Phylotranscriptomic Analysis of Pigment Biosynthesis in the Caryophyllales

Abstract

In plants, color is given by secondary metabolites, pigments, that absorb and emit color due to their chemical structure. Betalains are a class of tyrosine-derived pigments found exclusively in the Caryophyllales order, where they are concurrent with the anthocyanin pigments. These two types of pigments show a mutually exclusive pattern of expression rooted in a complex homoplastic distribution. Although the genetic events that led to the emergence of betalains in the Caryophyllales is known, the exact genetic evolutionary path that led to mutual exclusion remains elusive with multiple theories with a single or multiple emergences being proposed. This thesis combines orthology-based phylogenetic correlation analyses with comparative transcriptomics to investigate the molecular and evolutionary drivers of pigment biosynthesis, focusing on transcriptional regulation, pigment structural modification, and transport mechanisms. Co-expression analysis revealed potential regulatory co-option, suggesting that betalain-producing species may have repurposed ancestral anthocyanin regulatory mechanisms to drive their pigment emergence. Additionally, candidate enzymes such as UGT, SCPL, and MT were identified as key players in pigment structural modification and stabilization in betalain-producing species. The research also presents novel insights into the role of cellular transport mechanisms in pigment exclusion. Genes in orthogroups with statistically different occupancy annotated in processes related to vesicle trafficking were found to coexpress with biosynthetic modules, suggesting that transport may contribute significantly to the mutual exclusion of anthocyanins and betalains. These findings hint at a possible loss and co-option of anthocyanin transport mechanisms for betalain sequestration in vacuoles, raising questions about how shifts in transport specificity may drive pigment divergence.