Polyploid speciation is exceptionally common in plants, often operating sympatrically to saltationally generate new lineages. The reunion between two diverged diploid genomes during hybridization and polyploidization sets in motion a wide spectrum of genetic and genomic phenomena whose mechanistic underpinnings remain mostly mysterious and that have largely unknown evolutionary consequences. To advance our understanding of the evolutionary response dynamics of genome doubling, we have focused on illustrating the consequences of allopolyploid speciation on pathways and networks, using a number of different networks, including the seed oil biosynthetic network (Hu et al., 2017, Genome Biol. Evol. 8(12):3765–3783. doi:10.1093/gbe/evw280) the anthocyanin biosynthetic pathway and flowering time regulation systems.
This research entails complementary experimental approaches, including genetic and phylogenetic characterization of pathway/network components, transcriptomic profiling of gene expression dynamics accompanying genome evolution, and quantitative comparison of metabolite accumulation in response to pathway duplication. Our overall objective in these and similar studies is to enhance our understanding of polyploid genome evolution and function. We also hope to shed light on how two different regulatory systems, operating in isolation in diploid species, become accommodated into a new nucleus and context where all genes are doubled but with diverged cis and trans regulatory interactions.