Supplementary data for the publication: Genome assembly and analysis of Lactuca virosa: implications for lettuce breeding

This dataset supports the <em>Lactuca virosa</em> genome assembly manuscript published on <strong>G3:Genes|Genomes|Genetics</strong> journal, entitled: Genome assembly and analysis of <em>Lactuca virosa</em>: implications for lettuce breeding. <em style="color:black;">Lactuca virosa</em> (bitter lettuce) belongs to the Asteraceae, the largest flowing plant family, and is a wild relative of the economic crop lettuce (<em style="color:black;">Lactuca sativa</em> L.) found across Eurasia. Despite the hybrid barrier, <em style="color:black;">L. virosa</em> can still be crossed with lettuce via the bridge of <em style="color:black;">L. serriola</em> or embryo rescue techniques. <em style="color:black;">L. virosa</em> is resistant to various pests and pathogens and therefore an essential donor of genetic variation for lettuce breeding, especially resistance to the currant-lettuce aphid (<em style="color:black;">Nasonovia ribisnigri</em>). Moreover, <em style="color:black;">L. virosa</em> contributes to agronomic traits like a robust root system and mitigated defoliation in modern crisphead cultivars via introgression breeding. To date, the genetic variation of the mentioned traits and the pedigree history of hybridization remains primarily unknown for <em style="color:black;">L. virosa</em>. In contrast to other species within the lettuce gene pool, <em>L. virosa</em> has a significantly larger genome size, potentially hampering chromosome pairing. This combination of breeding and fundamental interests has attracted collaborators with diverse expertise from different fields to participate in this project. To obtain a high-quality genome sequence for <em style="color:black;">L. virosa</em>, we employed a mixed dataset of long-read (Pacbio 20x) and short-read (Illumina 70x) sequencing and scaffolding approaches of Bionano and Hi-C technologies. The resulting assembly has 5,855 super-scaffolds with an N50 of 316.9 Mb. The final assembly contains 3.45 Gb (96% complete BUSCOs) and 39,887 predicted gene models (90% complete BUSCOs). This reference genome sequence of <em style="color:black;">L. virosa</em> obtained in this study provides knowledge about genomic and genetic variation within this species. It facilitates various genomic comparisons to two other available <em style="color:black;">Lactuca</em> genome assemblies (<em style="color:black;">L. sativa</em> and <em style="color:black;">L. saligna</em>), forming a complete spectrum of the lettuce germplasm for lettuce breeding. This dataset contains five files, containing the detailed outputs of the genome assembling, genome annotation, homology grouping and whole-genome screening.

本数据集支撑发表于《G3:Genes|Genomes|Genetics》期刊的研究论文，论文标题为《毛山莴苣（Lactuca virosa）基因组组装与分析：对生菜育种的启示》。毛山莴苣（Lactuca virosa，又名苦莴苣）隶属于显花植物最大的科——菊科（Asteraceae），是经济作物栽培生菜（Lactuca sativa L.）的野生近缘种，自然分布于欧亚大陆。尽管存在生殖隔离，但通过糙叶莴苣（L. serriola）作为桥梁亲本或胚胎拯救技术，仍可实现毛山莴苣与栽培生菜的杂交。毛山莴苣对多种害虫与病原物具有抗性，因此是生菜育种关键的遗传变异供体资源，尤其在抗茶藨子莴苣蚜（Nasonovia ribisnigri）方面价值显著。此外，通过渐渗育种，毛山莴苣的优良农艺性状（如发达根系、减轻的落叶情况）已被引入现代脆叶生菜品种中。迄今为止，关于毛山莴苣上述性状的遗传变异以及杂交育种的系谱历史仍不明晰。与生菜基因库中的其他物种相比，毛山莴苣的基因组规模显著更大，这可能会阻碍染色体配对。这种兼具育种应用价值与基础研究意义的特性，吸引了多领域不同专长的科研人员参与本项目。为获得高质量的毛山莴苣基因组序列，本研究采用了长读长（PacBio，20×覆盖度）与短读长（Illumina，70×覆盖度）测序混合数据，并结合Bionano与Hi-C技术进行基因组支架构建。最终组装得到的基因组包含5855个超级支架，N50长度为316.9 Mb。最终组装的基因组大小为3.45 Gb，BUSCO评估完整度达96%；共预测得到39887个基因模型，BUSCO评估完整度达90%。本研究获得的毛山莴苣参考基因组序列，为该物种的基因组与遗传变异研究提供了核心数据支撑。其可与已发布的另外两个莴苣属（Lactuca）基因组组装结果（栽培生菜L. sativa与细叶莴苣L. saligna）开展各类基因组比较分析，从而构建覆盖生菜种质资源的完整研究谱系，服务于生菜育种工作。本数据集包含5个文件，涵盖了基因组组装、基因组注释、同源基因聚类以及全基因组筛选的详细结果。