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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 L. Fulton,Tina Graves,Patrick Minx,Amy Denise Reily,Laura Courtney,Scott Kruchowski,Chad Tomlinson,Cindy Strong,Kim D. Delehaunty,Catrina C. Fronick,Bill Courtney,Susan M. Rock,Eddie Belter,Feiyu Du,Kyung Kim,Rachel M. Abbott,Marc Cotton,Andy Levy,Pamela Marchetto,Kerri Ochoa,Stephanie Jackson,Barbara Gillam,Weizu Chen,Le Yan,Jamey Higginbotham,Marco Cardenas,Jason Waligorski,Elizabeth Applebaum,Lindsey Phelps,Jason Falcone,Krishna L. 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 T. Chinwalla,Shawn Leonard,Kevin Crouse,Kristi Collura,Dave Kudrna,Jennifer Currie,Rong He,Angelina Angelova,Shanmugam Rajasekar,Teri Mueller,Rene Lomeli,Gabriel Scara,Ara Ko,Krista Delaney,Marina Wissotski,Georgina Espinosa López,David Campos,Michele Braidotti,Elizabeth Ashley,Wolfgang Golser,Hye‐Ran Kim,Seung‐Hee Lee,Juan Lin,Zeljko Dujmic,Woojin Kim,Jayson Talag,Andrea Zuccolo,Chuanzhu Fan,Aswathy Sebastian,Melissa Kramer,Lori Spiegel,Lidia Nascimento,Theresa Zutavern,Beth A. Miller,Claude Ambroise,Stéphanie Muller,Stefan Will,Apurva Narechania,Liya Ren,Sharon Wei,Sunita Kumari,Ben Faga,Michael J. Levy,Linda McMahan,Peter Van Buren,Matthew Vaughn,Kai Ying,Cheng‐Ting Yeh,Scott 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 Lisch,Sanzhen Liu,Zhijie Liu,Dawn H. Nagel,Maureen C. McCann,Phillip SanMiguel,Alan M. Myers,Dan Nettleton,John D. Nguyen,Bryan W. Penning,Lalit Ponnala,Kevin Schneider,David C. Schwartz,Anupma Sharma,Carol Soderlund,Nathan M. Springer,Qi Sun,Hao Wang,Michael S. Waterman,Richard P. Westerman,Thomas 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

Transposable element

Biology

Genome

2009

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 methylation-poor 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.

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“The B73 Maize Genome: Complexity, Diversity, and Dynamics” is a paper by Patrick S. Schnable Doreen Ware Robert S. Fulton Joshua C. Stein Fusheng Wei Shiran Pasternak Chengzhi Liang Jianwei Zhang Lucinda L. Fulton Tina Graves Patrick Minx Amy Denise Reily Laura Courtney Scott Kruchowski Chad Tomlinson Cindy Strong Kim D. Delehaunty Catrina C. Fronick Bill Courtney Susan M. Rock Eddie Belter Feiyu Du Kyung Kim Rachel M. Abbott Marc Cotton Andy Levy Pamela Marchetto Kerri Ochoa Stephanie Jackson Barbara Gillam Weizu Chen Le Yan Jamey Higginbotham Marco Cardenas Jason Waligorski Elizabeth Applebaum Lindsey Phelps Jason Falcone Krishna L. 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 T. Chinwalla Shawn Leonard Kevin Crouse Kristi Collura Dave Kudrna Jennifer Currie Rong He Angelina Angelova Shanmugam Rajasekar Teri Mueller Rene Lomeli Gabriel Scara Ara Ko Krista Delaney Marina Wissotski Georgina Espinosa López David Campos Michele Braidotti Elizabeth Ashley Wolfgang Golser Hye‐Ran Kim Seung‐Hee Lee Juan Lin Zeljko Dujmic Woojin Kim Jayson Talag Andrea Zuccolo Chuanzhu Fan Aswathy Sebastian Melissa Kramer Lori Spiegel Lidia Nascimento Theresa Zutavern Beth A. Miller Claude Ambroise Stéphanie Muller Stefan Will Apurva Narechania Liya Ren Sharon Wei Sunita Kumari Ben Faga Michael J. Levy Linda McMahan Peter Van Buren Matthew Vaughn Kai Ying Cheng‐Ting Yeh Scott 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 Lisch Sanzhen Liu Zhijie Liu Dawn H. Nagel Maureen C. McCann Phillip SanMiguel Alan M. Myers Dan Nettleton John D. Nguyen Bryan W. Penning Lalit Ponnala Kevin Schneider David C. Schwartz Anupma Sharma Carol Soderlund Nathan M. Springer Qi Sun Hao Wang Michael S. Waterman Richard P. Westerman Thomas 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 published in 2009. It has an Open Access status of “green”. You can read and download a PDF Full Text of this paper here.