Carfora, Angela (2026) Adaptive genomic and transcriptomic variation in Raphanus raphanistrum in urban environments. [Tesi di dottorato]

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Abstract

Urbanization represents one of the most transformative contemporary environmental changes, significantly altering biodiversity through habitat loss and fragmentation. Beyond their destructive impact, urban environments also serve as unique ecosystems that promote rapid evolutionary adaptation through novel selective pressures. Identifying which species prosper or decline as urbanization intensifies is essential for effective biodiversity management and conservation strategies. Plants are continually exposed to adverse conditions and, although sessile, have evolved complex cellular, molecular, and biochemical mechanisms to withstand environmental challenges. However, many resistance strategies deployed under chronic urban stress remain insufficiently characterized. Addressing these knowledge gaps is critical for understanding the ecology and evolution of species in anthropogenic landscapes, making targeted urban biodiversity research necessary to clarify how species adapt and establish in these complex environments. Raphanus raphanistrum (Brassicaceae) can be used as a model due to its notable plasticity and capacity to thrive in diverse and disturbed habitats. To investigate the molecular pathways underlying urban adaptation, samples were collected from sites selected based on impervious surface percentages and soil types, providing a robust framework to examine how urban-induced stressors affect the genetic and functional architecture of this species. Although R. raphanistrum demonstrates ecological success in urban environments, the genetic and transcriptomic mechanisms underlying its resilience remain poorly understood. This study addressed these gaps using an integrated approach combining RNA sequencing, whole-genome sequencing, and genome-wide association studies. Transcriptomic analysis revealed substantial gene expression reprogramming in urban populations, particularly within the flavonoid biosynthesis pathway. This coordinated upregulation indicates that enhanced antioxidant and UV-protective mechanisms represent a primary adaptive response to oxidative stress and altered light conditions typical of urban environments. Building on these findings, genome-wide scans detected signatures of selection. Integration of multiple independent statistical methods enabled the identification of high-confidence candidate loci, where selection appears to promote the incorporation of specific variants into haplotype blocks that could enhance the regulation of genes involved in stress signaling and cellular homeostasis. To establish the relationship between molecular signals and organismal fitness, two morphological traits, leaf area and fruit weight, were evaluated through genome-wide association studies. The identification of pleiotropic loci associated with reduced vegetative and reproductive organ size suggests an adaptive life-history shift toward size reduction, potentially improving survival under heat and water limitations characteristic of urban heat islands. Population structure analysis of RNA-seq data confirmed the intra-population genetic variability observed in both genomic and transcriptomic datasets. Finally, to capture the full spectrum of genetic diversity, a genus-level pangenome was constructed, that could be used in future studies to explore structural variations as drivers of genomic plasticity beyond single-nucleotide polymorphisms. Collectively, these findings demonstrate that urban adaptation in R. raphanistrum is a multifaceted process involving coordinated modifications of both transcriptome and genome architecture. This research offers new insights into how resilient species modify their genetic identity in response to evolutionary forces. These results have direct implications for predicting species responses to ongoing urbanization and informing evidence-based conservation strategies in rapidly changing urban landscapes.

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