RT Journal
A1 Bruggmann, Rémy
A1 Bharti, Arvind K.
A1 Gundlach, Heidrun
A1 Lai, Jinsheng
A1 Young, Sarah
A1 Pontaroli, Ana C.
A1 Wei, Fusheng
A1 Haberer, Georg
A1 Fuks, Galina
A1 Du, Chunguang
A1 Raymond, Christina
A1 Estep, Matt C.
A1 Liu, Renyi
A1 Bennetzen, Jeffrey L.
A1 Chan, Agnes P.
A1 Rabinowicz, Pablo D.
A1 Quackenbush, John
A1 Barbazuk, W. Brad
A1 Wing, Rod A.
A1 Birren, Bruce
A1 Nusbaum, Chad
A1 Rounsley, Steve
A1 Mayer, Klaus F.X.
A1 Messing, Joachim
T1 Uneven chromosome contraction and expansion in the maize genome
JF Genome Research 
JO Genome Research 
YR 2006 
FD October 01 
VO 16 
IS 10 
SP 1241 
OP 1251 
DO 10.1101/gr.5338906 
UL http://genome.cshlp.org/content/16/10/1241.abstract 
AB 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.