title: Uneven chromosome contraction and expansion in the maize genome.
abstract: 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.
authors.affiliation: Munich Information Center for Protein Sequences (MIPS), Institute for Bioinformatics, GSF Research Center for Environment and Health, D-85764 Neuherberg, Germany.
authors.forename: Rémy
authors.initials: R
authors.lastname: Bruggmann
authors.forename: Arvind K
authors.initials: AK
authors.lastname: Bharti
authors.forename: Heidrun
authors.initials: H
authors.lastname: Gundlach
authors.forename: Jinsheng
authors.initials: J
authors.lastname: Lai
authors.forename: Sarah
authors.initials: S
authors.lastname: Young
authors.forename: Ana C
authors.initials: AC
authors.lastname: Pontaroli
authors.forename: Fusheng
authors.initials: F
authors.lastname: Wei
authors.forename: Georg
authors.initials: G
authors.lastname: Haberer
authors.forename: Galina
authors.initials: G
authors.lastname: Fuks
authors.forename: Chunguang
authors.initials: C
authors.lastname: Du
authors.forename: Christina
authors.initials: C
authors.lastname: Raymond
authors.forename: Matt C
authors.initials: MC
authors.lastname: Estep
authors.forename: Renyi
authors.initials: R
authors.lastname: Liu
authors.forename: Jeffrey L
authors.initials: JL
authors.lastname: Bennetzen
authors.forename: Agnes P
authors.initials: AP
authors.lastname: Chan
authors.forename: Pablo D
authors.initials: PD
authors.lastname: Rabinowicz
authors.forename: John
authors.initials: J
authors.lastname: Quackenbush
authors.forename: W Brad
authors.initials: WB
authors.lastname: Barbazuk
authors.forename: Rod A
authors.initials: RA
authors.lastname: Wing
authors.forename: Bruce
authors.initials: B
authors.lastname: Birren
authors.forename: Chad
authors.initials: C
authors.lastname: Nusbaum
authors.forename: Steve
authors.initials: S
authors.lastname: Rounsley
authors.forename: Klaus F X
authors.initials: KF
authors.lastname: Mayer
authors.forename: Joachim
authors.initials: J
authors.lastname: Messing
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics*; D019143:Evolution, Molecular; D020131:Genes, Duplicate / Q000235:genetics*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D011003:Ploidies; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D026801:Synteny / Q000235:genetics; D003313:Zea mays / Q000235:genetics*