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PMID: 19965430 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S.

The B73 maize genome: complexity, diversity, and dynamics.

Science (New York, N.Y.) ·Vol. 326 ·No. 5956 ·2009-11-20 ·Pages 1112-5

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

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.

MeSH Terms
Base Sequence Centromere/genetics Chromosome Mapping Chromosomes, Plant/genetics Crops, Agricultural/genetics DNA Copy Number Variations DNA Methylation DNA Transposable Elements DNA, Plant/genetics Genes, Plant Genetic Variation Genome, Plant Inbreeding MicroRNAs/genetics Molecular Sequence Data Ploidies RNA, Plant/genetics Recombination, Genetic Retroelements Sequence Analysis, DNA Zea mays/genetics
Chemicals
DNA Transposable Elements DNA, Plant MicroRNAs RNA, Plant Retroelements
Authors & Affiliations
157 authors, click to expand affiliations / ORCID
Schnable Patrick S
Center for Plant Genomics, Iowa State University, Ames, IA 50011, USA.
Ware Doreen
Fulton Robert S
Stein Joshua C
Wei Fusheng
Pasternak Shiran
Liang Chengzhi
Zhang Jianwei
Fulton Lucinda
Graves Tina A
Minx Patrick
Reily Amy Denise
Courtney Laura
Kruchowski Scott S
Tomlinson Chad
Strong Cindy
Delehaunty Kim
Fronick Catrina
Courtney Bill
Rock Susan M
Belter Eddie
Du Feiyu
Kim Kyung
Abbott Rachel M
Cotton Marc
Levy Andy
Marchetto Pamela
Ochoa Kerri
Jackson Stephanie M
Gillam Barbara
Chen Weizu
Yan Le
Higginbotham Jamey
Cardenas Marco
Waligorski Jason
Applebaum Elizabeth
Phelps Lindsey
Falcone Jason
Kanchi Krishna
Thane Thynn
Scimone Adam
Thane Nay
Henke Jessica
Wang Tom
Ruppert Jessica
Shah Neha
Rotter Kelsi
Hodges Jennifer
Ingenthron Elizabeth
Cordes Matt
Kohlberg Sara
Sgro Jennifer
Delgado Brandon
Mead Kelly
Chinwalla Asif
Leonard Shawn
Crouse Kevin
Collura Kristi
Kudrna Dave
Currie Jennifer
He Ruifeng
Angelova Angelina
Rajasekar Shanmugam
Mueller Teri
Lomeli Rene
Scara Gabriel
Ko Ara
Delaney Krista
Wissotski Marina
Lopez Georgina
Campos David
Braidotti Michele
Ashley Elizabeth
Golser Wolfgang
Kim HyeRan
Lee Seunghee
Lin Jinke
Dujmic Zeljko
Kim Woojin
Talag Jayson
Zuccolo Andrea
Fan Chuanzhu
Sebastian Aswathy
Kramer Melissa
Spiegel Lori
Nascimento Lidia
Zutavern Theresa
Miller Beth
Ambroise Claude
Muller Stephanie
Spooner Will
Narechania Apurva
Ren Liya
Wei Sharon
Kumari Sunita
Faga Ben
Levy Michael J
McMahan Linda
Van Buren Peter
Vaughn Matthew W
Ying Kai
Yeh Cheng-Ting
Emrich Scott J
Jia Yi
Kalyanaraman Ananth
Hsia An-Ping
Barbazuk W Brad
Baucom Regina S
Brutnell Thomas P
Carpita Nicholas C
Chaparro Cristian
Chia Jer-Ming
Deragon Jean-Marc
Estill James C
Fu Yan
Jeddeloh Jeffrey A
Han Yujun
Lee Hyeran
Li Pinghua
Lisch Damon R
Liu Sanzhen
Liu Zhijie
Nagel Dawn Holligan
McCann Maureen C
SanMiguel Phillip
Myers Alan M
Nettleton Dan
Nguyen John
Penning Bryan W
Ponnala Lalit
Schneider Kevin L
Schwartz David C
Sharma Anupma
Soderlund Carol
Springer Nathan M
Sun Qi
Wang Hao
Waterman Michael
Westerman Richard
Wolfgruber Thomas K
Yang Lixing
Yu Yeisoo
Zhang Lifang
Zhou Shiguo
Zhu Qihui
Bennetzen Jeffrey L
Dawe R Kelly
Jiang Jiming
Jiang Ning
Presting Gernot G
Wessler Susan R
Aluru Srinivas
Martienssen Robert A
Clifton Sandra W
McCombie W Richard
Wing Rod A
Wilson Richard K
Article Info
Journal
Science (New York, N.Y.)
Abbr.
Science
ISSN
1095-9203
Published
2009-11-20
Pages
1112-5
Language
English
Region
United States
NLM ID
0404511
Subset
IM
Databases
GENBANK
CM000777, CM000778, CM000779, CM000780, CM000781, CM000782, CM000783, CM000784, CM000785, CM000786
Corrections
ErratumIn
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