title: Structure and architecture of the maize genome.
abstract: Maize (Zea mays or corn) plays many varied and important roles in society. It is not only an important experimental model plant, but also a major livestock feed crop and a significant source of industrial products such as sweeteners and ethanol. In this study we report the systematic analysis of contiguous sequences of the maize genome. We selected 100 random regions averaging 144 kb in size, representing about 0.6% of the genome, and generated a high-quality dataset for sequence analysis. This sampling contains 330 annotated genes, 91% of which are supported by expressed sequence tag data from maize and other cereal species. Genes averaged 4 kb in size with five exons, although the largest was over 59 kb with 31 exons. Gene density varied over a wide range from 0.5 to 10.7 genes per 100 kb and genes did not appear to cluster significantly. The total repetitive element content we observed (66%) was slightly higher than previous whole-genome estimates (58%-63%) and consisted almost exclusively of retroelements. The vast majority of genes can be aligned to at least one sequence read derived from gene-enrichment procedures, but only about 30% are fully covered. Our results indicate that much of the increase in genome size of maize relative to rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana) is attributable to an increase in number of both repetitive elements and genes.
authors.affiliation: Munich Information Center for Protein Sequences, Institute for Bioinformatics, Gesellschaft für Strahlenforschung Research Center for Environment and Health, D-85764 Neuherberg, Germany.
authors.forename: Georg
authors.initials: G
authors.lastname: Haberer
authors.forename: Sarah
authors.initials: S
authors.lastname: Young
authors.forename: Arvind K
authors.initials: AK
authors.lastname: Bharti
authors.forename: Heidrun
authors.initials: H
authors.lastname: Gundlach
authors.forename: Christina
authors.initials: C
authors.lastname: Raymond
authors.forename: Galina
authors.initials: G
authors.lastname: Fuks
authors.forename: Ed
authors.initials: E
authors.lastname: Butler
authors.forename: Rod A
authors.initials: RA
authors.lastname: Wing
authors.forename: Steve
authors.initials: S
authors.lastname: Rounsley
authors.forename: Bruce
authors.initials: B
authors.lastname: Birren
authors.forename: Chad
authors.initials: C
authors.lastname: Nusbaum
authors.forename: Klaus F X
authors.initials: KF
authors.lastname: Mayer
authors.forename: Joachim
authors.initials: J
authors.lastname: Messing
mesh_terms: D001482:Base Composition; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D003062:Codon / Q000235:genetics; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics; D015870:Gene Expression; D015723:Gene Library; D017343:Genes, Plant; D018745:Genome, Plant; D005810:Multigene Family; D012091:Repetitive Sequences, Nucleic Acid; D003313:Zea mays / Q000235:genetics*
chemical_list: D003062:Codon; D018744:DNA, Plant