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）草稿基因组组装所用基因型的测序数据汇总
表S2：基于连锁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：基于k-mer分析估算的可可树基因型基因组特征
表S4：各可可树元组装的BUSCO完整度评分
表S5：可可树参考基因组Matina、Criollo以及新增元组装的基因组汇总统计量
表S6：用于基因组注释的混合RNA样本
表S7：用于克隆TcCSE（SCA-6_Chr6v1_17513）的引物及其酶切位点
表S8：游动孢子侵染过程中采集的LC-MS/MS数据对应的MS2碎裂模式注释结果
表S9：在各自群体分支统计量（Population Branch Statistic，PBS）分布中处于前1%且与差异表达基因重叠的基因
表S10：在各自群体分支统计量（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受棕榈疫霉（Phytophthora palmivora）侵染后差异表达的直系同源组
表S12：RNA-seq实验的元数据
表S13：各遗传组在病原体处理下的前1000个基因，按绝对对数倍变（|LFC|）排序
表S14：各遗传组在耐受/易感表型下的前1000个基因，按绝对对数倍变（|LFC|）排序
表S15：RNA-seq实验组织的代谢物提取元数据