Supplementary materials for PhD thesis: Comparative Genomics and Trait Evolution in Lettuce, its Wild Relatives and the Asteraceae

This dataset includes the supplementary materials of Wei Xiong's Ph.D. thesis book for different chapters. It contains the evidence that supports the main findings or the important intermediate results. The work was conducted in the Biosystematics group, at Wageningen University<br>Improved crops are needed to provide healthy and nutritious food for the growing global population. Genome assembly helps understand genetic diversity and chromosome organization, which is crucial for breeding improved crops.This study focuses on lettuce (<em>Lactuca sativa</em>) and its wild relatives, which serve as important genetic resources for breeding. Chapter 1 discusses sequencing technologies for genome assembly and introduces three key species for lettuce breeding: <em>L. saligna</em>, <em>L. virosa</em>, and dandelion (<em>Taraxacum officinale</em>).<em>L. saligna</em> belongs to lettuce’s secondary gene pool and provides resistance to downy mildew. Chapter 2 presents a high-quality genome assembly of <em>L. saligna</em>, describing genetic variants, structural differences compared to lettuce, and potential genetic barriers in hybridization.<em>L. virosa</em> is part of the tertiary gene pool and is naturally difficult to cross with lettuce. Chapter 3 details the genome assembly of <em>L. virosa</em> and compares its genetic structure with <em>L. saligna</em> and <em>L. sativa</em>, identifying major structural differences and repetitive elements.Chapter 4 introduces a genome assembly of diploid dandelion as a reference for lettuce breeding and a phylogenomic study within the Asteraceae family. The evolution of resistance and floral traits is explored, with a focus on MADS-box genes.Chapter 5 provides a synthesizing discussion and perspectives for future research, including improved genome assembly strategies, the use of model plants, and the role of specific genes in disease resistance and flower development. This study contributes to genetic knowledge and breeding possibilities for lettuce species and related crops. (Summary by ChatGPT)