(Pan)Genomics Approaches for Plant Agrobiodiversity Conservation and Valorisation

The unfolding biodiversity crisis threatens ecosystems health, species adaptability, genetic diversity, and food security. The study of biodiversity and agrobiodiversity is crucial for identifying conservation strategies. Genomic data are key to understanding many of the major challenges in biodiversity conservation. Indeed, the new DNA sequencing technologies revolutionised our capacity to extensively characterise and monitor genetic diversity, greatly accelerating the acquisition of high-quality de novo genome assemblies and permitting the availability of more than one single reference genome per species. This is hastening the shift in genomics from single reference-based studies, which frequently suffer from biases, to a pangenome-based approach. Pangenomes are collections of genomic sequences of a species or population that comprehensively capture the genetic diversity. The purpose of this thesis was the development of bioinformatics pipelines for de novo genome assembly and pangenome analysis. Several bioinformatics tools were benchmarked to identify the most accurate in generating de novo genome assemblies. An automated, open-source, portable, and user-friendly pipeline for complete, chromosome-scale de novo genome assembly was built. A 93-assemblies reference-free pangenome of the model plant Arabidopsis thaliana was constructed and used to set up an analysis workflow. The developed methods were then applied to Sardinian genetic resources. Two complete, chromosome-scale de novo genome assemblies were generated for two genotypes of the Sardinian barley landrace S’Orgiu Sardu, which were included in a reference-free pangenome for a comparative study. Haploid consensus and phased de novo genome assemblies for the Sardinian emblematic grapevine cultivar Cannonau were produced. This thesis delivered open-source tools that will be available to the whole biodiversity genomics community and its results will contribute to the conservation and valorisation of Sardinian biodiversity.