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Published online before print
August 10, 2006 Genome Research, DOI: 10.1101/gr.5338906
Uneven chromosome contraction and expansion in the maize genome1Munich Information Center for Protein Sequences (MIPS), Institute for Bioinformatics, GSF Research Center for Environment and Health, D-85764 Neuherberg, Germany; 2The Plant Genome Initiative at Rutgers (PGIR), Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA; 3Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA; 4Department of Genetics, University of Georgia, Athens, Georgia 30602, USA; 5Arizona Genomics Institute (AGI), University of Arizona, Tucson, Arizona 85721, USA; 6The Institute for Genomic Research (TIGR), Rockville, Maryland 20850, USA; 7Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
Maize (Zea mays or corn), both a major food source and an important cytogenetic model, evolved from a tetraploid that arose about 4.8 million years ago (Mya). As a result, maize has extensive duplicated regions within its genome. We have sequenced the two copies of one such region, generating 7.8 Mb of sequence spanning 17.4 cM of the short arm of chromosome 1 and 6.6 Mb (25.6 cM) from the long arm of chromosome 9. Rice, which did not undergo a similar whole genome duplication event, has only one orthologous region (4.9 Mb) on the short arm of chromosome 3, and can be used as reference for the maize homoeologous regions. Alignment of the three regions allowed identification of syntenic blocks, and indicated that the maize regions have undergone differential contraction in genic and intergenic regions and expansion by the insertion of retrotransposable elements. Approximately 9% of the predicted genes in each duplicated region are completely missing in the rice genome, and almost 20% have moved to other genomic locations. Predicted genes within these regions tend to be larger in maize than in rice, primarily because of the presence of predicted genes in maize with larger introns. Interestingly, the general gene methylation patterns in the maize homoeologous regions do not appear to have changed with contraction or expansion of their chromosomes. In addition, no differences in methylation of single genes and tandemly repeated gene copies have been detected. These results, therefore, provide new insights into the diploidization of polyploid species.
8 These authors contributed equally to this work. E-mail messing{at}mbcl.rutgers.edu; fax (732) 445-0072. Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.5338906 [Supplemental material is available online at www.genome.org. The list of the accessions deposited into GenBank can be found in Supplemental Tables D (chromosome 1S) and E (chromosome 9L).]
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