and Kerri Topham and Ira Topping and Tsamla Tsamla and Helen Vassiliev and Andy Vo and Tsering Wangchuk and Tsering Wangdi and Michael Weiand and Jane Wilkinson and Adam Wilson and Shailendra Yadav and Geneva Young and Qing Yu and Lisa Zembek and Danni Zhong and Andrew Zimmer and Zac Zwirko and Jaffe, {David B.} and Pablo Alvarez and Will Brockman and Jonathan Butler and Chin, {Chee Whye} and Sante Gnerre and Iain MacCallum and Graves, {Jennifer A.Marshall} and Ponting, {Chris P.} and Matthew Breen and Samollow, {Paul B.} and Lander, {Eric S.} and Kerstin Lindblad-Toh",

note = "Funding Information: Acknowledgements Generation of the Monodelphis domestica sequence at the Broad Institute of MIT and Harvard was supported by grants from the National Human Genome Research Institute (NHGRI). For work from other members of the Opossum Genome Sequencing Consortium, we acknowledge the support of the National Institutes of Health (NHGRI, NIAID, NLM), the National Science Foundation, the Robert J. Kleberg Jr and Helen C. Kleberg Foundation, the State of Louisiana Board of Regents Support Fund, State of Colorado support funds, the Pittsburgh Foundation, TATRC/DoD, the UK Medical Research Council and the Australian Research Council. We thank colleagues at the UCSC genome browser for providing data (BLASTZ/MULTIZ alignments, synteny nets, and annotations). We thank L. Gaffney for assistance in preparing the manuscript and figures, and J. Danke for flow cytometry data.",

year = "2007",

month = may,

day = "10",

doi = "10.1038/nature05805",

language = "English (US)",

volume = "447",

pages = "167--177",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Publishing Group",

number = "7141",

}

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, CW, 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

TY - JOUR

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

AU - Mikkelsen, Tarjei S.

AU - Wakefield, Matthew J.

AU - Aken, Bronwen

AU - Amemiya, Chris T.

AU - Chang, Jean L.

AU - Duke, Shannon

AU - Garber, Manuel

AU - Gentles, Andrew J.

AU - Goodstadt, Leo

AU - Heger, Andreas

AU - Jurka, Jerzy

AU - Kamal, Michael

AU - Mauceli, Evan

AU - Searle, Stephen M.J.

AU - Sharpe, Ted

AU - Baker, Michelle L.

AU - Batzer, Mark A.

AU - Benos, Panayiotis V.

AU - Belov, Katherine

AU - Clamp, Michele

AU - Cook, April

AU - Cuff, James

AU - Das, Radhika

AU - Davidow, Lance

AU - Deakin, Janine E.

AU - Fazzari, Melissa J.

AU - Glass, Jacob L.

AU - Grabherr, Manfred

AU - Greally, John M.

AU - Gu, Wanjun

AU - Hore, Timothy A.

AU - Huttley, Gavin A.

AU - Kleber, Michael

AU - Jirtle, Randy L.

AU - Koina, Edda

AU - Lee, Jeannie T.

AU - Mahony, Shaun

AU - Marra, Marco A.

AU - Miller, Robert D.

AU - Nicholls, Robert D.

AU - Oda, Mayumi

AU - Papenfuss, Anthony T.

AU - Parra, Zuly E.

AU - Pollock, David D.

AU - Ray, David A.

AU - Schein, Jacqueline E.

AU - Speed, Terence P.

AU - Thompson, Katherine

AU - VandeBerg, John L.

AU - Wade, Claire M.

AU - Walker, Jerilyn A.

AU - Waters, Paul D.

AU - Webber, Caleb

AU - Weidman, Jennifer R.

AU - Xie, Xiaohui

AU - Zody, Michael C.

AU - Baldwin, Jennifer

AU - Abdouelleil, Amr

AU - Abdulkadir, Jamal

AU - Abebe, Adal

AU - Abera, Brikti

AU - Abreu, Justin

AU - Acer, St Christophe

AU - Aftuck, Lynne

AU - Alexander, Allen

AU - An, Peter

AU - Anderson, Erica

AU - Anderson, Scott

AU - Arachi, Harindra

AU - Azer, Marc

AU - Bachantsang, Pasang

AU - Barry, Andrew

AU - Bayul, Tashi

AU - Berlin, Aaron

AU - Bessette, Daniel

AU - Bloom, Toby

AU - Blye, Jason

AU - Boguslavskiy, Leonid

AU - Bonnet, Claude

AU - Boukhgalter, Boris

AU - Bourzgui, Imane

AU - Brown, Adam

AU - Cahill, Patrick

AU - Channer, Sheridon

AU - Cheshatsang, Yama

AU - Chuda, Lisa

AU - Citroen, Mieke

AU - Collymore, Alville

AU - Cooke, Patrick

AU - Costello, Maura

AU - D'Aco, Katie

AU - Daza, Riza

AU - De Haan, Georgius

AU - DeGray, Stuart

AU - DeMaso, Christina

AU - Dhargay, Norbu

AU - Dooley, Kimberly

AU - Dooley, Erin

AU - Doricent, Missole

AU - Dorje, Passang

AU - Dorjee, Kunsang

AU - Dupes, Alan

AU - Elong, Richard

AU - Falk, Jill

AU - Farina, Abderrahim

AU - Faro, Susan

AU - Ferguson, Diallo

AU - Fisher, Sheila

AU - Foley, Chelsea D.

AU - Franke, Alicia

AU - Friedrich, Dennis

AU - Gadbois, Loryn

AU - Gearin, Gary

AU - Gearin, Christina R.

AU - Giannoukos, Georgia

AU - Goode, Tina

AU - Graham, Joseph

AU - Grandbois, Edward

AU - Grewal, Sharleen

AU - Gyaltsen, Kunsang

AU - Hafez, Nabil

AU - Hagos, Birhane

AU - Hall, Jennifer

AU - Henson, Charlotte

AU - Hollinger, Andrew

AU - Honan, Tracey

AU - Huard, Monika D.

AU - Hughes, Leanne

AU - Hurhula, Brian

AU - Husby, M. Erii

AU - Kamat, Asha

AU - Kanga, Ben

AU - Kashin, Seva

AU - Khazanovich, Dmitry

AU - Kisner, Peter

AU - Lance, Krista

AU - Lara, Marcia

AU - Lee, William

AU - Lennon, Niall

AU - Letendre, Frances

AU - LeVine, Rosie

AU - Lipovsky, Alex

AU - Liu, Xiaohong

AU - Liu, Jinlei

AU - Liu, Shangtao

AU - Lokyitsang, Tashi

AU - Lokyitsang, Yeshi

AU - Lubonja, Rakela

AU - Lui, Annie

AU - MacDonald, Pen

AU - Magnisalis, Vasilia

AU - Maru, Kebede

AU - Matthews, Charles

AU - McCusker, William

AU - McDonough, Susan

AU - Mehta, Teena

AU - Meldrim, James

AU - Meneus, Louis

AU - Mihai, Oana

AU - Mihalev, Atanas

AU - Mihova, Tanya

AU - Mittelman, Rachel

AU - Mlenga, Valentine

AU - Montmayeur, Anna

AU - Mulrain, Leonidas

AU - Navidi, Adam

AU - Naylor, Jerome

AU - Negash, Tamrat

AU - Nguyen, Thu

AU - Nguyen, Nga

AU - Nicol, Robert

AU - Norbu, Choe

AU - Norbu, Nyima

AU - Novod, Nathaniel

AU - O'Neill, Barry

AU - Osman, Sahal

AU - Markiewicz, Eva

AU - Oyono, Otero L.

AU - Patti, Christopher

AU - Phunkhang, Pema

AU - Pierre, Fritz

AU - Priest, Margaret

AU - Raghuraman, Sujaa

AU - Rege, Filip

AU - Reyes, Rebecca

AU - Rise, Cecil

AU - Rogov, Peter

AU - Ross, Keenan

AU - Ryan, Elizabeth

AU - Settipalli, Sampath

AU - Shea, Terry

AU - Sherpa, Ngawang

AU - Shi, Lu

AU - Shih, Diana

AU - Sparrow, Todd

AU - Spaulding, Jessica

AU - Stalker, John

AU - Stange-Thomann, Nicole

AU - Stavropoulos, Sharon

AU - Stone, Catherine

AU - Strader, Christopher

AU - Tesfaye, Senait

AU - Thomson, Talene

AU - Thoulutsang, Yama

AU - Thoulutsang, Dawa

AU - Topham, Kerri

AU - Topping, Ira

AU - Tsamla, Tsamla

AU - Vassiliev, Helen

AU - Vo, Andy

AU - Wangchuk, Tsering

AU - Wangdi, Tsering

AU - Weiand, Michael

AU - Wilkinson, Jane

AU - Wilson, Adam

AU - Yadav, Shailendra

AU - Young, Geneva

AU - Yu, Qing

AU - Zembek, Lisa

AU - Zhong, Danni

AU - Zimmer, Andrew

AU - Zwirko, Zac

AU - Jaffe, David B.

AU - Alvarez, Pablo

AU - Brockman, Will

AU - Butler, Jonathan

AU - Chin, Chee Whye

AU - Gnerre, Sante

AU - MacCallum, Iain

AU - Graves, Jennifer A.Marshall

AU - Ponting, Chris P.

AU - Breen, Matthew

AU - Samollow, Paul B.

AU - Lander, Eric S.

AU - Lindblad-Toh, Kerstin

N1 - Funding Information: Acknowledgements Generation of the Monodelphis domestica sequence at the Broad Institute of MIT and Harvard was supported by grants from the National Human Genome Research Institute (NHGRI). For work from other members of the Opossum Genome Sequencing Consortium, we acknowledge the support of the National Institutes of Health (NHGRI, NIAID, NLM), the National Science Foundation, the Robert J. Kleberg Jr and Helen C. Kleberg Foundation, the State of Louisiana Board of Regents Support Fund, State of Colorado support funds, the Pittsburgh Foundation, TATRC/DoD, the UK Medical Research Council and the Australian Research Council. We thank colleagues at the UCSC genome browser for providing data (BLASTZ/MULTIZ alignments, synteny nets, and annotations). We thank L. Gaffney for assistance in preparing the manuscript and figures, and J. Danke for flow cytometry data.

PY - 2007/5/10

Y1 - 2007/5/10

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.

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.

UR - http://www.scopus.com/inward/record.url?scp=34248576291&partnerID=8YFLogxK

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U2 - 10.1038/nature05805

DO - 10.1038/nature05805

M3 - Article

C2 - 17495919

AN - SCOPUS:34248576291

SN - 0028-0836

VL - 447

SP - 167

EP - 177

JO - Nature

JF - Nature

IS - 7141

ER -

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

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