Gene and Genome Duplications and the Origin of C4 photosynthesis: Birth of a Trait in the Cleomaceae

C₄ photosynthesis is a trait that has evolved in sixty-six independent plant lineages and increases the efficiency of carbon fixation. The shift from C₃ to C₄ photosynthesis requires many new genes or gene functions effecting phenotypic, physiological and enzymatic changes. We investigate the role of gene duplication from Whole Genome Duplication (WGD) and more recent gene duplications in the development of this trait. We compare Gynandropsis gynandra, the closest relative of Arabidopsis that uses C₄ photosynthesis, with its C₃ relative Tarenaya hassleriana that underwent a WGD named Ch-α. It is established through analysis of synonymous substitutions in gene duplicates that G. gynandra shares the Ch-α WGD event with T. hassleriana, meaning that this WGD occurred before their divergence. A GO enrichment analysis shows that the duplicated genes in G. gynandra are enriched for the organization of photosynthetic machinery. It is found that gene pairs from the Ch-α event form a large portion of the genome of both species and that duplicate genes that organize the photosynthetic machinery have been conserved in G. gynandra, whereas T. hassleriana has more genes remaining from the Ch-α WGD overall. Phylogenetic analysis shows that photosynthetic duplicate genes in G. gynandra tend to span a smaller phylogenetic distance than the orthologs in T. hassleriana suggesting a higher degree of conservation.