Authors

Fusheng Wei, University of Arizona
Joshua C. Stein
Chengzhi Liang
Jianwei Zhang, University of Arizona
Robert S. Fulton, Washington University School of Medicine in St. Louis
Regina S. Baucom, University of Georgia
Emanuele De Paoli, University of Delaware
Shiguo Zhou, University of Wisconsin - Madison
Lixing Yang, University of Georgia
Yujun Han, University of Georgia
Shiran Pasternak
Apurva Narechania
Lifang Zhang
Cheng-Ting Yeh, Iowa State University
Kai Ying, Iowa State University
Dawn H. Nagel, University of Georgia
Kristi Collura, University of Arizona
David Kudrna, University of Arizona
Jennifer Currie, University of Arizona
Jinke Lin, University of Arizona
HyeRan Kim, University of Arizona
Angelina Angelova, University of Arizona
Gabriel Scara, University of Arizona
Marina Wissotski, University of Arizona
Wolfgang Golser, University of Arizona
Laura Courtney, Washington University School of Medicine in St. Louis
Scott Kruchowski, Washington University School of Medicine in St. Louis
Tina A. Graves, Washington University School of Medicine in St. Louis
Susan M. Rock, Washington University School of Medicine in St. Louis
Stephanie Adams, Washington University School of Medicine in St. Louis
Lucinda A. Fulton, Washington University School of Medicine in St. Louis
Catrina Fronick, Washington University School of Medicine in St. Louis
William Courtney, Washington University School of Medicine in St. Louis
Melissa Kramer
Lori Spiegel
Lydia Nascimento
Ananth Kalyanaraman, Washington State University
Cristian Chaparro, Université de Perpignan Via Domitia
Jean-Marc Deragon, Université de Perpignan Via Domitia
Phillip SanMiguel, Purdue UniversityFollow
Ning Jiang, Michigan State University
Susan R. Wessler, University of Georgia
Pamela J. Green, University of Delaware
Yeisoo Yu, University of Arizona
David C. Schwartz, University of Wisconsin - Madison
Blake C. Meyers, University of Delaware
Jeffrey L. Bennetzen, University of Georgia
Robert A. Martienssen
W. Richard McCombie
Srinivas Aluru, Iowa State University
Sandra W. Clifton, Washington University School of Medicine in St. Louis
Patrick S. Schnable, Iowa State University
Doreen Ware
Richard K. Wilson, Washington University School of Medicine in St. Louis
Rod A. Wing, University of Arizona

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 ~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.

Comments

This is the publisher pdf of Wei F, Stein JC, Liang C, Zhang J, Fulton RS, et al. (2009) Detailed Analysis of a Contiguous 22-Mb Region of the Maize Genome. PLoS Genet 5(11): e1000728 and is available at: 10.1371/journal.pgen.1000728.

Date of this Version

11-20-2009

DOI

10.1371/journal.pgen.1000728

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