Abstract
BackgroundGenes duplicated by polyploidy (homoeologs) may be differentially expressed in plant tissues. Recent research using DNA microarrays and RNAseq data have described a cacophony of complex expression patterns during development of cotton fibers, petals, and leaves. Because of its highly canalized development, petal tissue has been used as a model tissue for gene expression in cotton. Recent advances in cotton genome annotation and assembly now permit an enhanced analysis of duplicate gene deployment in petals from allopolyploid cotton.ResultsHomoeologous gene expression levels were quantified in diploid and tetraploid flower petals of Gossypium using the Gossypium raimondii genome sequence as a reference. In the polyploid, most homoeologous genes were expressed at equal levels, though a subset had an expression bias of AT and DT copies. 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.ConclusionsCompared to previous studies, a surprising level of expression homeostasis was observed in the expression patterns of polyploid genomes. Conserved expression bias in polyploid petals may have resulted from cis-acting modifications that occurred prior to polyploidization. Some duplicated genes were intriguing exceptions to general trends. Mechanisms of gene regulation for these and other genes in the cotton genome warrants further investigation.
Highlights
Genes duplicated by polyploidy may be differentially expressed in plant tissues
One consequence of polyploidization is unequal expression of homoeologous loci. This phenomenon was first described in cotton, for single duplicate gene pairs using Single-Strand Conformation Polymorphism (SSCP) [1,2,8] and genome-wide using custom DNA microarrays [3,4,9]
Of the genes with biased expression in petal tissue, approximately 76% of homoeolog expression biases were immediately apparent after genomic merger, while the remaining 24% of homoeolog expression biases had been molded by evolutionary forces over time [20]
Summary
Genes duplicated by polyploidy (homoeologs) may be differentially expressed in plant tissues. Recent research using DNA microarrays and RNAseq data have described a cacophony of complex expression patterns during development of cotton fibers, petals, and leaves. The six polyploid species of this genus formed between 1–2 million years ago [3,4] While these polyploid species are currently geographically separated, their monophyletic origin makes this genus an ideal system to study the effects of polyploidization on gene expression. One consequence of polyploidization is unequal expression of homoeologous loci This phenomenon was first described in cotton, for single duplicate gene pairs using Single-Strand Conformation Polymorphism (SSCP) [1,2,8] and genome-wide using custom DNA microarrays [3,4,9]. The expression level changes that accompanied polyploidization were considered two distinct phases of duplication gene evolution and have been reported in other natural and synthetic allopolyploid species [6,21,22,23,24,25,26]
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