The maize and sorghum genomes are both functionally diploid and contain ten chromosomes. However, the maize genome underwent a tetraploidy event sometime after the divergence of the maize and sorghum lineages. Many of the duplicate genes (homeologs) in maize have not been maintained. This gene loss combined with chromosomal rearrangements have created a dynamic maize genome that has winnowed the genes and chromosomes back to the ancestral chromosomal number. Interestingly, the gene loss did not occur equally among the subgenomes produced by the maize tetraploidy event. By comparison of syntenic regions of the maize and sorghum genomes, the authors of this paper show that the process of gene loss has been concentrated in one of the maize subgenomes. Furthermore, presence absence variation for genes in diverse maize and teosinte lines shows that polymorphism for gene loss appears to be more frequent in one genome suggesting that the process of gene loss in maize is ongoing. Finally, the authors show that among duplicate genes that have been maintained there are frequent expression differences among the subgenomes, with the same subgenome that frequently loses genes showing reduced expression levels. They suggest a mechanism whereby deletion rates are equal among both subgenomes, but purifying selection maintains genes from the dominant subgenome that exhibits higher expression.
Schnable J, Springer N, Freeling M (2011) Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proc Natl Acad Sci, USA 0:doi: 10.1073/pnas.1101368108
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