Duplicate genes increase expression diversity in closely related species and allopolyploids

Polyploidy or whole genome duplication (WGD) provides raw genetic materials for sequence and expression evolution of duplicate genes. However, the mode and tempo of expression divergence between WGD duplicate genes in closely relates species and recurrent allopolyploids are poorly understood. Arabidopsis is a suitable system for testing the hypothesis that duplicate genes increase expression diversity and regulatory networks. In Arabidopsis, WGD occurred more than once prior to the split between Arabidopsis thaliana and Arabidopsis arenosa, and both natural and human-made allotetraploids are available. Comparative genomic hybridization analysis indicated that single-copy and duplicate genes after WGD were well preserved in A. thaliana and A. arenosa. Analysis of gene expression microarrays showed that duplicate genes generally had higher levels of expression divergence between two closely related species than single-copy genes. The proportion of the progenitors' duplicate genes that were nonadditively expressed in the resynthesized and natural allotetraploids was significantly higher than that of single-copy genes. Duplicate genes related to environmental stresses tended to be differentially expressed, and multi-copy duplicate genes were likely to diverge expression between progenitors and in the allotetraploids. Compared to single-copy genes, duplicate genes tend to contain TATA boxes and less DNA methylation in the promoter regions, facilitating transcriptional regulation by binding transcription factors and/or cis-and trans- acting proteins. The data suggest an important role of WGD duplicate genes in modulating diverse and novel gene expression changes in response to external environmental cues as well as internal genetic turmoil such as recurrent polyploidy events. To analyze expression change of duplicate genes conserved in A.thaliana and A.arenosa, we selected the duplicate genes with the same hybridization intensities in comparative genomic hybridization (CGH) between A. thaliana and A. arenosa. To test the hypothesis that duplicate genes change expression regulation among different polyploid species, we first compared expression divergences of single-copy and duplicate genes between A. thaliana and A. arenosa. We then examined how duplicate genes affect expression change in new round of polyploidy detecting expression variations of single-copy and duplicate genes between each resynthesized allopolyploid and their progenitors.