The B73 Maize Genome: Complexity, Diversity, and Dynamics

Date
2009-11-20
Authors
Schnable, Patrick
Ware, Doreen
Ying, Kai
Yeh, Cheng-Ting
Emrich, Scott
Jia, Yi
Kalyanaraman, Ananth
Nettleton, Dan
Hsia, An-Ping
Fu, Yan
Liu, Sanzhen
Myers, Alan
Nettleton, Dan
Aluru, Srinivas
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Statistics
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Agronomy
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StatisticsAgronomyElectrical and Computer EngineeringGenetics, Development and Cell BiologyStatisticsCenter for Plant Genomics
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 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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This article is published as Schnable, Patrick S., Doreen Ware, Robert S. Fulton, Joshua C. Stein, Fusheng Wei, Shiran Pasternak, Chengzhi Liang et al. "The B73 maize genome: complexity, diversity, and dynamics." science 326, no. 5956 (2009): 1112-1115. doi: 10.1126/science.1178534.

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