title: Detailed analysis of a contiguous 22-Mb region of the maize genome.
abstract: 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.
authors: 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.
authors: Fusheng
authors: F
authors: Wei
authors: Joshua C
authors: JC
authors: Stein
authors: Chengzhi
authors: C
authors: Liang
authors: Jianwei
authors: J
authors: Zhang
authors: Robert S
authors: RS
authors: Fulton
authors: Regina S
authors: RS
authors: Baucom
authors: Emanuele
authors: E
authors: De Paoli
authors: Shiguo
authors: S
authors: Zhou
authors: Lixing
authors: L
authors: Yang
authors: Yujun
authors: Y
authors: Han
authors: Shiran
authors: S
authors: Pasternak
authors: Apurva
authors: A
authors: Narechania
authors: Lifang
authors: L
authors: Zhang
authors: Cheng-Ting
authors: CT
authors: Yeh
authors: Kai
authors: K
authors: Ying
authors: Dawn H
authors: DH
authors: Nagel
authors: Kristi
authors: K
authors: Collura
authors: David
authors: D
authors: Kudrna
authors: Jennifer
authors: J
authors: Currie
authors: Jinke
authors: J
authors: Lin
authors: Hyeran
authors: H
authors: Kim
authors: Angelina
authors: A
authors: Angelova
authors: Gabriel
authors: G
authors: Scara
authors: Marina
authors: M
authors: Wissotski
authors: Wolfgang
authors: W
authors: Golser
authors: Laura
authors: L
authors: Courtney
authors: Scott
authors: S
authors: Kruchowski
authors: Tina A
authors: TA
authors: Graves
authors: Susan M
authors: SM
authors: Rock
authors: Stephanie
authors: S
authors: Adams
authors: Lucinda A
authors: LA
authors: Fulton
authors: Catrina
authors: C
authors: Fronick
authors: William
authors: W
authors: Courtney
authors: Melissa
authors: M
authors: Kramer
authors: Lori
authors: L
authors: Spiegel
authors: Lydia
authors: L
authors: Nascimento
authors: Ananth
authors: A
authors: Kalyanaraman
authors: Cristian
authors: C
authors: Chaparro
authors: Jean-Marc
authors: JM
authors: Deragon
authors: Phillip San
authors: PS
authors: Miguel
authors: Ning
authors: N
authors: Jiang
authors: Susan R
authors: SR
authors: Wessler
authors: Pamela J
authors: PJ
authors: Green
authors: Yeisoo
authors: Y
authors: Yu
authors: David C
authors: DC
authors: Schwartz
authors: Blake C
authors: BC
authors: Meyers
authors: Jeffrey L
authors: JL
authors: Bennetzen
authors: Robert A
authors: RA
authors: Martienssen
authors: W Richard
authors: WR
authors: McCombie
authors: Srinivas
authors: S
authors: Aluru
authors: Sandra W
authors: SW
authors: Clifton
authors: Patrick S
authors: PS
authors: Schnable
authors: Doreen
authors: D
authors: Ware
authors: Richard K
authors: RK
authors: Wilson
authors: Rod A
authors: RA
authors: Wing
mesh_terms: 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*
chemical_list: D004251:DNA Transposable Elements; D018749:RNA, Plant