Genome reconstruction for the analysis of functional diversity

Supervisor: Prof. Fabio Marroni

Third-generation sequencing technologies, like PacBio HiFi and Oxford Nanopore, with their longer, high-quality reads, enable genome assembly from telomere to telomere, including complex regions and structural variations that were previously unexplored. This supports haplotype-specific reconstructions, crucial for diploid or polyploid species with heterozygous regions. These advances can greatly help the study of biodiversity, enhancing our understanding of genetic diversity between individuals. In addition, complete genomes assemblies and pangenomes have applications in crop improvement, species discovery, and industrial sectors. Key to these analyses are generating comprehensive references and automating pipelines across species.
The project's goals include developing unified pipelines for data processing, from raw sequencing data cleaning to haplotype-specific assembly and structural/functional annotation. Additionally, the project focuses on comparing data to unveil species relationships, genome similarities, and unique elements, advancing our knowledge of biology and evolution.