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Published online on September 23, 2004, 10.1073/pnas.0406163101
PNAS | October 5, 2004 | vol. 101 | no. 40 | 14349-14354
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AGRICULTURAL SCIENCES
Sequence composition and genome organization of maize

Joachim Messing *, {dagger}, Arvind K. Bharti *, Wojciech M. Karlowski {ddagger}, Heidrun Gundlach {ddagger}, Hye Ran Kim §, Yeisoo Yu §, Fusheng Wei §, Galina Fuks *, Carol A. Soderlund ¶, Klaus F. X. Mayer {ddagger}, and Rod A. Wing §

*Plant Genome Initiative at Rutgers, Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, NJ 08854; {ddagger}Munich Information Center for Protein Sequences, Institute for Bioinformatics, GSF Research Center for Environment and Health, D-85764 Neuherberg, Germany; and §Arizona Genomics Institute and Arizona Genomics Computational Laboratory, University of Arizona, Tucson, AZ 85721

Communicated by Brian A. Larkins, University of Arizona, Tucson, AZ, August 20, 2004 (received for review July 22, 2004)

Zea mays L. ssp. mays, or corn, one of the most important crops and a model for plant genetics, has a genome {approx}80% the size of the human genome. To gain global insight into the organization of its genome, we have sequenced the ends of large insert clones, yielding a cumulative length of one-eighth of the genome with a DNA sequence read every 6.2 kb, thereby describing a large percentage of the genes and transposable elements of maize in an unbiased approach. Based on the accumulative 307 Mb of sequence, repeat sequences occupy 58% and genic regions occupy 7.5%. A conservative estimate predicts {approx}59,000 genes, which is higher than in any other organism sequenced so far. Because the sequences are derived from bacterial artificial chromosome clones, which are ordered in overlapping bins, tagged genes are also ordered along continuous chromosomal segments. Based on this positional information, roughly one-third of the genes appear to consist of tandemly arrayed gene families. Although the ancestor of maize arose by tetraploidization, fewer than half of the genes appear to be present in two orthologous copies, indicating that the maize genome has undergone significant gene loss since the duplication event.

maize genome | whole-genome sequence tags | map-based sequence | whole-genome duplication | gene families

Author contributions: J.M., K.F.X.M., and R.A.W. designed research; A.K.B., H.R.K., Y.Y., and F.W. performed research; A.K.B. contributed new reagents/analytic tools; J.M., A.K.B., W.M.K., H.G., G.F., C.A.S., K.F.X.M., and R.A.W. analyzed data; and J.M. wrote the paper.

Freely available online through the PNAS open access option.

Abbreviations: Gb, gigabase(s); Mb, megabase(s); BAC, bacterial artificial chromosome; BES, BAC end sequence; TE, transposable element; GSS, genome survey sequence; TC, tentative consensus; HC, high C0t-derived; MF, methyl-filtered; GFS, gene family signature.

Data deposition: The sequences reported in this paper have been deposited in the GenBank database (accession nos. can be found in Table 4, which is published as supporting information on the PNAS web site).

{dagger} To whom correspondence should be addressed. E-mail: messing{at}mbcl.rutgers.edu.

© 2004 by The National Academy of Sciences of the USA


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