Sequence composition and genome organization of maize

Zea mays L. ssp. mays, or corn, one of the most important crops and a model for plant genetics, has a genome ≈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...

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Bibliographic Details
Published in:	Proceedings of the National Academy of Sciences - PNAS Vol. 101; no. 40; pp. 14349 - 14354
Main Authors:	Messing, J, Bharti, A.K, Karlowski, W.M, Gundlach, H, Kim, H.R, Yu, Y, Wei, F, Fuks, G, Soderlund, C.A, Mayer, K.F.X
Format:	Journal Article
Language:	English
Published:	United States National Academy of Sciences 05-10-2004 National Acad Sciences
Subjects:	Agriculture Biological Sciences Chromosomes, Artificial, Bacterial - genetics Corn Databases, Nucleic Acid Datasets DNA DNA Transposable Elements - genetics DNA, Plant - genetics Genes Genetics Genome, Plant Genomes Genomics Libraries Plants Repetitive Sequences, Nucleic Acid Retrotransposons Rice Zea mays Zea mays - genetics
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Summary:	Zea mays L. ssp. mays, or corn, one of the most important crops and a model for plant genetics, has a genome ≈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 ≈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.
Bibliography:	ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Feature-1 content type line 23 ObjectType-Article-1 ObjectType-Feature-2 To whom correspondence should be addressed. E-mail: messing@mbcl.rutgers.edu. 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. Communicated by Brian A. Larkins, University of Arizona, Tucson, AZ, August 20, 2004 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).
ISSN:	0027-8424 1091-6490
DOI:	10.1073/pnas.0406163101