Additional file 1 of A combination of conserved and diverged responses underlies Theobroma cacao’s defense response to Phytophthora palmivora

Additional file 1: Table S1. Summary of sequence data for Theobroma cacao genotypes used in the draft assemblies for Theobroma cacao genotypes. Table S2. The length-weighted mean molecule length for Supernova genotype assemblies at different read depths estimated from linked reads. Table S3. Estimated k-mer based genome characteristics for Theobroma cacao genotypes Table S4. BUSCO completeness scores for each cacao meta-assembly. Table S5. Genome summary statistics for the T. cacao reference genomes, Matina and Criollo, and new meta-assemblies. Table S6. RNA samples pooled for genome annotation. Table S7. Primers used to clone TcCSE (SCA-6_Chr6v1_17513) and their cut sites. Table S8. Annotated MS2 fragmentation patterns from LC-MS/MS data collected during zoospore infection. Table S9. Genes in the top 1% of their respective PBS distributions that also overlap a differentially expressed gene. Table S10. Genes in the top 1% of their respective population branch statistic (PBS) distributions. Table S11. Orthogroups that are differentially expressed in response to P. palmivora challenge in both wild Theobroma spp. and Theobroma cacao. Table S12. Meta-data for the RNA-seq experiment. Table S13. Top 1000 genes from each genetic group in response to pathogen treatment, ranked by absolute log fold change (|LFC|). Table S14. Top 1000 genes from each genetic group in response tolerance/susceptibility phenotype, ranked by absolute log fold change (|LFC|). Table S15. Meta-data for metabolite extraction from the RNA-seq experimental tissues.

附加文件1：
表S1。可可树（Theobroma cacao）草图组装所用基因型的测序数据汇总
表S2。基于链接读长（linked reads）估算的不同测序深度下Supernova基因型组装的长度加权平均分子长度
表S3。可可树（Theobroma cacao）基因型基于k-mer的基因组特征估算结果
表S4。各可可树（Theobroma cacao）整合组装的单拷贝通用直系同源基因基准评估（BUSCO）完整性评分
表S5。可可树参考基因组Matina、Criollo以及新构建的整合组装的基因组统计汇总
表S6。用于基因组注释的混合RNA样本汇总
表S7。用于克隆TcCSE（SCA-6_Chr6v1_17513）的引物及其酶切位点
表S8。游动孢子侵染实验中获取的液相色谱-串联质谱（LC-MS/MS）数据对应的MS2片段化模式注释结果
表S9。在各自群体分支统计（PBS）分布中处于前1%且与差异表达基因存在重叠的基因
表S10。在各自群体分支统计（PBS）分布中处于前1%的基因
表S11。在野生可可属物种及可可树（Theobroma cacao）中响应棕榈疫霉（P. palmivora）侵染的差异表达直系同源基因簇
表S12。RNA测序实验的元数据
表S13。各遗传类群中响应病原菌处理的前1000个基因，按绝对对数倍变化量（|LFC|）排序
表S14。各遗传类群中响应耐受性/感病性表型的前1000个基因，按绝对对数倍变化量（|LFC|）排序
表S15。取自RNA测序实验组织的代谢物提取元数据