Fates of duplicated genes : sub-localization, intracellular gene transfer, and concerted evolution

Gene duplication is a major contributor to genome evolution. There are several evolutionary fates of duplicated genes, such as retention with redundancy, subfunctionalization and neofunctionalization. I proposed and characterized examples of three new models here. The first is duplication of an alternatively spliced gene with dual-targeted products, followed by partitioning of the splice forms between the duplicates so that the products of each duplicate are sub-localized. I report the plastid ascorbate peroxidase (cpAPX) genes as an example of sub-localization. I show angiosperms typically have one cpAPX gene that generates both thylakoidal tAPX and stromal sAPX through alternative splicing. I then identified several independent, lineage-specific sub-localization events with paralogs of specialized tAPX and sAPX. I determined that the sub-localization happened through two types of sequence evolution patterns. Second, I show an unreported type of duplicative intracellular transfer: transfer of a nuclear gene to the mitochondrial genome and transcription of the gene. The transcribed orf164 gene in the mitochondrial genome of several Brassicaceae species is derived from a nuclear gene that codes for an auxin responsive protein. Third, I studied POLYCOMB REPRESSIVE COMPLEX2 (PRC2) in Brassicaceae to demonstrate concerted divergence of simultaneously duplicated genes whose products function in the same complex. The VERNALIZATION (VRN)-PRC2 complex contains VRN2 and SWINGER (SWN), and both genes were duplicated during a whole-genome duplication to generate FERTILIZATION INDEPENDENT SEED2 (FIS2) and MEDEA (MEA), which function in the Brassicaceae-specific FIS-PRC2 complex that regulates reproductive development. I found that FIS2 and MEA have correlated reproductive-specific expression patterns that are derived from the broadly expressed VRN2 and SWN. In vegetative tissues of Arabidopsis thaliana, repressive methylation marks are enriched in FIS2 and MEA, whereas active marks are associated with their paralogs. I detected comparable accelerated amino acid substitution rates in FIS2 and MEA but not in their paralogs. These lines of evidence indicate that FIS2 and MEA have diverged in concert, resulting in functional divergence of the PRC2 complexes in Brassicaceae. Overall, the three projects provide new insights into the retention and divergence of duplicated genes.Science, Faculty ofBotany, Department ofGraduat