Phylogenomic investigations of the photosynthetic and genomic diversification of Molluginacea

Abstract During evolution, organisms acquired many traits that allowed them to colonize almost all possible environments. Some of these tools result from the coordinated action of numerous cells and enzymes and are consequently referred to as complex traits. Due to their apparent complexity, the evolutionary paths leading to the emergence of complex traits remain incompletely understood. C4 photosynthesis is a derived physiology that boosts productivity in warm and dry habitats. It results from the coordinated action of multiple anatomical and biochemical components and therefore is an excellent example of a complex trait. The C4 trait has evolved more 62 times independently, offering natural replicates to understand the processes leading to the emergence of complex traits. In particular, the Molluginaceae encompasses multiple C4 species, species using the ancestral C3 type, and C3-C4 species with intermediate characters. In this work, this study system is used to evaluate the evolutionary dynamics of the leaf anatomy, genes for C4 enzymes, and chloroplast genomes during the diversification of photosynthetic types. Using a phylogenetic framework, I first compared the leaf anatomies of Molluginaceae species with distinct photosynthetic types, showing that the emergence of C4 leaf anatomy in Molluginaceae resulted from the constraint combination of characters that individually existed in C3 ancestors. I then used comparative transcriptomes to show that the C4 biochemistry emerged from the upregulation of multiple genes, specifically in the C4 lineages. Finally, I compare the chloroplast genomes of members of the family, showing that a large subgroup of Molluginaceae containing C4, C3-C4 and C3 species is characterized by sustained increased rates of chloroplast evolution. Overall, this work brings new insights into the events that led to C4 emergence of Molluginaceae. C4 leaf anatomical components evolved early in the history of the group and were later recurrently co-opted for transitions to C4 photosynthesis through gene upregulation and positive selection adapting the encoding enzymes. C3-C4 species only occasionally bridge the gap to C4 anatomy, but in the case of Molluginaceae, they do not decrease the distance to a C4 biochemistry. The function of C3-C4 intermediates as evolutionary facilitators therefore depends on the details of their photosynthetic machinery and their eco-physiological strategies. Transcriptome data moreover suggest that hybridization might have contributed to independent transitions to C4 photosynthesis in the group. In the future, analyses of complete nuclear genomes will be needed to precisely assess how such processes affected the evolutionary dynamics in the group. My work forms a solid foundation on which to build such efforts