Evolution of dosage compensation at transcriptional and post-transcriptional levels in plants

Objective

This project will address a key question in evolutionary biology: the evolution of sex chromosomes and the origin and regulation of dosage compensation (DC). Degeneration of non-recombining sex-specific chromosomes (e.g., Y in mammals, W in birds) causes gene loss and dosage imbalances between sexes. While some organisms with ancient sex chromosomes (e.g., Drosophila, mammals) evolved chromosome-wide DC, such systems are not universally observed in birds, reptiles, amphibians, fish, or plants. Emerging evidence in animals suggests that incomplete transcriptional DC may be buffered by post-transcriptional regulation, but whether this mechanism extends to plants remains entirely untested. To fill this gap, I will study two phylogenetically dioicous plants, Silene and Rumex, each with independently evolved sex chromosomes, using hermaphroditic outgroups as ancestral references. This will be the first study to integrate post-transcriptional regulation into the analysis of plant DC. For each species, I will generate three complementary omics: long-read, short-read transcriptomics and proteomics from the same individuals, tissues and developmental stages. I will test whether incomplete transcriptional DC is offset by post-transcriptional regulation. To trace the origin and tempo of DC, I will compare expression balance between sexes across evolutionary strata of varying ages, classifying sex-linked genes by synonymous substitution rates (dS) and functional categories. Long-read sequencing will further allow the first systematic test of whether alternative splicing (AS) contributes to DC in plants. Finally, integrating multi-omics from both vegetative and reproductive tissues of both sexes will enable a comprehensive view of tissue- and sex-specific regulatory dynamics. Overall, this project will provide unprecedented insights into the early stages of DC evolution and the interplay between transcriptional and post-transcriptional regulation in sex chromosome evolution.