Gene Retention Following Polyploidy in Angiosperms for a Single Biosynthetic Pathway

Polyploidy, the duplication of a whole genome, is a common occurrence throughout the eukaryotes, particularly in plants.  Doubling the genetic material in a nucleus generates many short-term effects, including global and local epigenetic modifications and alterations in gene expression patterns, as well as longer-term consequences such as subfunctionalization and fractionation. Here we examine the effects of polyploidy in angiosperms on the anthocyanin biosynthetic pathway.  We evaluate copy number variability across a wide spectrum of angiosperms and compare the number observed with that predicted by the various rounds of polyploidy affecting each lineage.  We find that these genes have typically been reduced in copy number, although signatures of more recent polyploidy events in several species are still present.  Genes that encode different proteins in the anthocyanin biosynthetic pathway are differentially retained.  These data may reflect relative position in the pathway, differential levels of subfunctionalization leading to expression partitioning, and/or protein-protein interactions or other aspects of the gene balance hypothesis. The perspectives of exploring polyploidy in the context of pathways, as opposed to genes in isolation, will be discussed.