Lineage-specific biology revealed by a finished genome assembly of the mouse

Deanna M. Church; Leo Goodstadt; Ladeana W. Hillier; Michael C. Zody; Steve Goldstein; Xinwe She; Carol J. Bult; Richa Agarwala; Joshua L. Cherry; Michael DiCuccio; Wratko Hlavina; Yuri Kapustin; Peter Meric; Donna Maglott; Zoë Birtle; Ana C. Marques; Tina Graves; Shiguo Zhou; Brian Teague; Konstantinos Potamousis; Christopher Churas; Michael Place; Jill Herschleb; Ron Runnheim; Daniel Forrest; James Amos-Landgraf; David C. Schwartz; Ze Cheng; Kerstin Lindblad-Toh; Evan E. Eichler; Chris P. Ponting; Donna M. Muzny; Shannon Dugan-Rocha; Yan Ding; Steven E. Scherer; Christian J. Buhay; Andrew Cree; Judith Hernandez; Michael Holder; Jennifer Hume; Laronda R. Jackson; Christie Kovar; Sandra L. Lee; Lora R. Lewis; Michael L. Metzker; Lynne V. Narareth; Aniko Sabo; Erica Sodergren; Richard A. Gibbs; Michael FitzGerald; April Cook; David B. Jaffe; Manuel Garber; Andrew R. Zimmer; Mono Pirun; Lyndsey Russell; Ted Sharpe; Michael Kamal Kabir Chaturvedi; Jane Wilkinson; Kurt LaButti; Xiaoping Yang; Daniel Bessette; Nicole R. Allen; Cindy Nguyen; Thu Nguyen; Chelsea Dunbar; Rakela Lubonja; Charles Matthews; Xiaohong Liu; Mostafa Benamara; Tamrat Negash; Tashi Lokyitsang; Karin Decktor; Bruno Piqani; Glen Munson; Pema Tenzin; Sabrina Stone; Pendexter Macdonald; Harindra Arachchi; Amr Abouelleil; Annie Lui; Margaret Priest; Gary Gearin; Adam Brown; Lynne Aftuck; Terrance Shea; Sean Sykes; Aaron Berlin; Jeff Chu; Kathleen Dooley; Daniel Hagopian; Jennifer Hall; Nabil Hafez; Cherylyn L. Smith; Peter Olandt; Karen Miller; Vijay Ventkataraman; Anthony Rachupka; Lester Dorris; Laura Ayotte; Richard Mabbitt; Jeffrey Erickson; Andrea Horn; Peter An; Jerome W. Naylor; Sampath Settipalli; Eric S. Lander; Richard K. Wilson; Tina A. Graves; Robert S. Fulton; Susan M. Rock; Asif T. Chinwalla; Kelly Bernard; Laura P. Courtney; Catrina Fronick; Lucinda L. Fulton; Michelle O'Laughlin; Colin L. Kremitzki; Patrick J. Minx; Joanne O. Nelson; Kyriena L. Schatzkamer; Cynthia Strong; Aye M. Wollam; George M. Weinstock; Shiaw Pyng Yang; Jane Rogers; Darren Grafham; Sean Humphray; Christine Nicholson; Christine Bird; Andrew J. Brown; John Burton; Chris Clee; Adrienne Hunt; Matt C. Jones; Christine Lloyd; Lucy Matthews; Karen Mclaren; Stuart Mclaren; Kirsten McLay; Sophie A. Palmer; Robert Plumb; Ratna Shownkeen; Sarah Sims; Mike A. Quail; Siobhan L. Whitehead; David L. Willey; Stephane Deschamps; Steven Kenton; Lin Song; Trang Do; Bruce Roe; Gerard G. Bouffard; Robert W. Blakesley; Eric D. Green; Raju Kucherlapati; George Grills; Li Li; Kate T. Montgomery; Melissa Kramer; Lori Speigel; W. Richard McCombie; Susan Lucas; Astrid Terry; Laurie Gordon; Lisa Stubbs; Paul Denny; Steve D.M. Brown; Anne Marie Mallon; R. Duncan Campbell; Marc R.M. Botherby; Ian J. Jackson; Marc J. Rubenfield; Andrea M. Rogosin; Douglas R. Smith

doi:10.1371/journal.pbio.1000112

Lineage-specific biology revealed by a finished genome assembly of the mouse

Deanna M. Church, Leo Goodstadt, Ladeana W. Hillier, Michael C. Zody, Steve Goldstein, Xinwe She, Carol J. Bult, Richa Agarwala, Joshua L. Cherry, Michael DiCuccio, Wratko Hlavina, Yuri Kapustin, Peter Meric, Donna Maglott, Zoë Birtle, Ana C. Marques, Tina Graves, Shiguo Zhou, Brian Teague, Konstantinos PotamousisChristopher Churas, Michael Place, Jill Herschleb, Ron Runnheim, Daniel Forrest, James Amos-Landgraf, David C. Schwartz, Ze Cheng, Kerstin Lindblad-Toh, Evan E. Eichler, Chris P. Ponting, Donna M. Muzny, Shannon Dugan-Rocha, Yan Ding, Steven E. Scherer, Christian J. Buhay, Andrew Cree, Judith Hernandez, Michael Holder, Jennifer Hume, Laronda R. Jackson, Christie Kovar, Sandra L. Lee, Lora R. Lewis, Michael L. Metzker, Lynne V. Narareth, Aniko Sabo, Erica Sodergren, Richard A. Gibbs, Michael FitzGerald, April Cook, David B. Jaffe, Manuel Garber, Andrew R. Zimmer, Mono Pirun, Lyndsey Russell, Ted Sharpe, Michael Kamal Kabir Chaturvedi, Jane Wilkinson, Kurt LaButti, Xiaoping Yang, Daniel Bessette, Nicole R. Allen, Cindy Nguyen, Thu Nguyen, Chelsea Dunbar, Rakela Lubonja, Charles Matthews, Xiaohong Liu, Mostafa Benamara, Tamrat Negash, Tashi Lokyitsang, Karin Decktor, Bruno Piqani, Glen Munson, Pema Tenzin, Sabrina Stone, Pendexter Macdonald, Harindra Arachchi, Amr Abouelleil, Annie Lui, Margaret Priest, Gary Gearin, Adam Brown, Lynne Aftuck, Terrance Shea, Sean Sykes, Aaron Berlin, Jeff Chu, Kathleen Dooley, Daniel Hagopian, Jennifer Hall, Nabil Hafez, Cherylyn L. Smith, Peter Olandt, Karen Miller, Vijay Ventkataraman, Anthony Rachupka, Lester Dorris, Laura Ayotte, Richard Mabbitt, Jeffrey Erickson, Andrea Horn, Peter An, Jerome W. Naylor, Sampath Settipalli, Eric S. Lander, Richard K. Wilson, Tina A. Graves, Robert S. Fulton, Susan M. Rock, Asif T. Chinwalla, Kelly Bernard, Laura P. Courtney, Catrina Fronick, Lucinda L. Fulton, Michelle O'Laughlin, Colin L. Kremitzki, Patrick J. Minx, Joanne O. Nelson, Kyriena L. Schatzkamer, Cynthia Strong, Aye M. Wollam, George M. Weinstock, Shiaw Pyng Yang, Jane Rogers, Darren Grafham, Sean Humphray, Christine Nicholson, Christine Bird, Andrew J. Brown, John Burton, Chris Clee, Adrienne Hunt, Matt C. Jones, Christine Lloyd, Lucy Matthews, Karen Mclaren, Stuart Mclaren, Kirsten McLay, Sophie A. Palmer, Robert Plumb, Ratna Shownkeen, Sarah Sims, Mike A. Quail, Siobhan L. Whitehead, David L. Willey, Stephane Deschamps, Steven Kenton, Lin Song, Trang Do, Bruce Roe, Gerard G. Bouffard, Robert W. Blakesley, Eric D. Green, Raju Kucherlapati, George Grills, Li Li, Kate T. Montgomery, Melissa Kramer, Lori Speigel, W. Richard McCombie, Susan Lucas, Astrid Terry, Laurie Gordon, Lisa Stubbs, Paul Denny, Steve D.M. Brown, Anne Marie Mallon, R. Duncan Campbell, Marc R.M. Botherby, Ian J. Jackson, Marc J. Rubenfield, Andrea M. Rogosin, Douglas R. Smith

McDonnell Genome Institute (MGI)

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

351 Scopus citations

Abstract

The mouse (Mus musculus) is the premier animal model for understanding human disease and development. Here we show that a comprehensive understanding of mouse biology is only possible with the availability of a finished, high-quality genome assembly. The finished clone-based assembly of the mouse strain C57BL/6J reported here has over 175,000 fewer gaps and over 139 Mb more of novel sequence, compared with the earlier MGSCv3 draft genome assembly. In a comprehensive analysis of this revised genome sequence, we are now able to define 20,210 protein-coding genes, over a thousand more than predicted in the human genome (19,042 genes). In addition, we identified 439 long, non-proteincoding RNAs with evidence for transcribed orthologs in human. We analyzed the complex and repetitive landscape of 267 Mb of sequence that was missing or misassembled in the previously published assembly, and we provide insights into the reasons for its resistance to sequencing and assembly by whole-genome shotgun approaches. Duplicated regions within newly assembled sequence tend to be of more recent ancestry than duplicates in the published draft, correcting our initial understanding of recent evolution on the mouse lineage. These duplicates appear to be largely composed of sequence regions containing transposable elements and duplicated protein-coding genes; of these, some may be fixed in the mouse population, but at least 40% of segmentally duplicated sequences are copy number variable even among laboratory mouse strains. Mouse lineage-specific regions contain 3,767 genes drawn mainly from rapidly-changing gene families associated with reproductive functions. The finished mouse genome assembly, therefore, greatly improves our understanding of rodent-specific biology and allows the delineation of ancestral biological functions that are shared with human from derived functions that are not.

Original language	English
Article number	e1000112
Journal	PLoS biology
Volume	7
Issue number	5
DOIs	https://doi.org/10.1371/journal.pbio.1000112
State	Published - May 2009

Access to Document

10.1371/journal.pbio.1000112

Cite this

Church, D. M., Goodstadt, L., Hillier, L. W., Zody, M. C., Goldstein, S., She, X., Bult, C. J., Agarwala, R., Cherry, J. L., DiCuccio, M., Hlavina, W., Kapustin, Y., Meric, P., Maglott, D., Birtle, Z., Marques, A. C., Graves, T., Zhou, S., Teague, B., ... Smith, D. R. (2009). Lineage-specific biology revealed by a finished genome assembly of the mouse. PLoS biology, 7(5), [e1000112]. https://doi.org/10.1371/journal.pbio.1000112

Church, Deanna M. ; Goodstadt, Leo ; Hillier, Ladeana W. ; Zody, Michael C. ; Goldstein, Steve ; She, Xinwe ; Bult, Carol J. ; Agarwala, Richa ; Cherry, Joshua L. ; DiCuccio, Michael ; Hlavina, Wratko ; Kapustin, Yuri ; Meric, Peter ; Maglott, Donna ; Birtle, Zoë ; Marques, Ana C. ; Graves, Tina ; Zhou, Shiguo ; Teague, Brian ; Potamousis, Konstantinos ; Churas, Christopher ; Place, Michael ; Herschleb, Jill ; Runnheim, Ron ; Forrest, Daniel ; Amos-Landgraf, James ; Schwartz, David C. ; Cheng, Ze ; Lindblad-Toh, Kerstin ; Eichler, Evan E. ; Ponting, Chris P. ; Muzny, Donna M. ; Dugan-Rocha, Shannon ; Ding, Yan ; Scherer, Steven E. ; Buhay, Christian J. ; Cree, Andrew ; Hernandez, Judith ; Holder, Michael ; Hume, Jennifer ; Jackson, Laronda R. ; Kovar, Christie ; Lee, Sandra L. ; Lewis, Lora R. ; Metzker, Michael L. ; Narareth, Lynne V. ; Sabo, Aniko ; Sodergren, Erica ; Gibbs, Richard A. ; FitzGerald, Michael ; Cook, April ; Jaffe, David B. ; Garber, Manuel ; Zimmer, Andrew R. ; Pirun, Mono ; Russell, Lyndsey ; Sharpe, Ted ; Chaturvedi, Michael Kamal Kabir ; Wilkinson, Jane ; LaButti, Kurt ; Yang, Xiaoping ; Bessette, Daniel ; Allen, Nicole R. ; Nguyen, Cindy ; Nguyen, Thu ; Dunbar, Chelsea ; Lubonja, Rakela ; Matthews, Charles ; Liu, Xiaohong ; Benamara, Mostafa ; Negash, Tamrat ; Lokyitsang, Tashi ; Decktor, Karin ; Piqani, Bruno ; Munson, Glen ; Tenzin, Pema ; Stone, Sabrina ; Macdonald, Pendexter ; Arachchi, Harindra ; Abouelleil, Amr ; Lui, Annie ; Priest, Margaret ; Gearin, Gary ; Brown, Adam ; Aftuck, Lynne ; Shea, Terrance ; Sykes, Sean ; Berlin, Aaron ; Chu, Jeff ; Dooley, Kathleen ; Hagopian, Daniel ; Hall, Jennifer ; Hafez, Nabil ; Smith, Cherylyn L. ; Olandt, Peter ; Miller, Karen ; Ventkataraman, Vijay ; Rachupka, Anthony ; Dorris, Lester ; Ayotte, Laura ; Mabbitt, Richard ; Erickson, Jeffrey ; Horn, Andrea ; An, Peter ; Naylor, Jerome W. ; Settipalli, Sampath ; Lander, Eric S. ; Wilson, Richard K. ; Graves, Tina A. ; Fulton, Robert S. ; Rock, Susan M. ; Chinwalla, Asif T. ; Bernard, Kelly ; Courtney, Laura P. ; Fronick, Catrina ; Fulton, Lucinda L. ; O'Laughlin, Michelle ; Kremitzki, Colin L. ; Minx, Patrick J. ; Nelson, Joanne O. ; Schatzkamer, Kyriena L. ; Strong, Cynthia ; Wollam, Aye M. ; Weinstock, George M. ; Yang, Shiaw Pyng ; Rogers, Jane ; Grafham, Darren ; Humphray, Sean ; Nicholson, Christine ; Bird, Christine ; Brown, Andrew J. ; Burton, John ; Clee, Chris ; Hunt, Adrienne ; Jones, Matt C. ; Lloyd, Christine ; Matthews, Lucy ; Mclaren, Karen ; Mclaren, Stuart ; McLay, Kirsten ; Palmer, Sophie A. ; Plumb, Robert ; Shownkeen, Ratna ; Sims, Sarah ; Quail, Mike A. ; Whitehead, Siobhan L. ; Willey, David L. ; Deschamps, Stephane ; Kenton, Steven ; Song, Lin ; Do, Trang ; Roe, Bruce ; Bouffard, Gerard G. ; Blakesley, Robert W. ; Green, Eric D. ; Kucherlapati, Raju ; Grills, George ; Li, Li ; Montgomery, Kate T. ; Kramer, Melissa ; Speigel, Lori ; McCombie, W. Richard ; Lucas, Susan ; Terry, Astrid ; Gordon, Laurie ; Stubbs, Lisa ; Denny, Paul ; Brown, Steve D.M. ; Mallon, Anne Marie ; Campbell, R. Duncan ; Botherby, Marc R.M. ; Jackson, Ian J. ; Rubenfield, Marc J. ; Rogosin, Andrea M. ; Smith, Douglas R. / Lineage-specific biology revealed by a finished genome assembly of the mouse. In: PLoS biology. 2009 ; Vol. 7, No. 5.

@article{05b07037b0a743ff87ed0db9d43e352a,

title = "Lineage-specific biology revealed by a finished genome assembly of the mouse",

abstract = "The mouse (Mus musculus) is the premier animal model for understanding human disease and development. Here we show that a comprehensive understanding of mouse biology is only possible with the availability of a finished, high-quality genome assembly. The finished clone-based assembly of the mouse strain C57BL/6J reported here has over 175,000 fewer gaps and over 139 Mb more of novel sequence, compared with the earlier MGSCv3 draft genome assembly. In a comprehensive analysis of this revised genome sequence, we are now able to define 20,210 protein-coding genes, over a thousand more than predicted in the human genome (19,042 genes). In addition, we identified 439 long, non-proteincoding RNAs with evidence for transcribed orthologs in human. We analyzed the complex and repetitive landscape of 267 Mb of sequence that was missing or misassembled in the previously published assembly, and we provide insights into the reasons for its resistance to sequencing and assembly by whole-genome shotgun approaches. Duplicated regions within newly assembled sequence tend to be of more recent ancestry than duplicates in the published draft, correcting our initial understanding of recent evolution on the mouse lineage. These duplicates appear to be largely composed of sequence regions containing transposable elements and duplicated protein-coding genes; of these, some may be fixed in the mouse population, but at least 40% of segmentally duplicated sequences are copy number variable even among laboratory mouse strains. Mouse lineage-specific regions contain 3,767 genes drawn mainly from rapidly-changing gene families associated with reproductive functions. The finished mouse genome assembly, therefore, greatly improves our understanding of rodent-specific biology and allows the delineation of ancestral biological functions that are shared with human from derived functions that are not.",

author = "Church, {Deanna M.} and Leo Goodstadt and Hillier, {Ladeana W.} and Zody, {Michael C.} and Steve Goldstein and Xinwe She and Bult, {Carol J.} and Richa Agarwala and Cherry, {Joshua L.} and Michael DiCuccio and Wratko Hlavina and Yuri Kapustin and Peter Meric and Donna Maglott and Zo{\"e} Birtle and Marques, {Ana C.} and Tina Graves and Shiguo Zhou and Brian Teague and Konstantinos Potamousis and Christopher Churas and Michael Place and Jill Herschleb and Ron Runnheim and Daniel Forrest and James Amos-Landgraf and Schwartz, {David C.} and Ze Cheng and Kerstin Lindblad-Toh and Eichler, {Evan E.} and Ponting, {Chris P.} and Muzny, {Donna M.} and Shannon Dugan-Rocha and Yan Ding and Scherer, {Steven E.} and Buhay, {Christian J.} and Andrew Cree and Judith Hernandez and Michael Holder and Jennifer Hume and Jackson, {Laronda R.} and Christie Kovar and Lee, {Sandra L.} and Lewis, {Lora R.} and Metzker, {Michael L.} and Narareth, {Lynne V.} and Aniko Sabo and Erica Sodergren and Gibbs, {Richard A.} and Michael FitzGerald and April Cook and Jaffe, {David B.} and Manuel Garber and Zimmer, {Andrew R.} and Mono Pirun and Lyndsey Russell and Ted Sharpe and Chaturvedi, {Michael Kamal Kabir} and Jane Wilkinson and Kurt LaButti and Xiaoping Yang and Daniel Bessette and Allen, {Nicole R.} and Cindy Nguyen and Thu Nguyen and Chelsea Dunbar and Rakela Lubonja and Charles Matthews and Xiaohong Liu and Mostafa Benamara and Tamrat Negash and Tashi Lokyitsang and Karin Decktor and Bruno Piqani and Glen Munson and Pema Tenzin and Sabrina Stone and Pendexter Macdonald and Harindra Arachchi and Amr Abouelleil and Annie Lui and Margaret Priest and Gary Gearin and Adam Brown and Lynne Aftuck and Terrance Shea and Sean Sykes and Aaron Berlin and Jeff Chu and Kathleen Dooley and Daniel Hagopian and Jennifer Hall and Nabil Hafez and Smith, {Cherylyn L.} and Peter Olandt and Karen Miller and Vijay Ventkataraman and Anthony Rachupka and Lester Dorris and Laura Ayotte and Richard Mabbitt and Jeffrey Erickson and Andrea Horn and Peter An and Naylor, {Jerome W.} and Sampath Settipalli and Lander, {Eric S.} and Wilson, {Richard K.} and Graves, {Tina A.} and Fulton, {Robert S.} and Rock, {Susan M.} and Chinwalla, {Asif T.} and Kelly Bernard and Courtney, {Laura P.} and Catrina Fronick and Fulton, {Lucinda L.} and Michelle O'Laughlin and Kremitzki, {Colin L.} and Minx, {Patrick J.} and Nelson, {Joanne O.} and Schatzkamer, {Kyriena L.} and Cynthia Strong and Wollam, {Aye M.} and Weinstock, {George M.} and Yang, {Shiaw Pyng} and Jane Rogers and Darren Grafham and Sean Humphray and Christine Nicholson and Christine Bird and Brown, {Andrew J.} and John Burton and Chris Clee and Adrienne Hunt and Jones, {Matt C.} and Christine Lloyd and Lucy Matthews and Karen Mclaren and Stuart Mclaren and Kirsten McLay and Palmer, {Sophie A.} and Robert Plumb and Ratna Shownkeen and Sarah Sims and Quail, {Mike A.} and Whitehead, {Siobhan L.} and Willey, {David L.} and Stephane Deschamps and Steven Kenton and Lin Song and Trang Do and Bruce Roe and Bouffard, {Gerard G.} and Blakesley, {Robert W.} and Green, {Eric D.} and Raju Kucherlapati and George Grills and Li Li and Montgomery, {Kate T.} and Melissa Kramer and Lori Speigel and McCombie, {W. Richard} and Susan Lucas and Astrid Terry and Laurie Gordon and Lisa Stubbs and Paul Denny and Brown, {Steve D.M.} and Mallon, {Anne Marie} and Campbell, {R. Duncan} and Botherby, {Marc R.M.} and Jackson, {Ian J.} and Rubenfield, {Marc J.} and Rogosin, {Andrea M.} and Smith, {Douglas R.}",

year = "2009",

month = may,

doi = "10.1371/journal.pbio.1000112",

language = "English",

volume = "7",

journal = "PLoS Biology",

issn = "1544-9173",

number = "5",

}

Church, DM, Goodstadt, L, Hillier, LW, Zody, MC, Goldstein, S, She, X, Bult, CJ, Agarwala, R, Cherry, JL, DiCuccio, M, Hlavina, W, Kapustin, Y, Meric, P, Maglott, D, Birtle, Z, Marques, AC, Graves, T, Zhou, S, Teague, B, Potamousis, K, Churas, C, Place, M, Herschleb, J, Runnheim, R, Forrest, D, Amos-Landgraf, J, Schwartz, DC, Cheng, Z, Lindblad-Toh, K, Eichler, EE, Ponting, CP, Muzny, DM, Dugan-Rocha, S, Ding, Y, Scherer, SE, Buhay, CJ, Cree, A, Hernandez, J, Holder, M, Hume, J, Jackson, LR, Kovar, C, Lee, SL, Lewis, LR, Metzker, ML, Narareth, LV, Sabo, A, Sodergren, E, Gibbs, RA, FitzGerald, M, Cook, A, Jaffe, DB, Garber, M, Zimmer, AR, Pirun, M, Russell, L, Sharpe, T, Chaturvedi, MKK, Wilkinson, J, LaButti, K, Yang, X, Bessette, D, Allen, NR, Nguyen, C, Nguyen, T, Dunbar, C, Lubonja, R, Matthews, C, Liu, X, Benamara, M, Negash, T, Lokyitsang, T, Decktor, K, Piqani, B, Munson, G, Tenzin, P, Stone, S, Macdonald, P, Arachchi, H, Abouelleil, A, Lui, A, Priest, M, Gearin, G, Brown, A, Aftuck, L, Shea, T, Sykes, S, Berlin, A, Chu, J, Dooley, K, Hagopian, D, Hall, J, Hafez, N, Smith, CL, Olandt, P, Miller, K, Ventkataraman, V, Rachupka, A, Dorris, L, Ayotte, L, Mabbitt, R, Erickson, J, Horn, A, An, P, Naylor, JW, Settipalli, S, Lander, ES, Wilson, RK, Graves, TA , Fulton, RS, Rock, SM, Chinwalla, AT, Bernard, K, Courtney, LP, Fronick, C, Fulton, LL, O'Laughlin, M, Kremitzki, CL, Minx, PJ, Nelson, JO, Schatzkamer, KL, Strong, C, Wollam, AM, Weinstock, GM, Yang, SP, Rogers, J, Grafham, D, Humphray, S, Nicholson, C, Bird, C, Brown, AJ, Burton, J, Clee, C, Hunt, A, Jones, MC, Lloyd, C, Matthews, L, Mclaren, K, Mclaren, S, McLay, K, Palmer, SA, Plumb, R, Shownkeen, R, Sims, S, Quail, MA, Whitehead, SL, Willey, DL, Deschamps, S, Kenton, S, Song, L, Do, T, Roe, B, Bouffard, GG, Blakesley, RW, Green, ED, Kucherlapati, R, Grills, G, Li, L, Montgomery, KT, Kramer, M, Speigel, L, McCombie, WR, Lucas, S, Terry, A, Gordon, L, Stubbs, L, Denny, P, Brown, SDM, Mallon, AM, Campbell, RD, Botherby, MRM, Jackson, IJ, Rubenfield, MJ, Rogosin, AM & Smith, DR 2009, 'Lineage-specific biology revealed by a finished genome assembly of the mouse', PLoS biology, vol. 7, no. 5, e1000112. https://doi.org/10.1371/journal.pbio.1000112

Lineage-specific biology revealed by a finished genome assembly of the mouse. / Church, Deanna M.; Goodstadt, Leo; Hillier, Ladeana W.; Zody, Michael C.; Goldstein, Steve; She, Xinwe; Bult, Carol J.; Agarwala, Richa; Cherry, Joshua L.; DiCuccio, Michael; Hlavina, Wratko; Kapustin, Yuri; Meric, Peter; Maglott, Donna; Birtle, Zoë; Marques, Ana C.; Graves, Tina; Zhou, Shiguo; Teague, Brian; Potamousis, Konstantinos; Churas, Christopher; Place, Michael; Herschleb, Jill; Runnheim, Ron; Forrest, Daniel; Amos-Landgraf, James; Schwartz, David C.; Cheng, Ze; Lindblad-Toh, Kerstin; Eichler, Evan E.; Ponting, Chris P.; Muzny, Donna M.; Dugan-Rocha, Shannon; Ding, Yan; Scherer, Steven E.; Buhay, Christian J.; Cree, Andrew; Hernandez, Judith; Holder, Michael; Hume, Jennifer; Jackson, Laronda R.; Kovar, Christie; Lee, Sandra L.; Lewis, Lora R.; Metzker, Michael L.; Narareth, Lynne V.; Sabo, Aniko; Sodergren, Erica; Gibbs, Richard A.; FitzGerald, Michael; Cook, April; Jaffe, David B.; Garber, Manuel; Zimmer, Andrew R.; Pirun, Mono; Russell, Lyndsey; Sharpe, Ted; Chaturvedi, Michael Kamal Kabir; Wilkinson, Jane; LaButti, Kurt; Yang, Xiaoping; Bessette, Daniel; Allen, Nicole R.; Nguyen, Cindy; Nguyen, Thu; Dunbar, Chelsea; Lubonja, Rakela; Matthews, Charles; Liu, Xiaohong; Benamara, Mostafa; Negash, Tamrat; Lokyitsang, Tashi; Decktor, Karin; Piqani, Bruno; Munson, Glen; Tenzin, Pema; Stone, Sabrina; Macdonald, Pendexter; Arachchi, Harindra; Abouelleil, Amr; Lui, Annie; Priest, Margaret; Gearin, Gary; Brown, Adam; Aftuck, Lynne; Shea, Terrance; Sykes, Sean; Berlin, Aaron; Chu, Jeff; Dooley, Kathleen; Hagopian, Daniel; Hall, Jennifer; Hafez, Nabil; Smith, Cherylyn L.; Olandt, Peter; Miller, Karen; Ventkataraman, Vijay; Rachupka, Anthony; Dorris, Lester; Ayotte, Laura; Mabbitt, Richard; Erickson, Jeffrey; Horn, Andrea; An, Peter; Naylor, Jerome W.; Settipalli, Sampath; Lander, Eric S.; Wilson, Richard K.; Graves, Tina A.; Fulton, Robert S.; Rock, Susan M.; Chinwalla, Asif T.; Bernard, Kelly; Courtney, Laura P.; Fronick, Catrina; Fulton, Lucinda L.; O'Laughlin, Michelle; Kremitzki, Colin L.; Minx, Patrick J.; Nelson, Joanne O.; Schatzkamer, Kyriena L.; Strong, Cynthia; Wollam, Aye M.; Weinstock, George M.; Yang, Shiaw Pyng; Rogers, Jane; Grafham, Darren; Humphray, Sean; Nicholson, Christine; Bird, Christine; Brown, Andrew J.; Burton, John; Clee, Chris; Hunt, Adrienne; Jones, Matt C.; Lloyd, Christine; Matthews, Lucy; Mclaren, Karen; Mclaren, Stuart; McLay, Kirsten; Palmer, Sophie A.; Plumb, Robert; Shownkeen, Ratna; Sims, Sarah; Quail, Mike A.; Whitehead, Siobhan L.; Willey, David L.; Deschamps, Stephane; Kenton, Steven; Song, Lin; Do, Trang; Roe, Bruce; Bouffard, Gerard G.; Blakesley, Robert W.; Green, Eric D.; Kucherlapati, Raju; Grills, George; Li, Li; Montgomery, Kate T.; Kramer, Melissa; Speigel, Lori; McCombie, W. Richard; Lucas, Susan; Terry, Astrid; Gordon, Laurie; Stubbs, Lisa; Denny, Paul; Brown, Steve D.M.; Mallon, Anne Marie; Campbell, R. Duncan; Botherby, Marc R.M.; Jackson, Ian J.; Rubenfield, Marc J.; Rogosin, Andrea M.; Smith, Douglas R.

In: PLoS biology, Vol. 7, No. 5, e1000112, 05.2009.

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

TY - JOUR

T1 - Lineage-specific biology revealed by a finished genome assembly of the mouse

AU - Church, Deanna M.

AU - Goodstadt, Leo

AU - Hillier, Ladeana W.

AU - Zody, Michael C.

AU - Goldstein, Steve

AU - She, Xinwe

AU - Bult, Carol J.

AU - Agarwala, Richa

AU - Cherry, Joshua L.

AU - DiCuccio, Michael

AU - Hlavina, Wratko

AU - Kapustin, Yuri

AU - Meric, Peter

AU - Maglott, Donna

AU - Birtle, Zoë

AU - Marques, Ana C.

AU - Graves, Tina

AU - Zhou, Shiguo

AU - Teague, Brian

AU - Potamousis, Konstantinos

AU - Churas, Christopher

AU - Place, Michael

AU - Herschleb, Jill

AU - Runnheim, Ron

AU - Forrest, Daniel

AU - Amos-Landgraf, James

AU - Schwartz, David C.

AU - Cheng, Ze

AU - Lindblad-Toh, Kerstin

AU - Eichler, Evan E.

AU - Ponting, Chris P.

AU - Muzny, Donna M.

AU - Dugan-Rocha, Shannon

AU - Ding, Yan

AU - Scherer, Steven E.

AU - Buhay, Christian J.

AU - Cree, Andrew

AU - Hernandez, Judith

AU - Holder, Michael

AU - Hume, Jennifer

AU - Jackson, Laronda R.

AU - Kovar, Christie

AU - Lee, Sandra L.

AU - Lewis, Lora R.

AU - Metzker, Michael L.

AU - Narareth, Lynne V.

AU - Sabo, Aniko

AU - Sodergren, Erica

AU - Gibbs, Richard A.

AU - FitzGerald, Michael

AU - Cook, April

AU - Jaffe, David B.

AU - Garber, Manuel

AU - Zimmer, Andrew R.

AU - Pirun, Mono

AU - Russell, Lyndsey

AU - Sharpe, Ted

AU - Chaturvedi, Michael Kamal Kabir

AU - Wilkinson, Jane

AU - LaButti, Kurt

AU - Yang, Xiaoping

AU - Bessette, Daniel

AU - Allen, Nicole R.

AU - Nguyen, Cindy

AU - Nguyen, Thu

AU - Dunbar, Chelsea

AU - Lubonja, Rakela

AU - Matthews, Charles

AU - Liu, Xiaohong

AU - Benamara, Mostafa

AU - Negash, Tamrat

AU - Lokyitsang, Tashi

AU - Decktor, Karin

AU - Piqani, Bruno

AU - Munson, Glen

AU - Tenzin, Pema

AU - Stone, Sabrina

AU - Macdonald, Pendexter

AU - Arachchi, Harindra

AU - Abouelleil, Amr

AU - Lui, Annie

AU - Priest, Margaret

AU - Gearin, Gary

AU - Brown, Adam

AU - Aftuck, Lynne

AU - Shea, Terrance

AU - Sykes, Sean

AU - Berlin, Aaron

AU - Chu, Jeff

AU - Dooley, Kathleen

AU - Hagopian, Daniel

AU - Hall, Jennifer

AU - Hafez, Nabil

AU - Smith, Cherylyn L.

AU - Olandt, Peter

AU - Miller, Karen

AU - Ventkataraman, Vijay

AU - Rachupka, Anthony

AU - Dorris, Lester

AU - Ayotte, Laura

AU - Mabbitt, Richard

AU - Erickson, Jeffrey

AU - Horn, Andrea

AU - An, Peter

AU - Naylor, Jerome W.

AU - Settipalli, Sampath

AU - Lander, Eric S.

AU - Wilson, Richard K.

AU - Graves, Tina A.

AU - Fulton, Robert S.

AU - Rock, Susan M.

AU - Chinwalla, Asif T.

AU - Bernard, Kelly

AU - Courtney, Laura P.

AU - Fronick, Catrina

AU - Fulton, Lucinda L.

AU - O'Laughlin, Michelle

AU - Kremitzki, Colin L.

AU - Minx, Patrick J.

AU - Nelson, Joanne O.

AU - Schatzkamer, Kyriena L.

AU - Strong, Cynthia

AU - Wollam, Aye M.

AU - Weinstock, George M.

AU - Yang, Shiaw Pyng

AU - Rogers, Jane

AU - Grafham, Darren

AU - Humphray, Sean

AU - Nicholson, Christine

AU - Bird, Christine

AU - Brown, Andrew J.

AU - Burton, John

AU - Clee, Chris

AU - Hunt, Adrienne

AU - Jones, Matt C.

AU - Lloyd, Christine

AU - Matthews, Lucy

AU - Mclaren, Karen

AU - Mclaren, Stuart

AU - McLay, Kirsten

AU - Palmer, Sophie A.

AU - Plumb, Robert

AU - Shownkeen, Ratna

AU - Sims, Sarah

AU - Quail, Mike A.

AU - Whitehead, Siobhan L.

AU - Willey, David L.

AU - Deschamps, Stephane

AU - Kenton, Steven

AU - Song, Lin

AU - Do, Trang

AU - Roe, Bruce

AU - Bouffard, Gerard G.

AU - Blakesley, Robert W.

AU - Green, Eric D.

AU - Kucherlapati, Raju

AU - Grills, George

AU - Li, Li

AU - Montgomery, Kate T.

AU - Kramer, Melissa

AU - Speigel, Lori

AU - McCombie, W. Richard

AU - Lucas, Susan

AU - Terry, Astrid

AU - Gordon, Laurie

AU - Stubbs, Lisa

AU - Denny, Paul

AU - Brown, Steve D.M.

AU - Mallon, Anne Marie

AU - Campbell, R. Duncan

AU - Botherby, Marc R.M.

AU - Jackson, Ian J.

AU - Rubenfield, Marc J.

AU - Rogosin, Andrea M.

AU - Smith, Douglas R.

PY - 2009/5

Y1 - 2009/5

N2 - The mouse (Mus musculus) is the premier animal model for understanding human disease and development. Here we show that a comprehensive understanding of mouse biology is only possible with the availability of a finished, high-quality genome assembly. The finished clone-based assembly of the mouse strain C57BL/6J reported here has over 175,000 fewer gaps and over 139 Mb more of novel sequence, compared with the earlier MGSCv3 draft genome assembly. In a comprehensive analysis of this revised genome sequence, we are now able to define 20,210 protein-coding genes, over a thousand more than predicted in the human genome (19,042 genes). In addition, we identified 439 long, non-proteincoding RNAs with evidence for transcribed orthologs in human. We analyzed the complex and repetitive landscape of 267 Mb of sequence that was missing or misassembled in the previously published assembly, and we provide insights into the reasons for its resistance to sequencing and assembly by whole-genome shotgun approaches. Duplicated regions within newly assembled sequence tend to be of more recent ancestry than duplicates in the published draft, correcting our initial understanding of recent evolution on the mouse lineage. These duplicates appear to be largely composed of sequence regions containing transposable elements and duplicated protein-coding genes; of these, some may be fixed in the mouse population, but at least 40% of segmentally duplicated sequences are copy number variable even among laboratory mouse strains. Mouse lineage-specific regions contain 3,767 genes drawn mainly from rapidly-changing gene families associated with reproductive functions. The finished mouse genome assembly, therefore, greatly improves our understanding of rodent-specific biology and allows the delineation of ancestral biological functions that are shared with human from derived functions that are not.

AB - The mouse (Mus musculus) is the premier animal model for understanding human disease and development. Here we show that a comprehensive understanding of mouse biology is only possible with the availability of a finished, high-quality genome assembly. The finished clone-based assembly of the mouse strain C57BL/6J reported here has over 175,000 fewer gaps and over 139 Mb more of novel sequence, compared with the earlier MGSCv3 draft genome assembly. In a comprehensive analysis of this revised genome sequence, we are now able to define 20,210 protein-coding genes, over a thousand more than predicted in the human genome (19,042 genes). In addition, we identified 439 long, non-proteincoding RNAs with evidence for transcribed orthologs in human. We analyzed the complex and repetitive landscape of 267 Mb of sequence that was missing or misassembled in the previously published assembly, and we provide insights into the reasons for its resistance to sequencing and assembly by whole-genome shotgun approaches. Duplicated regions within newly assembled sequence tend to be of more recent ancestry than duplicates in the published draft, correcting our initial understanding of recent evolution on the mouse lineage. These duplicates appear to be largely composed of sequence regions containing transposable elements and duplicated protein-coding genes; of these, some may be fixed in the mouse population, but at least 40% of segmentally duplicated sequences are copy number variable even among laboratory mouse strains. Mouse lineage-specific regions contain 3,767 genes drawn mainly from rapidly-changing gene families associated with reproductive functions. The finished mouse genome assembly, therefore, greatly improves our understanding of rodent-specific biology and allows the delineation of ancestral biological functions that are shared with human from derived functions that are not.

UR - http://www.scopus.com/inward/record.url?scp=66249148986&partnerID=8YFLogxK

U2 - 10.1371/journal.pbio.1000112

DO - 10.1371/journal.pbio.1000112

M3 - Article

C2 - 19468303

AN - SCOPUS:66249148986

VL - 7

JO - PLoS Biology

JF - PLoS Biology

SN - 1544-9173

IS - 5

M1 - e1000112

ER -

Lineage-specific biology revealed by a finished genome assembly of the mouse

Abstract

Access to Document

Other files and links

Fingerprint

Cite this