Genome sequencing and analysis of the model grass Brachypodium distachyon

John P. Vogel; David F. Garvin; Todd C. Mockler; Jeremy Schmutz; Dan Rokhsar; Michael W. Bevan; Kerrie Barry; Susan Lucas; Miranda Harmon-Smith; Kathleen Lail; Hope Tice; Jane Grimwood; Neil McKenzie; Naxin Huo; Yong Q. Gu; Gerard R. Lazo; Olin D. Anderson; Frank M. You; Ming Cheng Luo; Jan Dvorak; Jonathan Wright; Melanie Febrer; Dominika Idziak; Robert Hasterok; Erika Lindquist; Mei Wang; Samuel E. Fox; Henry D. Priest; Sergei A. Filichkin; Scott A. Givan; Douglas W. Bryant; Jeff H. Chang; Haiyan Wu; Wei Wu; An Ping Hsia; Patrick S. Schnable; Anantharaman Kalyanaraman; Brad Barbazuk; Todd P. Michael; Samuel P. Hazen; Jennifer N. Bragg; Debbie Laudencia-Chingcuanco; Yiqun Weng; Georg Haberer; Manuel Spannagl; Klaus Mayer; Thomas Rattei; Therese Mitros; Sang Jik Lee; Jocelyn K.C. Rose; Lukas A. Mueller; Thomas L. York; Thomas Wicker; Jan P. Buchmann; Jaakko Tanskanen; Alan H. Schulman; Heidrun Gundlach; Michael Beven; Antonio Costa De Oliveira; Luciano Da C. Maia; William Belknap; Ning Jiang; Jinsheng Lai; Liucun Zhu; Jianxin Ma; Cheng Sun; Ellen Pritham; Jerome Salse; Florent Murat; Michael Abrouk; Remy Bruggmann; Joachim Messing; Noah Fahlgren; Christopher M. Sullivan; James C. Carrington; Elisabeth J. Chapman; Greg D. May; Jixian Zhai; Matthias Ganssmann; Sai Guna Ranjan Gurazada; Marcelo German; Blake C. Meyers; Pamela J. Green; Ludmila Tyler; Jiajie Wu; James Thomson; Shan Chen; Henrik V. Scheller; Jesper Harholt; Peter Ulvskov; Jeffrey A. Kimbrel; Laura E. Bartley; Peijian Cao; Ki Hong Jung; Manoj K. Sharma; Miguel Vega-Sanchez; Pamela Ronald; Christopher D. Dardick; Stefanie De Bodt; Wim Verelst; Dirk Inzé; Maren Heese; Arp Schnittger; Xiaohan Yang; Udaya C. Kalluri; Gerald A. Tuskan; Zhihua Hua; Richard D. Vierstra; Yu Cui; Shuhong Ouyang; Qixin Sun; Zhiyong Liu; Alper Yilmaz; Erich Grotewold; Richard Sibout; Kian Hematy; Gregory Mouille; Herman Höfte; Todd Micheel; Jérome Pelloux; Devin O'Connor; James Schnable; Scott Rowe; Frank Harmon; Cynthia L. Cass; John C. Sedbrook; Mary E. Byrne; Sean Walsh; Janet Higgins; Pinghua Li; Thomas Brutnell; Turgay Unver; Hikmet Budak; Harry Belcram; Mathieu Charles; Boulos Chalhoub; Ivan Baxter

doi:10.1038/nature08747

Genome sequencing and analysis of the model grass Brachypodium distachyon

John P. Vogel, David F. Garvin, Todd C. Mockler, Jeremy Schmutz, Dan Rokhsar, Michael W. Bevan, Kerrie Barry, Susan Lucas, Miranda Harmon-Smith, Kathleen Lail, Hope Tice, Jane Grimwood, Neil McKenzie, Naxin Huo, Yong Q. Gu, Gerard R. Lazo, Olin D. Anderson, Frank M. You, Ming Cheng Luo, Jan DvorakJonathan Wright, Melanie Febrer, Dominika Idziak, Robert Hasterok, Erika Lindquist, Mei Wang, Samuel E. Fox, Henry D. Priest, Sergei A. Filichkin, Scott A. Givan, Douglas W. Bryant, Jeff H. Chang, Haiyan Wu, Wei Wu, An Ping Hsia, Patrick S. Schnable, Anantharaman Kalyanaraman, Brad Barbazuk, Todd P. Michael, Samuel P. Hazen, Jennifer N. Bragg, Debbie Laudencia-Chingcuanco, Yiqun Weng, Georg Haberer, Manuel Spannagl, Klaus Mayer, Thomas Rattei, Therese Mitros, Sang Jik Lee, Jocelyn K.C. Rose, Lukas A. Mueller, Thomas L. York, Thomas Wicker, Jan P. Buchmann, Jaakko Tanskanen, Alan H. Schulman, Heidrun Gundlach, Michael Beven, Antonio Costa De Oliveira, Luciano Da C. Maia, William Belknap, Ning Jiang, Jinsheng Lai, Liucun Zhu, Jianxin Ma, Cheng Sun, Ellen Pritham, Jerome Salse, Florent Murat, Michael Abrouk, Remy Bruggmann, Joachim Messing, Noah Fahlgren, Christopher M. Sullivan, James C. Carrington, Elisabeth J. Chapman, Greg D. May, Jixian Zhai, Matthias Ganssmann, Sai Guna Ranjan Gurazada, Marcelo German, Blake C. Meyers, Pamela J. Green, Ludmila Tyler, Jiajie Wu, James Thomson, Shan Chen, Henrik V. Scheller, Jesper Harholt, Peter Ulvskov, Jeffrey A. Kimbrel, Laura E. Bartley, Peijian Cao, Ki Hong Jung, Manoj K. Sharma, Miguel Vega-Sanchez, Pamela Ronald, Christopher D. Dardick, Stefanie De Bodt, Wim Verelst, Dirk Inzé, Maren Heese, Arp Schnittger, Xiaohan Yang, Udaya C. Kalluri, Gerald A. Tuskan, Zhihua Hua, Richard D. Vierstra, Yu Cui, Shuhong Ouyang, Qixin Sun, Zhiyong Liu, Alper Yilmaz, Erich Grotewold, Richard Sibout, Kian Hematy, Gregory Mouille, Herman Höfte, Todd Micheel, Jérome Pelloux, Devin O'Connor, James Schnable, Scott Rowe, Frank Harmon, Cynthia L. Cass, John C. Sedbrook, Mary E. Byrne, Sean Walsh, Janet Higgins, Pinghua Li, Thomas Brutnell, Turgay Unver, Hikmet Budak, Harry Belcram, Mathieu Charles, Boulos Chalhoub, Ivan Baxter

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

1480 Scopus citations

Abstract

Three subfamilies of grasses, the Ehrhartoideae, Panicoideae and Pooideae, provide the bulk of human nutrition and are poised to become major sources of renewable energy. Here we describe the genome sequence of the wild grass Brachypodium distachyon (Brachypodium), which is, to our knowledge, the first member of the Pooideae subfamily to be sequenced. Comparison of the Brachypodium, rice and sorghum genomes shows a precise history of genome evolution across a broad diversity of the grasses, and establishes a template for analysis of the large genomes of economically important pooid grasses such as wheat. The high-quality genome sequence, coupled with ease of cultivation and transformation, small size and rapid life cycle, will help Brachypodium reach its potential as an important model system for developing new energy and food crops.

Original language	English
Pages (from-to)	763-768
Number of pages	6
Journal	Nature
Volume	463
Issue number	7282
DOIs	https://doi.org/10.1038/nature08747
State	Published - Feb 11 2010

Funding

Acknowledgements We acknowledge the contributions of the late M. Gale, who identified the importance of conserved gene order in grass genomes. This work was mainly supported by the US Department of Energy Joint Genome Institute Community Sequencing Program project with J.P.V., D.F.G., T.C.M. and M.W.B., a BBSRC grant to M.W.B., an EU Contract Agronomics grant to M.W.B. and K.F.X.M., and GABI Barlex grant to K.F.X.M. Illumina transcriptome sequencing was supported by a DOE Plant Feedstock Genomics for Bioenergy grant and an Oregon State Agricultural Research Foundation grant to T.C.M.; small RNA research was supported by the DOE Plant Feedstock Genomics for Bioenergy grants to P.J.G. and T.C.M.; annotation was supported by a DOE Plant Feedstocks for Genomics Bioenergy grant to J.P.V. A full list of support and acknowledgements is in the Supplementary Information.

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1038/nature08747

Cite this

Vogel, J. P., Garvin, D. F., Mockler, T. C., Schmutz, J., Rokhsar, D., Bevan, M. W., Barry, K., Lucas, S., Harmon-Smith, M., Lail, K., Tice, H., Grimwood, J., McKenzie, N., Huo, N., Gu, Y. Q., Lazo, G. R., Anderson, O. D., You, F. M., Luo, M. C., ... Baxter, I. (2010). Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature, 463(7282), 763-768. https://doi.org/10.1038/nature08747

@article{bbda598b117846468ebf813f7ecf7129,

title = "Genome sequencing and analysis of the model grass Brachypodium distachyon",

abstract = "Three subfamilies of grasses, the Ehrhartoideae, Panicoideae and Pooideae, provide the bulk of human nutrition and are poised to become major sources of renewable energy. Here we describe the genome sequence of the wild grass Brachypodium distachyon (Brachypodium), which is, to our knowledge, the first member of the Pooideae subfamily to be sequenced. Comparison of the Brachypodium, rice and sorghum genomes shows a precise history of genome evolution across a broad diversity of the grasses, and establishes a template for analysis of the large genomes of economically important pooid grasses such as wheat. The high-quality genome sequence, coupled with ease of cultivation and transformation, small size and rapid life cycle, will help Brachypodium reach its potential as an important model system for developing new energy and food crops.",

author = "Vogel, {John P.} and Garvin, {David F.} and Mockler, {Todd C.} and Jeremy Schmutz and Dan Rokhsar and Bevan, {Michael W.} and Kerrie Barry and Susan Lucas and Miranda Harmon-Smith and Kathleen Lail and Hope Tice and Jane Grimwood and Neil McKenzie and Naxin Huo and Gu, {Yong Q.} and Lazo, {Gerard R.} and Anderson, {Olin D.} and You, {Frank M.} and Luo, {Ming Cheng} and Jan Dvorak and Jonathan Wright and Melanie Febrer and Dominika Idziak and Robert Hasterok and Erika Lindquist and Mei Wang and Fox, {Samuel E.} and Priest, {Henry D.} and Filichkin, {Sergei A.} and Givan, {Scott A.} and Bryant, {Douglas W.} and Chang, {Jeff H.} and Haiyan Wu and Wei Wu and Hsia, {An Ping} and Schnable, {Patrick S.} and Anantharaman Kalyanaraman and Brad Barbazuk and Michael, {Todd P.} and Hazen, {Samuel P.} and Bragg, {Jennifer N.} and Debbie Laudencia-Chingcuanco and Yiqun Weng and Georg Haberer and Manuel Spannagl and Klaus Mayer and Thomas Rattei and Therese Mitros and Lee, {Sang Jik} and Rose, {Jocelyn K.C.} and Mueller, {Lukas A.} and York, {Thomas L.} and Thomas Wicker and Buchmann, {Jan P.} and Jaakko Tanskanen and Schulman, {Alan H.} and Heidrun Gundlach and Michael Beven and {Costa De Oliveira}, Antonio and {Da C. Maia}, Luciano and William Belknap and Ning Jiang and Jinsheng Lai and Liucun Zhu and Jianxin Ma and Cheng Sun and Ellen Pritham and Jerome Salse and Florent Murat and Michael Abrouk and Remy Bruggmann and Joachim Messing and Noah Fahlgren and Sullivan, {Christopher M.} and Carrington, {James C.} and Chapman, {Elisabeth J.} and May, {Greg D.} and Jixian Zhai and Matthias Ganssmann and Gurazada, {Sai Guna Ranjan} and Marcelo German and Meyers, {Blake C.} and Green, {Pamela J.} and Ludmila Tyler and Jiajie Wu and James Thomson and Shan Chen and Scheller, {Henrik V.} and Jesper Harholt and Peter Ulvskov and Kimbrel, {Jeffrey A.} and Bartley, {Laura E.} and Peijian Cao and Jung, {Ki Hong} and Sharma, {Manoj K.} and Miguel Vega-Sanchez and Pamela Ronald and Dardick, {Christopher D.} and {De Bodt}, Stefanie and Wim Verelst and Dirk Inz{\'e} and Maren Heese and Arp Schnittger and Xiaohan Yang and Kalluri, {Udaya C.} and Tuskan, {Gerald A.} and Zhihua Hua and Vierstra, {Richard D.} and Yu Cui and Shuhong Ouyang and Qixin Sun and Zhiyong Liu and Alper Yilmaz and Erich Grotewold and Richard Sibout and Kian Hematy and Gregory Mouille and Herman H{\"o}fte and Todd Micheel and J{\'e}rome Pelloux and Devin O'Connor and James Schnable and Scott Rowe and Frank Harmon and Cass, {Cynthia L.} and Sedbrook, {John C.} and Byrne, {Mary E.} and Sean Walsh and Janet Higgins and Pinghua Li and Thomas Brutnell and Turgay Unver and Hikmet Budak and Harry Belcram and Mathieu Charles and Boulos Chalhoub and Ivan Baxter",

year = "2010",

month = feb,

day = "11",

doi = "10.1038/nature08747",

language = "English",

volume = "463",

pages = "763--768",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Research",

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Vogel, JP, Garvin, DF, Mockler, TC, Schmutz, J, Rokhsar, D, Bevan, MW, Barry, K, Lucas, S, Harmon-Smith, M, Lail, K, Tice, H, Grimwood, J, McKenzie, N, Huo, N, Gu, YQ, Lazo, GR, Anderson, OD, You, FM, Luo, MC, Dvorak, J, Wright, J, Febrer, M, Idziak, D, Hasterok, R, Lindquist, E, Wang, M, Fox, SE, Priest, HD, Filichkin, SA, Givan, SA, Bryant, DW, Chang, JH, Wu, H, Wu, W, Hsia, AP, Schnable, PS, Kalyanaraman, A, Barbazuk, B, Michael, TP, Hazen, SP, Bragg, JN, Laudencia-Chingcuanco, D, Weng, Y, Haberer, G, Spannagl, M, Mayer, K, Rattei, T, Mitros, T, Lee, SJ, Rose, JKC, Mueller, LA, York, TL, Wicker, T, Buchmann, JP, Tanskanen, J, Schulman, AH, Gundlach, H, Beven, M, Costa De Oliveira, A, Da C. Maia, L, Belknap, W, Jiang, N, Lai, J, Zhu, L, Ma, J, Sun, C, Pritham, E, Salse, J, Murat, F, Abrouk, M, Bruggmann, R, Messing, J, Fahlgren, N, Sullivan, CM, Carrington, JC, Chapman, EJ, May, GD, Zhai, J, Ganssmann, M, Gurazada, SGR, German, M, Meyers, BC, Green, PJ, Tyler, L, Wu, J, Thomson, J, Chen, S, Scheller, HV, Harholt, J, Ulvskov, P, Kimbrel, JA, Bartley, LE, Cao, P, Jung, KH, Sharma, MK, Vega-Sanchez, M, Ronald, P, Dardick, CD, De Bodt, S, Verelst, W, Inzé, D, Heese, M, Schnittger, A, Yang, X , Kalluri, UC , Tuskan, GA, Hua, Z, Vierstra, RD, Cui, Y, Ouyang, S, Sun, Q, Liu, Z, Yilmaz, A, Grotewold, E, Sibout, R, Hematy, K, Mouille, G, Höfte, H, Micheel, T, Pelloux, J, O'Connor, D, Schnable, J, Rowe, S, Harmon, F, Cass, CL, Sedbrook, JC, Byrne, ME, Walsh, S, Higgins, J, Li, P, Brutnell, T, Unver, T, Budak, H, Belcram, H, Charles, M, Chalhoub, B & Baxter, I 2010, 'Genome sequencing and analysis of the model grass Brachypodium distachyon', Nature, vol. 463, no. 7282, pp. 763-768. https://doi.org/10.1038/nature08747

TY - JOUR

T1 - Genome sequencing and analysis of the model grass Brachypodium distachyon

AU - Vogel, John P.

AU - Garvin, David F.

AU - Mockler, Todd C.

AU - Schmutz, Jeremy

AU - Rokhsar, Dan

AU - Bevan, Michael W.

AU - Barry, Kerrie

AU - Lucas, Susan

AU - Harmon-Smith, Miranda

AU - Lail, Kathleen

AU - Tice, Hope

AU - Grimwood, Jane

AU - McKenzie, Neil

AU - Huo, Naxin

AU - Gu, Yong Q.

AU - Lazo, Gerard R.

AU - Anderson, Olin D.

AU - You, Frank M.

AU - Luo, Ming Cheng

AU - Dvorak, Jan

AU - Wright, Jonathan

AU - Febrer, Melanie

AU - Idziak, Dominika

AU - Hasterok, Robert

AU - Lindquist, Erika

AU - Wang, Mei

AU - Fox, Samuel E.

AU - Priest, Henry D.

AU - Filichkin, Sergei A.

AU - Givan, Scott A.

AU - Bryant, Douglas W.

AU - Chang, Jeff H.

AU - Wu, Haiyan

AU - Wu, Wei

AU - Hsia, An Ping

AU - Schnable, Patrick S.

AU - Kalyanaraman, Anantharaman

AU - Barbazuk, Brad

AU - Michael, Todd P.

AU - Hazen, Samuel P.

AU - Bragg, Jennifer N.

AU - Laudencia-Chingcuanco, Debbie

AU - Weng, Yiqun

AU - Haberer, Georg

AU - Spannagl, Manuel

AU - Mayer, Klaus

AU - Rattei, Thomas

AU - Mitros, Therese

AU - Lee, Sang Jik

AU - Rose, Jocelyn K.C.

AU - Mueller, Lukas A.

AU - York, Thomas L.

AU - Wicker, Thomas

AU - Buchmann, Jan P.

AU - Tanskanen, Jaakko

AU - Schulman, Alan H.

AU - Gundlach, Heidrun

AU - Beven, Michael

AU - Costa De Oliveira, Antonio

AU - Da C. Maia, Luciano

AU - Belknap, William

AU - Jiang, Ning

AU - Lai, Jinsheng

AU - Zhu, Liucun

AU - Ma, Jianxin

AU - Sun, Cheng

AU - Pritham, Ellen

AU - Salse, Jerome

AU - Murat, Florent

AU - Abrouk, Michael

AU - Bruggmann, Remy

AU - Messing, Joachim

AU - Fahlgren, Noah

AU - Sullivan, Christopher M.

AU - Carrington, James C.

AU - Chapman, Elisabeth J.

AU - May, Greg D.

AU - Zhai, Jixian

AU - Ganssmann, Matthias

AU - Gurazada, Sai Guna Ranjan

AU - German, Marcelo

AU - Meyers, Blake C.

AU - Green, Pamela J.

AU - Tyler, Ludmila

AU - Wu, Jiajie

AU - Thomson, James

AU - Chen, Shan

AU - Scheller, Henrik V.

AU - Harholt, Jesper

AU - Ulvskov, Peter

AU - Kimbrel, Jeffrey A.

AU - Bartley, Laura E.

AU - Cao, Peijian

AU - Jung, Ki Hong

AU - Sharma, Manoj K.

AU - Vega-Sanchez, Miguel

AU - Ronald, Pamela

AU - Dardick, Christopher D.

AU - De Bodt, Stefanie

AU - Verelst, Wim

AU - Inzé, Dirk

AU - Heese, Maren

AU - Schnittger, Arp

AU - Yang, Xiaohan

AU - Kalluri, Udaya C.

AU - Tuskan, Gerald A.

AU - Hua, Zhihua

AU - Vierstra, Richard D.

AU - Cui, Yu

AU - Ouyang, Shuhong

AU - Sun, Qixin

AU - Liu, Zhiyong

AU - Yilmaz, Alper

AU - Grotewold, Erich

AU - Sibout, Richard

AU - Hematy, Kian

AU - Mouille, Gregory

AU - Höfte, Herman

AU - Micheel, Todd

AU - Pelloux, Jérome

AU - O'Connor, Devin

AU - Schnable, James

AU - Rowe, Scott

AU - Harmon, Frank

AU - Cass, Cynthia L.

AU - Sedbrook, John C.

AU - Byrne, Mary E.

AU - Walsh, Sean

AU - Higgins, Janet

AU - Li, Pinghua

AU - Brutnell, Thomas

AU - Unver, Turgay

AU - Budak, Hikmet

AU - Belcram, Harry

AU - Charles, Mathieu

AU - Chalhoub, Boulos

AU - Baxter, Ivan

PY - 2010/2/11

Y1 - 2010/2/11

N2 - Three subfamilies of grasses, the Ehrhartoideae, Panicoideae and Pooideae, provide the bulk of human nutrition and are poised to become major sources of renewable energy. Here we describe the genome sequence of the wild grass Brachypodium distachyon (Brachypodium), which is, to our knowledge, the first member of the Pooideae subfamily to be sequenced. Comparison of the Brachypodium, rice and sorghum genomes shows a precise history of genome evolution across a broad diversity of the grasses, and establishes a template for analysis of the large genomes of economically important pooid grasses such as wheat. The high-quality genome sequence, coupled with ease of cultivation and transformation, small size and rapid life cycle, will help Brachypodium reach its potential as an important model system for developing new energy and food crops.

AB - Three subfamilies of grasses, the Ehrhartoideae, Panicoideae and Pooideae, provide the bulk of human nutrition and are poised to become major sources of renewable energy. Here we describe the genome sequence of the wild grass Brachypodium distachyon (Brachypodium), which is, to our knowledge, the first member of the Pooideae subfamily to be sequenced. Comparison of the Brachypodium, rice and sorghum genomes shows a precise history of genome evolution across a broad diversity of the grasses, and establishes a template for analysis of the large genomes of economically important pooid grasses such as wheat. The high-quality genome sequence, coupled with ease of cultivation and transformation, small size and rapid life cycle, will help Brachypodium reach its potential as an important model system for developing new energy and food crops.

UR - http://www.scopus.com/inward/record.url?scp=76749150030&partnerID=8YFLogxK

U2 - 10.1038/nature08747

DO - 10.1038/nature08747

M3 - Article

AN - SCOPUS:76749150030

SN - 0028-0836

VL - 463

SP - 763

EP - 768

JO - Nature

JF - Nature

IS - 7282

ER -

Genome sequencing and analysis of the model grass Brachypodium distachyon

Abstract

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UN SDGs

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