Format: ORAL

Gustavo A. Silva-Arias1,2, Kai Wei2, Edeline Gagnon3,4,5, Remco Stam5, Aurelien Tellier2

1 Instituto de Ciencias Naturales, Facultad de Ciencias, Universidad Nacional de Colombia, Colombia 2 Population Genetics, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Germany 3 Department of Integrative Biology, College of Biological Science, University of Guelph, Canada 4 Chair of Phytopathology, TUM School of Life Sciences, Technical University of Munich, Germany 5 Department of Phytopathology and Crop Protection, Institute of Phytopathology, Faculty of Agricultural and Nutritional Sciences, Christian Albrechts University, Germany

Species distributed across broad environmental gradients are ideal models for unraveling the intricate signals of demographic and adaptive variation in genome dynamics. Solanum chilense, a wild tomato relative, thrives in narrow valleys along steep altitudinal gradients in the Andes and has recently colonized isolated areas in highland and coastal regions around the Atacama desert. Utilizing whole-genome sequencing, we correlated climatic changes with demographic shifts and the emergence of adaptive variations. Selective sweeps at 112 genes associated with flowering time and other abiotic response networks, indicate concerted adaptation during colonization to new regions. Complementary, integrating transcriptomic data in response to water deprivation revealed two distinct drought-response networks: cell cycle and fundamental metabolic processes. Interestingly, genes with older selective sweeps exhibit greater network connectivity, illustrating the importance of network rewiring to improve the species ability to colonize new niches. To gain a more comprehensive understanding of gene network evolution in response to colonization of new habitats, we investigated gene copy number variation (CNVs), identifying 212,207 CNVs that reflect the species demographic history and reveal candidate genes associated with stress response and, intriguingly, flowering time regulation. Environmental associations link CNV dynamics to climatic variables, pointing to natural selections role in shaping genome structural variation. These findings provide insights into CNV-driven adaptation in marginal populations, enriching our comprehension of plant evolutionary responses to changing environments. Lastly, we comprehensively examine pathogen resistance genes (NLRs) in S. chilense. A refined genome and target-capture approach reveal larger within-population than between-population Presence-Absence Variation (PAV) of NLR loci. Contrary to abiotic-stress response networks, PAV in NLRs is linked to demographic history rather than environmental gradients, challenging prevailing notions about NLR diversity maintenance. This study enhances our understanding of evolutionary processes shaping genome diversity and structure in an outcrossing plant with high nucleotide diversity.