Uneven chromosome contraction and expansion in the maize genome.
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.
Bruggmann
Rémy
R
Munich Information Center for Protein Sequences (MIPS), Institute for Bioinformatics, GSF Research Center for Environment and Health, D-85764 Neuherberg, Germany.
Bharti
Arvind K
AK
Gundlach
Heidrun
H
Lai
Jinsheng
J
Young
Sarah
S
Pontaroli
Ana C
AC
Wei
Fusheng
F
Haberer
Georg
G
Fuks
Galina
G
Du
Chunguang
C
Raymond
Christina
C
Estep
Matt C
MC
Liu
Renyi
R
Bennetzen
Jeffrey L
JL
Chan
Agnes P
AP
Rabinowicz
Pablo D
PD
Quackenbush
John
J
Barbazuk
W Brad
WB
Wing
Rod A
RA
Birren
Bruce
B
Nusbaum
Chad
C
Rounsley
Steve
S
Mayer
Klaus F X
KF
Messing
Joachim
J
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*