Data underlying the publication: Lactuca super-pangenome reduces bias towards reference genes in lettuce research

Supplementary data belonging to "<em>Lactuca</em> super-pangenome reduces bias towards reference genes in lettuce research". In order to get an overview of the gene content of the genus <em>Lactuca</em>, we used WGS data of 474 accessions beloning to <em>L. sativa</em>, <em>L. serriola</em>, <em>L. saligna</em> and <em>L. virosa</em> for the construction of a linear pangenome per species. This linear pangenome was built using the assemble-and-iteratively-add approach. Once constructed, presence-absence variation (PAV) and copy-number variation (CNV) were calculated from the WGS data on the linear pangenomes. The PAV data was integrated across species into a <em>Lactuca</em> wide table that contains the variation for each of the 474 accessions for all genes in the super-pangenome. This super-pangenome resource was then used for functional characterisation of the core and variable genes, and a phylogeny of all accessions. Finally, we used the <em>L. sativa</em> PAV data to show its complementary and benefits in GWAS over SNPs. All data underlying these analyses is bundled together in one tarball including README.

本数据为《<em>Lactuca</em>超级泛基因组降低莴苣研究中对参考基因的偏倚》一文的补充数据集。为全面解析莴苣属（*Lactuca*）的基因组成，我们选取了分别隶属于栽培莴苣（*L. sativa*）、野莴苣（*L. serriola*）、柳枝莴苣（*L. saligna*）与毒莴苣（*L. virosa*）的474份种质材料的全基因组测序（Whole Genome Sequencing, WGS）数据，用于构建各物种的线性泛基因组。该线性泛基因组采用组装-迭代添加法完成构建。构建完成后，基于线性泛基因组，我们从WGS数据中计算得到存在/缺失变异（Presence-Absence Variation, PAV）与拷贝数变异（Copy Number Variation, CNV）。随后将跨物种的PAV数据整合为莴苣属全域表格，该表格涵盖超级泛基因组中所有基因在474份种质材料中的变异信息。依托该超级泛基因组资源，我们对核心基因与可变基因开展了功能注释，并构建了所有种质材料的系统发育树。最后，我们利用栽培莴苣（*L. sativa*）的PAV数据，验证了其相较于单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）在全基因组关联分析（Genome-Wide Association Study, GWAS）中的互补优势与应用价值。本研究所有分析所依托的原始数据均打包为一个包含说明文档（README）的tar压缩包。