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.