The B73 maize genome: complexity, diversity, and dynamics.
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.
Schnable
Patrick S
PS
Center for Plant Genomics, Iowa State University, Ames, IA 50011, USA.
Ware
Doreen
D
Fulton
Robert S
RS
Stein
Joshua C
JC
Wei
Fusheng
F
Pasternak
Shiran
S
Liang
Chengzhi
C
Zhang
Jianwei
J
Fulton
Lucinda
L
Graves
Tina A
TA
Minx
Patrick
P
Reily
Amy Denise
AD
Courtney
Laura
L
Kruchowski
Scott S
SS
Tomlinson
Chad
C
Strong
Cindy
C
Delehaunty
Kim
K
Fronick
Catrina
C
Courtney
Bill
B
Rock
Susan M
SM
Belter
Eddie
E
Du
Feiyu
F
Kim
Kyung
K
Abbott
Rachel M
RM
Cotton
Marc
M
Levy
Andy
A
Marchetto
Pamela
P
Ochoa
Kerri
K
Jackson
Stephanie M
SM
Gillam
Barbara
B
Chen
Weizu
W
Yan
Le
L
Higginbotham
Jamey
J
Cardenas
Marco
M
Waligorski
Jason
J
Applebaum
Elizabeth
E
Phelps
Lindsey
L
Falcone
Jason
J
Kanchi
Krishna
K
Thane
Thynn
T
Scimone
Adam
A
Thane
Nay
N
Henke
Jessica
J
Wang
Tom
T
Ruppert
Jessica
J
Shah
Neha
N
Rotter
Kelsi
K
Hodges
Jennifer
J
Ingenthron
Elizabeth
E
Cordes
Matt
M
Kohlberg
Sara
S
Sgro
Jennifer
J
Delgado
Brandon
B
Mead
Kelly
K
Chinwalla
Asif
A
Leonard
Shawn
S
Crouse
Kevin
K
Collura
Kristi
K
Kudrna
Dave
D
Currie
Jennifer
J
He
Ruifeng
R
Angelova
Angelina
A
Rajasekar
Shanmugam
S
Mueller
Teri
T
Lomeli
Rene
R
Scara
Gabriel
G
Ko
Ara
A
Delaney
Krista
K
Wissotski
Marina
M
Lopez
Georgina
G
Campos
David
D
Braidotti
Michele
M
Ashley
Elizabeth
E
Golser
Wolfgang
W
Kim
HyeRan
H
Lee
Seunghee
S
Lin
Jinke
J
Dujmic
Zeljko
Z
Kim
Woojin
W
Talag
Jayson
J
Zuccolo
Andrea
A
Fan
Chuanzhu
C
Sebastian
Aswathy
A
Kramer
Melissa
M
Spiegel
Lori
L
Nascimento
Lidia
L
Zutavern
Theresa
T
Miller
Beth
B
Ambroise
Claude
C
Muller
Stephanie
S
Spooner
Will
W
Narechania
Apurva
A
Ren
Liya
L
Wei
Sharon
S
Kumari
Sunita
S
Faga
Ben
B
Levy
Michael J
MJ
McMahan
Linda
L
Van Buren
Peter
P
Vaughn
Matthew W
MW
Ying
Kai
K
Yeh
Cheng-Ting
CT
Emrich
Scott J
SJ
Jia
Yi
Y
Kalyanaraman
Ananth
A
Hsia
An-Ping
AP
Barbazuk
W Brad
WB
Baucom
Regina S
RS
Brutnell
Thomas P
TP
Carpita
Nicholas C
NC
Chaparro
Cristian
C
Chia
Jer-Ming
JM
Deragon
Jean-Marc
JM
Estill
James C
JC
Fu
Yan
Y
Jeddeloh
Jeffrey A
JA
Han
Yujun
Y
Lee
Hyeran
H
Li
Pinghua
P
Lisch
Damon R
DR
Liu
Sanzhen
S
Liu
Zhijie
Z
Nagel
Dawn Holligan
DH
McCann
Maureen C
MC
SanMiguel
Phillip
P
Myers
Alan M
AM
Nettleton
Dan
D
Nguyen
John
J
Penning
Bryan W
BW
Ponnala
Lalit
L
Schneider
Kevin L
KL
Schwartz
David C
DC
Sharma
Anupma
A
Soderlund
Carol
C
Springer
Nathan M
NM
Sun
Qi
Q
Wang
Hao
H
Waterman
Michael
M
Westerman
Richard
R
Wolfgruber
Thomas K
TK
Yang
Lixing
L
Yu
Yeisoo
Y
Zhang
Lifang
L
Zhou
Shiguo
S
Zhu
Qihui
Q
Bennetzen
Jeffrey L
JL
Dawe
R Kelly
RK
Jiang
Jiming
J
Jiang
Ning
N
Presting
Gernot G
GG
Wessler
Susan R
SR
Aluru
Srinivas
S
Martienssen
Robert A
RA
Clifton
Sandra W
SW
McCombie
W Richard
WR
Wing
Rod A
RA
Wilson
Richard K
RK
D001483:Base Sequence; D002503:Centromere / Q000235:genetics; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D018556:Crops, Agricultural / Q000235:genetics; D056915:DNA Copy Number Variations; D019175:DNA Methylation; D004251:DNA Transposable Elements; D018744:DNA, Plant / Q000235:genetics; D017343:Genes, Plant; D014644:Genetic Variation; D018745:Genome, Plant; D007178:Inbreeding; D035683:MicroRNAs / Q000235:genetics; D008969:Molecular Sequence Data; D011003:Ploidies; D018749:RNA, Plant / Q000235:genetics; D011995:Recombination, Genetic; D018626:Retroelements; D017422:Sequence Analysis, DNA; D003313:Zea mays / Q000235:genetics*
D004251:DNA Transposable Elements; D018744:DNA, Plant; D035683:MicroRNAs; D018749:RNA, Plant; D018626:Retroelements