Detailed analysis of a contiguous 22-Mb region of the maize genome.
Most of our understanding of plant genome structure and evolution has come from the careful annotation of small (e.g., 100 kb) sequenced genomic regions or from automated annotation of complete genome sequences. Here, we sequenced and carefully annotated a contiguous 22 Mb region of maize chromosome 4 using an improved pseudomolecule for annotation. The sequence segment was comprehensively ordered, oriented, and confirmed using the maize optical map. Nearly 84% of the sequence is composed of transposable elements (TEs) that are mostly nested within each other, of which most families are low-copy. We identified 544 gene models using multiple levels of evidence, as well as five miRNA genes. Gene fragments, many captured by TEs, are prevalent within this region. Elimination of gene redundancy from a tetraploid maize ancestor that originated a few million years ago is responsible in this region for most disruptions of synteny with sorghum and rice. Consistent with other sub-genomic analyses in maize, small RNA mapping showed that many small RNAs match TEs and that most TEs match small RNAs. These results, performed on approximately 1% of the maize genome, demonstrate the feasibility of refining the B73 RefGen_v1 genome assembly by incorporating optical map, high-resolution genetic map, and comparative genomic data sets. Such improvements, along with those of gene and repeat annotation, will serve to promote future functional genomic and phylogenomic research in maize and other grasses.
Wei
Fusheng
F
Arizona Genomics Institute, School of Plant Sciences and Department of Ecology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America.
Stein
Joshua C
JC
Liang
Chengzhi
C
Zhang
Jianwei
J
Fulton
Robert S
RS
Baucom
Regina S
RS
De Paoli
Emanuele
E
Zhou
Shiguo
S
Yang
Lixing
L
Han
Yujun
Y
Pasternak
Shiran
S
Narechania
Apurva
A
Zhang
Lifang
L
Yeh
Cheng-Ting
CT
Ying
Kai
K
Nagel
Dawn H
DH
Collura
Kristi
K
Kudrna
David
D
Currie
Jennifer
J
Lin
Jinke
J
Kim
Hyeran
H
Angelova
Angelina
A
Scara
Gabriel
G
Wissotski
Marina
M
Golser
Wolfgang
W
Courtney
Laura
L
Kruchowski
Scott
S
Graves
Tina A
TA
Rock
Susan M
SM
Adams
Stephanie
S
Fulton
Lucinda A
LA
Fronick
Catrina
C
Courtney
William
W
Kramer
Melissa
M
Spiegel
Lori
L
Nascimento
Lydia
L
Kalyanaraman
Ananth
A
Chaparro
Cristian
C
Deragon
Jean-Marc
JM
Miguel
Phillip San
PS
Jiang
Ning
N
Wessler
Susan R
SR
Green
Pamela J
PJ
Yu
Yeisoo
Y
Schwartz
David C
DC
Meyers
Blake C
BC
Bennetzen
Jeffrey L
JL
Martienssen
Robert A
RA
McCombie
W Richard
WR
Aluru
Srinivas
S
Clifton
Sandra W
SW
Schnable
Patrick S
PS
Ware
Doreen
D
Wilson
Richard K
RK
Wing
Rod A
RA
D020029:Base Pairing / Q000235:genetics*; D001483:Base Sequence; D032461:Chromosomes, Plant / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication; D015321:Gene Rearrangement / Q000235:genetics; D017343:Genes, Plant; D056426:Genetic Loci / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics; D012275:Oryza / Q000235:genetics; D020161:Physical Chromosome Mapping; D018749:RNA, Plant / Q000235:genetics; D012689:Sequence Homology, Nucleic Acid; D045868:Sorghum / Q000235:genetics; D026801:Synteny / Q000235:genetics; D003313:Zea mays / Q000235:genetics*
D004251:DNA Transposable Elements; D018749:RNA, Plant