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

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

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

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

Fates of genes after duplication : sublocalization and regulatory neofunctionalization

Gene duplication has supplied the raw material for novel gene functions and evolutionary innovations in plants. Duplicated genes can have different fates over time such as neofunctionalization and subfunctionalization. Sublocalization, which is a type of subfunctionalization based on protein subcellular relocalization, happens when the products of the duplicate genes are each directed to only one of two subcellular locations that were previously targeted by the single ancestral gene. The goals of the first part of my project were to study changes in protein subcellular localization (relocalization) after gene duplication by finding cases of sublocalization and further characterizing them from an evolutionary perspective. I found that sublocalization is a relatively uncommon phenomenon in plants as only two out of the seven gene families that I analyzed demonstrated cases of sublocalization. I identified and analyzed multiple cases of sublocalization of the APX and PP5 genes by doing RT-PCR experiments and then performing phylogenetic analyses and sequence rate analyses to further characterize the genes from an evolutionary perspective. Regulatory neofunctionalization involves changes in expression patterns of a gene after duplication. The goals for the second part of my thesis were to study expression patterns of duplicated genes in Arabidopsis thaliana and to analyze the selective forces acting on the genes of interest. I focused on eight pairs of duplicates that showed one copy broadly expressed and the other copy having expression only in certain organ types. By analyzing the expression patterns of the orthologs in outgroup species and selective forces acting on the sequences, I obtained evidence for potential neofunctionalization for a few cases. The results from my thesis provide new insights into the frequency and process of sublocalization of duplicated genes, as well as characterizing new examples of neofunctionalization of duplicated genes.Science, Faculty ofBotany, Department ofGraduat