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)

本数据集涵盖魏雄博士学位论文各章节的补充材料，包含支撑核心研究发现与关键中间结果的佐证资料。本研究工作由瓦赫宁根大学生物系统学研究组完成。
为满足全球日益增长的人口对健康营养食品的需求，亟需培育优质改良作物。基因组组装（genome assembly）有助于解析遗传多样性与染色体组织架构，这对作物育种改良至关重要。
本研究聚焦栽培莴苣（*Lactuca sativa*）及其野生近缘种，它们是育种工作中重要的遗传资源。
第1章探讨了用于基因组组装的测序技术，并介绍了莴苣育种中的3个关键物种：腺毛莴苣（*L. saligna*）、毒莴苣（*L. virosa*）以及西洋蒲公英（*Taraxacum officinale*）。
腺毛莴苣属于莴苣的次级基因库，可抗霜霉病。
第2章呈现了腺毛莴苣的高质量基因组组装结果，描述了其遗传变异、与栽培莴苣的结构差异，以及杂交过程中潜在的遗传障碍。
毒莴苣属于莴苣的三级基因库，自然条件下难以与栽培莴苣杂交。
第3章详细阐述了毒莴苣的基因组组装，并将其遗传结构与腺毛莴苣和栽培莴苣进行比对，鉴定出二者间的主要结构差异与重复元件。
第4章介绍了二倍体西洋蒲公英的基因组组装，将其作为莴苣育种与菊科（Asteraceae）植物系统基因组学研究的参考序列。
本章节还探讨了抗性与花部性状的演化历程，重点关注MADS-box基因家族。
第5章给出了综合性的讨论与未来研究展望，包括优化基因组组装策略、模式植物的应用，以及特定基因在抗病与花发育过程中的作用。
本研究为莴苣属物种及相关作物的遗传认知与育种潜力提供了重要支撑。（摘要由ChatGPT生成）