The B73 maize genome: Complexity, diversity, and dynamics

Patrick S. Schnable; Doreen Ware; Robert S. Fulton; Joshua C. Stein; Fusheng Wei; Shiran Pasternak; Chengzhi Liang; Jianwei Zhang; Lucinda Fulton; Tina A. Graves; Patrick Minx; Amy Denise Reily; Laura Courtney; Scott S. Kruchowski; Chad Tomlinson; Cindy Strong; Kim Delehaunty; Catrina Fronick; Bill Courtney; Susan M. Rock; Eddie Belter; Feiyu Du; Kyung Kim; Rachel M. Abbott; Marc Cotton; Andy Levy; Pamela Marchetto; Kerri Ochoa; Stephanie M. Jackson; Barbara Gillam; Weizu Chen; Le Yan; Jamey Higginbotham; Marco Cardenas; Jason Waligorski; Elizabeth Applebaum; Lindsey Phelps; Jason Falcone; Krishna Kanchi; Thynn Thane; Adam Scimone; Nay Thane; Jessica Henke; Tom Wang; Jessica Ruppert; Neha Shah; Kelsi Rotter; Jennifer Hodges; Elizabeth Ingenthron; Matt Cordes; Sara Kohlberg; Jennifer Sgro; Brandon Delgado; Kelly Mead; Asif Chinwalla; Shawn Leonard; Kevin Crouse; Kristi Collura; Dave Kudrna; Jennifer Currie; Ruifeng He; Angelina Angelova; Shanmugam Rajasekar; Teri Mueller; Rene Lomeli; Gabriel Scara; Ara Ko; Krista Delaney; Marina Wissotski; Georgina Lopez; David Campos; Michele Braidotti; Elizabeth Ashley; Wolfgang Golser; Hyeran Kim; Seunghee Lee; Jinke Lin; Zeljko Dujmic; Woojin Kim; Jayson Talag; Andrea Zuccolo; Chuanzhu Fan; Aswathy Sebastian; Melissa Kramer; Lori Spiegel; Lidia Nascimento; Theresa Zutavern; Beth Miller; Claude Ambroise; Stephanie Muller; Will Spooner; Apurva Narechania; Liya Ren; Sharon Wei; Sunita Kumari; Ben Faga; Michael J. Levy; Linda McMahan; Peter Van Buren; Matthew W. Vaughn; Kai Ying; Cheng Ting Yeh; Scott J. Emrich; Yi Jia; Ananth Kalyanaraman; An Ping Hsia; W. Brad Barbazuk; Regina S. Baucom; Thomas P. Brutnell; Nicholas C. Carpita; Cristian Chaparro; Jer Ming Chia; Jean Marc Deragon; James C. Estill; Yan Fu; Jeffrey A. Jeddeloh; Yujun Han; Hyeran Lee; Pinghua Li; Damon R. Lisch; Sanzhen Liu; Zhijie Liu; Dawn Holligan Nagel; Maureen C. McCann; Phillip Sanmiguel; Alan M. Myers; Dan Nettleton; John Nguyen; Bryan W. Penning; Lalit Ponnala; Kevin L. Schneider; David C. Schwartz; Anupma Sharma; Carol Soderlund; Nathan M. Springer; Qi Sun; Hao Wang; Michael Waterman; Richard Westerman; Thomas K. Wolfgruber; Lixing Yang; Yeisoo Yu; Lifang Zhang; Shiguo Zhou; Qihui Zhu; Jeffrey L. Bennetzen; R. Kelly Dawe; Jiming Jiang; Ning Jiang; Gernot G. Presting; Susan R. Wessler; Srinivas Aluru; Robert A. Martienssen; Sandra W. Clifton; W. Richard McCombie; Rod A. Wing; Richard K. Wilson

doi:10.1126/science.1178534

The B73 maize genome: Complexity, diversity, and dynamics

Patrick S. Schnable, Doreen Ware, Robert S. Fulton, Joshua C. Stein, Fusheng Wei, Shiran Pasternak, Chengzhi Liang, Jianwei Zhang, Lucinda Fulton, Tina A. Graves, Patrick Minx, Amy Denise Reily, Laura Courtney, Scott S. Kruchowski, Chad Tomlinson, Cindy Strong, Kim Delehaunty, Catrina Fronick, Bill Courtney, Susan M. RockEddie Belter, Feiyu Du, Kyung Kim, Rachel M. Abbott, Marc Cotton, Andy Levy, Pamela Marchetto, Kerri Ochoa, Stephanie M. Jackson, Barbara Gillam, Weizu Chen, Le Yan, Jamey Higginbotham, Marco Cardenas, Jason Waligorski, Elizabeth Applebaum, Lindsey Phelps, Jason Falcone, Krishna Kanchi, Thynn Thane, Adam Scimone, Nay Thane, Jessica Henke, Tom Wang, Jessica Ruppert, Neha Shah, Kelsi Rotter, Jennifer Hodges, Elizabeth Ingenthron, Matt Cordes, Sara Kohlberg, Jennifer Sgro, Brandon Delgado, Kelly Mead, Asif Chinwalla, Shawn Leonard, Kevin Crouse, Kristi Collura, Dave Kudrna, Jennifer Currie, Ruifeng He, Angelina Angelova, Shanmugam Rajasekar, Teri Mueller, Rene Lomeli, Gabriel Scara, Ara Ko, Krista Delaney, Marina Wissotski, Georgina Lopez, David Campos, Michele Braidotti, Elizabeth Ashley, Wolfgang Golser, Hyeran Kim, Seunghee Lee, Jinke Lin, Zeljko Dujmic, Woojin Kim, Jayson Talag, Andrea Zuccolo, Chuanzhu Fan, Aswathy Sebastian, Melissa Kramer, Lori Spiegel, Lidia Nascimento, Theresa Zutavern, Beth Miller, Claude Ambroise, Stephanie Muller, Will Spooner, Apurva Narechania, Liya Ren, Sharon Wei, Sunita Kumari, Ben Faga, Michael J. Levy, Linda McMahan, Peter Van Buren, Matthew W. Vaughn, Kai Ying, Cheng Ting Yeh, Scott J. Emrich, Yi Jia, Ananth Kalyanaraman, An Ping Hsia, W. Brad Barbazuk, Regina S. Baucom, Thomas P. Brutnell, Nicholas C. Carpita, Cristian Chaparro, Jer Ming Chia, Jean Marc Deragon, James C. Estill, Yan Fu, Jeffrey A. Jeddeloh, Yujun Han, Hyeran Lee, Pinghua Li, Damon R. Lisch, Sanzhen Liu, Zhijie Liu, Dawn Holligan Nagel, Maureen C. McCann, Phillip Sanmiguel, Alan M. Myers, Dan Nettleton, John Nguyen, Bryan W. Penning, Lalit Ponnala, Kevin L. Schneider, David C. Schwartz, Anupma Sharma, Carol Soderlund, Nathan M. Springer, Qi Sun, Hao Wang, Michael Waterman, Richard Westerman, Thomas K. Wolfgruber, Lixing Yang, Yeisoo Yu, Lifang Zhang, Shiguo Zhou, Qihui Zhu, Jeffrey L. Bennetzen, R. Kelly Dawe, Jiming Jiang, Ning Jiang, Gernot G. Presting, Susan R. Wessler, Srinivas Aluru, Robert A. Martienssen, Sandra W. Clifton, W. Richard McCombie, Rod A. Wing, Richard K. Wilson

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

3247 Scopus citations

Abstract

We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylationpoor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize.

Original language	English (US)
Journal	Science
Volume	326
Issue number	5956
DOIs	https://doi.org/10.1126/science.1178534
State	Published - Nov 20 2009

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10.1126/science.1178534

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Schnable, P. S., Ware, D., Fulton, R. S., Stein, J. C., Wei, F., Pasternak, S., Liang, C., Zhang, J., Fulton, L., Graves, T. A., Minx, P., Reily, A. D., Courtney, L., Kruchowski, S. S., Tomlinson, C., Strong, C., Delehaunty, K., Fronick, C., Courtney, B., ... Wilson, R. K. (2009). The B73 maize genome: Complexity, diversity, and dynamics. Science, 326(5956). https://doi.org/10.1126/science.1178534

@article{357b2fe9c365478e8774ff2bb2b8a1e7,

title = "The B73 maize genome: Complexity, diversity, and dynamics",

abstract = "We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylationpoor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize.",

author = "Schnable, {Patrick S.} and Doreen Ware and Fulton, {Robert S.} and Stein, {Joshua C.} and Fusheng Wei and Shiran Pasternak and Chengzhi Liang and Jianwei Zhang and Lucinda Fulton and Graves, {Tina A.} and Patrick Minx and Reily, {Amy Denise} and Laura Courtney and Kruchowski, {Scott S.} and Chad Tomlinson and Cindy Strong and Kim Delehaunty and Catrina Fronick and Bill Courtney and Rock, {Susan M.} and Eddie Belter and Feiyu Du and Kyung Kim and Abbott, {Rachel M.} and Marc Cotton and Andy Levy and Pamela Marchetto and Kerri Ochoa and Jackson, {Stephanie M.} and Barbara Gillam and Weizu Chen and Le Yan and Jamey Higginbotham and Marco Cardenas and Jason Waligorski and Elizabeth Applebaum and Lindsey Phelps and Jason Falcone and Krishna Kanchi and Thynn Thane and Adam Scimone and Nay Thane and Jessica Henke and Tom Wang and Jessica Ruppert and Neha Shah and Kelsi Rotter and Jennifer Hodges and Elizabeth Ingenthron and Matt Cordes and Sara Kohlberg and Jennifer Sgro and Brandon Delgado and Kelly Mead and Asif Chinwalla and Shawn Leonard and Kevin Crouse and Kristi Collura and Dave Kudrna and Jennifer Currie and Ruifeng He and Angelina Angelova and Shanmugam Rajasekar and Teri Mueller and Rene Lomeli and Gabriel Scara and Ara Ko and Krista Delaney and Marina Wissotski and Georgina Lopez and David Campos and Michele Braidotti and Elizabeth Ashley and Wolfgang Golser and Hyeran Kim and Seunghee Lee and Jinke Lin and Zeljko Dujmic and Woojin Kim and Jayson Talag and Andrea Zuccolo and Chuanzhu Fan and Aswathy Sebastian and Melissa Kramer and Lori Spiegel and Lidia Nascimento and Theresa Zutavern and Beth Miller and Claude Ambroise and Stephanie Muller and Will Spooner and Apurva Narechania and Liya Ren and Sharon Wei and Sunita Kumari and Ben Faga and Levy, {Michael J.} and Linda McMahan and {Van Buren}, Peter and Vaughn, {Matthew W.} and Kai Ying and Yeh, {Cheng Ting} and Emrich, {Scott J.} and Yi Jia and Ananth Kalyanaraman and Hsia, {An Ping} and Barbazuk, {W. Brad} and Baucom, {Regina S.} and Brutnell, {Thomas P.} and Carpita, {Nicholas C.} and Cristian Chaparro and Chia, {Jer Ming} and Deragon, {Jean Marc} and Estill, {James C.} and Yan Fu and Jeddeloh, {Jeffrey A.} and Yujun Han and Hyeran Lee and Pinghua Li and Lisch, {Damon R.} and Sanzhen Liu and Zhijie Liu and Nagel, {Dawn Holligan} and McCann, {Maureen C.} and Phillip Sanmiguel and Myers, {Alan M.} and Dan Nettleton and John Nguyen and Penning, {Bryan W.} and Lalit Ponnala and Schneider, {Kevin L.} and Schwartz, {David C.} and Anupma Sharma and Carol Soderlund and Springer, {Nathan M.} and Qi Sun and Hao Wang and Michael Waterman and Richard Westerman and Wolfgruber, {Thomas K.} and Lixing Yang and Yeisoo Yu and Lifang Zhang and Shiguo Zhou and Qihui Zhu and Bennetzen, {Jeffrey L.} and Dawe, {R. Kelly} and Jiming Jiang and Ning Jiang and Presting, {Gernot G.} and Wessler, {Susan R.} and Srinivas Aluru and Martienssen, {Robert A.} and Clifton, {Sandra W.} and McCombie, {W. Richard} and Wing, {Rod A.} and Wilson, {Richard K.}",

note = "Generated from Scopus record by KAUST IRTS on 2019-11-20",

year = "2009",

month = nov,

day = "20",

doi = "10.1126/science.1178534",

language = "English (US)",

volume = "326",

journal = "Science",

issn = "0036-8075",

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Schnable, PS, Ware, D, Fulton, RS, Stein, JC, Wei, F, Pasternak, S, Liang, C, Zhang, J, Fulton, L, Graves, TA, Minx, P, Reily, AD, Courtney, L, Kruchowski, SS, Tomlinson, C, Strong, C, Delehaunty, K, Fronick, C, Courtney, B, Rock, SM, Belter, E, Du, F, Kim, K, Abbott, RM, Cotton, M, Levy, A, Marchetto, P, Ochoa, K, Jackson, SM, Gillam, B, Chen, W, Yan, L, Higginbotham, J, Cardenas, M, Waligorski, J, Applebaum, E, Phelps, L, Falcone, J, Kanchi, K, Thane, T, Scimone, A, Thane, N, Henke, J, Wang, T, Ruppert, J, Shah, N, Rotter, K, Hodges, J, Ingenthron, E, Cordes, M, Kohlberg, S, Sgro, J, Delgado, B, Mead, K, Chinwalla, A, Leonard, S, Crouse, K, Collura, K, Kudrna, D, Currie, J, He, R, Angelova, A, Rajasekar, S, Mueller, T, Lomeli, R, Scara, G, Ko, A, Delaney, K, Wissotski, M, Lopez, G, Campos, D, Braidotti, M, Ashley, E, Golser, W, Kim, H, Lee, S, Lin, J, Dujmic, Z, Kim, W, Talag, J, Zuccolo, A, Fan, C, Sebastian, A, Kramer, M, Spiegel, L, Nascimento, L, Zutavern, T, Miller, B, Ambroise, C, Muller, S, Spooner, W, Narechania, A, Ren, L, Wei, S, Kumari, S, Faga, B, Levy, MJ, McMahan, L, Van Buren, P, Vaughn, MW, Ying, K, Yeh, CT, Emrich, SJ, Jia, Y, Kalyanaraman, A, Hsia, AP, Barbazuk, WB, Baucom, RS, Brutnell, TP, Carpita, NC, Chaparro, C, Chia, JM, Deragon, JM, Estill, JC, Fu, Y, Jeddeloh, JA, Han, Y, Lee, H, Li, P, Lisch, DR, Liu, S, Liu, Z, Nagel, DH, McCann, MC, Sanmiguel, P, Myers, AM, Nettleton, D, Nguyen, J, Penning, BW, Ponnala, L, Schneider, KL, Schwartz, DC, Sharma, A, Soderlund, C, Springer, NM, Sun, Q, Wang, H, Waterman, M, Westerman, R, Wolfgruber, TK, Yang, L, Yu, Y, Zhang, L, Zhou, S, Zhu, Q, Bennetzen, JL, Dawe, RK, Jiang, J, Jiang, N, Presting, GG, Wessler, SR, Aluru, S, Martienssen, RA, Clifton, SW, McCombie, WR, Wing, RA & Wilson, RK 2009, 'The B73 maize genome: Complexity, diversity, and dynamics', Science, vol. 326, no. 5956. https://doi.org/10.1126/science.1178534

TY - JOUR

T1 - The B73 maize genome: Complexity, diversity, and dynamics

AU - Schnable, Patrick S.

AU - Ware, Doreen

AU - Fulton, Robert S.

AU - Stein, Joshua C.

AU - Wei, Fusheng

AU - Pasternak, Shiran

AU - Liang, Chengzhi

AU - Zhang, Jianwei

AU - Fulton, Lucinda

AU - Graves, Tina A.

AU - Minx, Patrick

AU - Reily, Amy Denise

AU - Courtney, Laura

AU - Kruchowski, Scott S.

AU - Tomlinson, Chad

AU - Strong, Cindy

AU - Delehaunty, Kim

AU - Fronick, Catrina

AU - Courtney, Bill

AU - Rock, Susan M.

AU - Belter, Eddie

AU - Du, Feiyu

AU - Kim, Kyung

AU - Abbott, Rachel M.

AU - Cotton, Marc

AU - Levy, Andy

AU - Marchetto, Pamela

AU - Ochoa, Kerri

AU - Jackson, Stephanie M.

AU - Gillam, Barbara

AU - Chen, Weizu

AU - Yan, Le

AU - Higginbotham, Jamey

AU - Cardenas, Marco

AU - Waligorski, Jason

AU - Applebaum, Elizabeth

AU - Phelps, Lindsey

AU - Falcone, Jason

AU - Kanchi, Krishna

AU - Thane, Thynn

AU - Scimone, Adam

AU - Thane, Nay

AU - Henke, Jessica

AU - Wang, Tom

AU - Ruppert, Jessica

AU - Shah, Neha

AU - Rotter, Kelsi

AU - Hodges, Jennifer

AU - Ingenthron, Elizabeth

AU - Cordes, Matt

AU - Kohlberg, Sara

AU - Sgro, Jennifer

AU - Delgado, Brandon

AU - Mead, Kelly

AU - Chinwalla, Asif

AU - Leonard, Shawn

AU - Crouse, Kevin

AU - Collura, Kristi

AU - Kudrna, Dave

AU - Currie, Jennifer

AU - He, Ruifeng

AU - Angelova, Angelina

AU - Rajasekar, Shanmugam

AU - Mueller, Teri

AU - Lomeli, Rene

AU - Scara, Gabriel

AU - Ko, Ara

AU - Delaney, Krista

AU - Wissotski, Marina

AU - Lopez, Georgina

AU - Campos, David

AU - Braidotti, Michele

AU - Ashley, Elizabeth

AU - Golser, Wolfgang

AU - Kim, Hyeran

AU - Lee, Seunghee

AU - Lin, Jinke

AU - Dujmic, Zeljko

AU - Kim, Woojin

AU - Talag, Jayson

AU - Zuccolo, Andrea

AU - Fan, Chuanzhu

AU - Sebastian, Aswathy

AU - Kramer, Melissa

AU - Spiegel, Lori

AU - Nascimento, Lidia

AU - Zutavern, Theresa

AU - Miller, Beth

AU - Ambroise, Claude

AU - Muller, Stephanie

AU - Spooner, Will

AU - Narechania, Apurva

AU - Ren, Liya

AU - Wei, Sharon

AU - Kumari, Sunita

AU - Faga, Ben

AU - Levy, Michael J.

AU - McMahan, Linda

AU - Van Buren, Peter

AU - Vaughn, Matthew W.

AU - Ying, Kai

AU - Yeh, Cheng Ting

AU - Emrich, Scott J.

AU - Jia, Yi

AU - Kalyanaraman, Ananth

AU - Hsia, An Ping

AU - Barbazuk, W. Brad

AU - Baucom, Regina S.

AU - Brutnell, Thomas P.

AU - Carpita, Nicholas C.

AU - Chaparro, Cristian

AU - Chia, Jer Ming

AU - Deragon, Jean Marc

AU - Estill, James C.

AU - Fu, Yan

AU - Jeddeloh, Jeffrey A.

AU - Han, Yujun

AU - Lee, Hyeran

AU - Li, Pinghua

AU - Lisch, Damon R.

AU - Liu, Sanzhen

AU - Liu, Zhijie

AU - Nagel, Dawn Holligan

AU - McCann, Maureen C.

AU - Sanmiguel, Phillip

AU - Myers, Alan M.

AU - Nettleton, Dan

AU - Nguyen, John

AU - Penning, Bryan W.

AU - Ponnala, Lalit

AU - Schneider, Kevin L.

AU - Schwartz, David C.

AU - Sharma, Anupma

AU - Soderlund, Carol

AU - Springer, Nathan M.

AU - Sun, Qi

AU - Wang, Hao

AU - Waterman, Michael

AU - Westerman, Richard

AU - Wolfgruber, Thomas K.

AU - Yang, Lixing

AU - Yu, Yeisoo

AU - Zhang, Lifang

AU - Zhou, Shiguo

AU - Zhu, Qihui

AU - Bennetzen, Jeffrey L.

AU - Dawe, R. Kelly

AU - Jiang, Jiming

AU - Jiang, Ning

AU - Presting, Gernot G.

AU - Wessler, Susan R.

AU - Aluru, Srinivas

AU - Martienssen, Robert A.

AU - Clifton, Sandra W.

AU - McCombie, W. Richard

AU - Wing, Rod A.

AU - Wilson, Richard K.

N1 - Generated from Scopus record by KAUST IRTS on 2019-11-20

PY - 2009/11/20

Y1 - 2009/11/20

N2 - We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylationpoor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize.

AB - We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylationpoor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize.

UR - http://www.sciencemag.org/cgi/doi/10.1126/science.1178534

UR - http://www.scopus.com/inward/record.url?scp=70450202132&partnerID=8YFLogxK

U2 - 10.1126/science.1178534

DO - 10.1126/science.1178534

M3 - Article

SN - 0036-8075

VL - 326

JO - Science

JF - Science

IS - 5956

ER -

The B73 maize genome: Complexity, diversity, and dynamics

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