In terms of the duplicated gene expression, we observed that two genes in a duplication set show a strongly contrasting expression pattern.
The regulation of duplicated gene expression in polyploids has been well-studied in several model species, but few of these studies have correlated expression divergence with sequence variations [ 10, 23, 34- 36].
We found it interesting that, although AtPrxIIA, AtPrxIIB, and AtPrxIIC are tandemly duplicated, their expression patterns were not similar.
During a study of duplicated gene expression in A. thaliana (Liu et al. 2011), we identified two class III peroxidase genes with organ-specific complementary expression patterns.
In addition, an investigation of gene duplications in genetically modified mice may help to distinguish between the different models involved in the regulation of duplicated gene expression.
For example, while both comparative synteny mapping and duplicated marker expression support the homeologies between RT6q/RT30, the region within RT6q possessing homology to ancestral region D is currently very small.
These duplicated gene expression variations may be signs of subfunctionalization among different tissues and contribute to an increased complexity in the regulatory networks of the carotenoid pathway after polyploidization.
Gene duplication is one of the most important mechanisms for understanding the evolutionary novelties, while divergence of the duplicated gene expression is highly correlated with their functional divergence [ 33].
To handle genes appearing in multiple pathways (i.e. groups), we first duplicated their expression levels for each group—as suggested by (Jacob et al., 2009)—and then used the SLEP software package (www.public.asu.edu/∼jye02/Software/SLEP/) for group lasso estimation.
Gene duplicates were unified according to the gene name annotation as the mean values of the duplicate expression levels.
