Interplay of Polyploid- and Tandem-Derived Gene Duplicates in Chemical Defense and Pathogen Recognition

Analysis of gene retention and fractionation has revealed an evident role of ancient polyploidy and tandem-gene duplication during the evolution of genes from distinct classes including ontology (GO) categories. However, little is known about the impact of plant genome and gene multiplication to the expansion of specific pathways and associated traits. Through a genome informatics approach, we have identified groups of syntenic duplicates embedded in collinear blocks (ohnologs) across nine high-quality genomes including those from six major crops. Using the model plant Arabidopsis as a reference, we performed large-scale mapping of 128 pathway entries manually curated in the KEGG database to every target genome leading to the identification of more than 50,000 associated genes involved in major pathways across all analyzed species. Comparing genome-wide abundance of pathway categories (as background) to abundance among ohnologs, we identified 14 pathways with above-average retention-score across all genomes. Moreover, we report 37 pathway categories differentially enriched in species-specific sets of retained genes, and inferred functional constraints towards preferential retention of traits associated with plant-pathogen interactions and secondary metabolites.