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.

本数据集为发表于<strong>G3:Genes|Genomes|Genetics</strong>期刊的<em>Lactuca virosa</em>基因组组装论文提供支持，该论文标题为：<em>Lactuca virosa</em>基因组组装与分析：对莴苣育种的启示。<em style="color:black;">Lactuca virosa</em>（毒莴苣，俗称苦莴苣）隶属于菊科（Asteraceae）——全球最大的开花植物科，是广泛分布于欧亚大陆的经济作物莴苣（<em style="color:black;">Lactuca sativa</em> L.）的野生近缘种。尽管存在杂交障碍（hybrid barrier），<em style="color:black;">L. virosa</em>仍可通过<em style="color:black;">L. serriola</em>作为桥梁或胚胎拯救技术（embryo rescue techniques）与莴苣杂交。<em style="color:black;">L. virosa</em>对多种病虫害具有抗性，因此是莴苣育种中遗传变异的重要供体，尤其在抗醋栗莴苣蚜（<em style="color:black;">Nasonovia ribisnigri</em>）方面。此外，通过渗入育种（introgression breeding），<em style="color:black;">L. virosa</em>可为现代结球莴苣品种提供健壮根系、减少落叶等优良农艺性状。迄今为止，<em style="color:black;">L. virosa</em>上述性状的遗传变异及杂交系谱历史仍主要未知。与莴苣基因库中的其他物种相比，<em style="color:black;">L. virosa</em>的基因组规模显著更大，可能阻碍染色体配对（chromosome pairing）。育种应用与基础研究的双重价值吸引了不同领域具有多元专业背景的合作者参与本项目。为获得<em style="color:black;">L. virosa</em>的高质量基因组序列，我们采用了长读长（Pacbio 20x）与短读长（Illumina 70x）测序的混合数据集，并结合Bionano和Hi-C技术的支架构建（scaffolding）方法。最终组装得到5855个超级支架，N50为316.9 Mb。最终组装基因组大小为3.45 Gb（BUSCO完整性96%），预测基因模型39887个（BUSCO完整性90%）。本研究获得的<em style="color:black;">L. virosa</em>参考基因组序列为该物种的基因组及遗传变异研究提供了基础。该基因组有助于与已发表的另外两个<em style="color:black;">Lactuca</em>属基因组组装体（<em style="color:black;">L. sativa</em>和<em style="color:black;">L. saligna</em>）进行多维度基因组比较，构建完整的莴苣种质资源谱，服务于莴苣育种。本数据集包含5个文件，涵盖基因组组装、基因组注释、同源分组（homology grouping）及全基因组筛选（whole-genome screening）的详细结果。