Divergence of duplicated genes by repeated partitioning of splice forms and subcellular localization

Abstract

Gene duplication is a prominent and recurrent process in plant genomes. Among the possible fates of duplicated genes, subfunctionalization refers to duplicates taking on different parts of the function or expression pattern of the ancestral gene. This partitioning could be accompanied by changes in subcellular localization of the protein products. We propose that when alternative splicing of gene products leads to protein products with different subcellular localizations, after gene duplication there will be partitioning of the alternatively spliced forms such that the products of each duplicate are localized to only one of the original locations which we refer to as sub‐localization. We identified the plastid ascorbate peroxidase (cpAPX) genes across angiosperms and analyzed their duplication history, alternative splicing, and subcellular targeting patterns, to identify cases of sub‐localization. We found angiosperms typically have one cpAPX gene that generates both thylakoidal APX (tAPX) and stromal APX (sAPX) through alternative splicing. We identified several independent lineage‐specific sub‐localization cases with specialized paralogs of tAPX and sAPX. We determined that the sub‐localization happened through two types of sequence evolution patterns. Our findings suggest that the divergence through sub‐localization is key to the retention of paralogous cpAPX genes in angiosperms