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Plant Physiology 139:1612-1624 (2005)
© 2005 American Society of Plant Biologists

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BIOINFORMATICS

Structure and Architecture of the Maize Genome1,[W]

Georg Haberer2, Sarah Young2, Arvind K. Bharti2, Heidrun Gundlach, Christina Raymond, Galina Fuks, Ed Butler, Rod A. Wing, Steve Rounsley, Bruce Birren, Chad Nusbaum, Klaus F.X. Mayer and Joachim Messing*

Munich Information Center for Protein Sequences, Institute for Bioinformatics, Gesellschaft für Strahlenforschung Research Center for Environment and Health, D–85764 Neuherberg, Germany (G.H., H.G., K.F.X.M.); Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02141 (S.Y., C.R., S.R., B.B., C.N.); Plant Genome Initiative at Rutgers, Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854 (A.K.B., G.F., J.M.); and Arizona Genomics Institute, University of Arizona, Tucson, Arizona 85721 (E.B., R.A.W.)

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.

1 This work was supported by the National Science Foundation Plant Genome (grant no. 0211851). Work at the Munich Information Center for Protein Sequences was in part supported by the Genomanalyse im biologischen System Pflanze program of the German Ministry for Education and Research.

2 These authors contributed equally to the paper.

The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Joachim Messing (messing{at}mbcl.rutgers.edu).

[W] The online version of this article contains Web-only data.

www.plantphysiol.org/cgi/doi/10.1104/pp.105.068718.

* Corresponding author; e-mail messing{at}mbcl.rutgers.edu; fax 732–445–0072.

Received July 21, 2005; returned for revision September 11, 2005; accepted October 5, 2005.




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