Gene Loss and Movement in the Maize Genome
Open Access
- 1 October 2004
- journal article
- Published by Cold Spring Harbor Laboratory in Genome Research
- Vol. 14 (10a) , 1924-1931
- https://doi.org/10.1101/gr.2701104
Abstract
Maize (Zea mays L. ssp. mays), one of the most important agricultural crops in the world, originated by hybridization of two closely related progenitors. To investigate the fate of its genes after tetraploidization, we analyzed the sequence of five duplicated regions from different chromosomal locations. We also compared corresponding regions from sorghum and rice, two important crops that have largely collinear maps with maize. The split of sorghum and maize progenitors was recently estimated to be 11.9 Mya, whereas rice diverged from the common ancestor of maize and sorghum ∼50 Mya. A data set of roughly 4 Mb yielded 206 predicted genes from the three species, excluding any transposon-related genes, but including eight gene remnants. On average, 14% of the genes within the aligned regions are noncollinear between any two species. However, scoring each maize region separately, the set of noncollinear genes between all four regions jumps to 68%. This is largely because at least 50% of the duplicated genes from the two progenitors of maize have been lost over a very short period of time, possibly as short as 5 million years. Using the nearly completed rice sequence, we found noncollinear genes in other chromosomal positions, frequently in more than one. This demonstrates that many genes in these species have moved to new chromosomal locations in the last 50 million years or less, most as single gene events that did not dramatically alter gene structure.Keywords
This publication has 55 references indexed in Scilit:
- Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiaeNature, 2004
- Contiguous Genomic DNA Sequence Comprising the 19-kD Zein Gene Family from MaizePlant Physiology, 2002
- Characterization of Three Maize Bacterial Artificial Chromosome Libraries toward Anchoring of the Physical Map to the Genetic Map Using High-Density Bacterial Artificial Chromosome Filter HybridizationPlant Physiology, 2002
- Splitting pairs: the diverging fates of duplicated genesNature Reviews Genetics, 2002
- Mosaic Organization of Orthologous Sequences in Grass GenomesGenome Research, 2002
- Comparative Genomics of Plant ChromosomesPlant Cell, 2000
- Comparative Sequence Analysis of Plant Nuclear Genomes: Microcolinearity and Its Many ExceptionsPlant Cell, 2000
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997
- Cereal Genome Evolution: Grasses, line up and form a circlePublished by Elsevier ,1995
- Duplicate Genes in MaizeThe American Naturalist, 1951