Journal Article

Detailed Analysis of a Contiguous 22-Mb Region of the Maize Genome

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

2009

Overview

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.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Base Pairing / Base Pairing - genetics / Base Sequence / Biochemistry / Biochemistry, Molecular Biology / Biodiversity / Bioinformatics / Cellular Biology / Chromosomes, Plant / Chromosomes, Plant - genetics / Climate change / Computer Science / Corn / DNA Transposable Elements / DNA Transposable Elements - genetics / Evolution, Molecular / Gene Duplication / Gene Rearrangement / Gene Rearrangement - genetics / Genes / Genes, Plant / Genetic aspects / Genetic Loci / Genetic Loci - genetics / Genetics / Genetics and Genomics/Bioinformatics / Genetics and Genomics/Comparative Genomics / Genetics and Genomics/Genome Projects / Genetics and Genomics/Genomics / Genetics and Genomics/Plant Genomes and Evolution / Genome, Plant / Genome, Plant - genetics / Genomes / Genomics / Life Sciences / Molecular biology / Molecular Networks / Molecular Sequence Data / Mutation / Mutation - genetics / Open Reading Frames / Open Reading Frames - genetics / Oryza - genetics / Oryza sativa / Physical Chromosome Mapping / Physiological aspects / Plant breeding / Plant genetics / Plants genetics / Populations and Evolution / Quantitative Methods / RNA / RNA, Plant / RNA, Plant - genetics / Sequence Homology, Nucleic Acid / Sorghum / Sorghum - genetics / Structural Biology / Synteny / Synteny - genetics / Systematics, Phylogenetics and taxonomy / Transposons / Vegetal Biology / Zea mays / Zea mays - genetics