Polyploidy and the petal transcriptome and of Gossypium. Gossypium

Background: Genes duplicated by polyploidy are called homoeologs and can be differentially expressed in plant tissues. Recent research using DNA microarrays have described a cacophony of complex expression patterns during development of cotton fibers, petals, and leaves. In addition, interpretation of these patterns was dependent on EST assemblies without a reference genome sequence of cotton. This combination of technology and resources resulted in a tentative understanding of gene expression in polyploids. Results: Using the Gossypium raimondii reference genome sequence, homoeologous gene expression levels were quantified in diploid and tetraploid flower petals of Gossypium. In the polyploid, most homoeologous genes were expressed at equal levels, though a subset had an expression bias of AT and DT loci. The direction of gene expression bias was conserved in natural and recent polyploids of cotton. Conservation of direction of bias and additional comparisons between the diploids and tetraploids suggested different regulation mechanisms of gene expression. We described three phases in the evolution of cotton genomes that contribute to gene expression in the polyploid nucleus. Conclusions: This is the first RNA-seq report to thoroughly describe comparative gene expression levels of multiple genomes within a polyploid. Compared to previous studies, a surprising level of expression homeostasis was observed in the evolution of polyploid genomes. Some duplicated genes were intriguing exceptions to general trends. The mechanism of gene regulation for these and other genes in the cotton genome warrants further investigation.