Project (Sophie de Vries)

Evolution of small RNA regulatory networks and the foundation of plant life cycles

Land plants are defined by having a phase change between haploid and diploid multicellular stages: the gametophyte and sporophyte. We will test (i) whether the gametophyte–sporophyte transitions are governed by similar molecular networks across key lineages of land plants, and (ii) whether these networks are evolutionarily conserved or instead represent cases of convergent recruitment. Small RNAs (sRNAs) are crucial upstream regulators that can, but need not necessarily, be highly dynamic in both sequence and target specificity. They play central roles in initiating reproduction and strongly influence reproductive organ formation and fertility in angiosperms. However, the degree to which sRNA regulatory networks are conserved across land plants remains largely unknown. To address this gap, we will investigate the reproductive networks, their evolutionary trajectories, and ancestral character states across representative model species: the fern Ceratopteris richardii and the two bryophytes Marchantia polymorpha and Physcomitrium patens. By tracing the functional evolution of miRNA–target interactions, we will determine which components of these reproductive networks are lineage-specific innovations and which have been evolutionarily conserved, taking into account the dynamic nature of miRNA regulation. Specifically, we will (i) identify miRNA families that play key roles in the gametophyte–sporophyte transition, (ii) examine how these relate to the evolution of reproductive organ patterning, and (iii) reconstruct the evolutionary history of these regulatory modules. To achieve this, we will first identify miRNAs enriched during the gametophyte-to-sporophyte transition by comparing them with homologs known from angiosperm models, and then determine miRNAs significantly enriched in gametophytic versus sporophytic tissues across key non-seed plant lineages. Using separate sequencing of gametophytic and sporophytic tissues, we will apply a two-pronged approach to identify both conserved and newly recruited miRNA-guided regulatory modules involved in reproductive organ formation. Candidate miRNA targets will be predicted and validated through degradome sequencing using the same tissues employed for sRNA profiling. The proposed work will illuminate the evolutionary origins and conservation of a fundamental regulatory network that underpins reproductive development across all land plants.