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March 2011

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[Beg-evodevo] Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss
by Klaas Vandepoele 23 Mar '11

23 Mar '11

Expression evolution following WGD and fractionation in maize Klaas *Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss* James C. Schnablea, Nathan M. Springer and Michael Freeling Abstract Ancient tetraploidies are found throughout the eukaryotes. After duplication, one copy of each duplicate gene pair tends to be lost (fractionate). For all studied tetraploidies, the loss of duplicated genes, known as homeologs, homoeologs, ohnologs, or syntenic paralogs, is uneven between duplicate regions. In maize, a species that experienced a tetraploidy 5--12 million years ago, we show that in addition to uneven ancient gene loss, the two complete genomes contained within maize are differentiated by ongoing fractionation among diverse inbreds as well as by a pattern of overexpression of genes from the genome that has experienced less gene loss. These expression differences are consistent over a range of experiments quantifying RNA abundance in different tissues. We propose that the universal bias in gene loss between the genomes of this ancient tetraploid, and perhaps all tetraploids, is the result of selection against loss of the gene responsible for the majority of total expression for a duplicate gene pair. Although the tetraploidy of maize is ancient, biased gene loss and expression continue today and explain, at least in part, the remarkable genetic diversity found among modern maize cultivars. -- Prof. Dr. Klaas Vandepoele Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, Belgium E-mail: Klaas.Vandepoele(a)psb.vib-ugent.be Website: http://bioinformatics.psb.ugent.be/cig/ --------------------------------------------------------- Conference& Workshop Comparative& Regulatory Genomics in Plants Website: http://bioinformatics.psb.ugent.be/crg_event/ ---------------------------------------------------------

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