Additional file 1 of Comparative genomic and transcriptomic analyses of trans-kingdom pathogen Fusarium solani species complex reveal degrees of compartmentalization

Additional file 1: Table S1. Read summary of genome assemblies from each sequencing platform. Table S2. Fusarium genomes and an outrgroup genome used in the phylogenomic analysis and comparative studies. Table S3. Scaffold assembly completeness. Table S4. FSSC genome assemblies used to compare N90. Table S5. Number of genes with predicted signal peptide and effector using SignalP and EffectorP, respectively. Table S6. Number of genes with predicted carbohydrate-active enzymes (CAZymes) and its categories using dbCAN2. Table S7. Number of secondary metabolites biosynthetic gene cluster detected via antiSMASH. Table S8. Type and presence of secondary metabolite products in each FSSC genomes predicted via antiSMASH. Table S9. Fusarium solani species complex (FSSC) sequences used in multi-locus sequence typing (MLST) phylogenetic tree in Fig. S2. Table S10. Structural features of FSSC genome assemblies. Table S11. Gene number and proportion of effector, carbohydrate active enzymes and secondary metabolite gene cluster in each FSSC chromosome. Table S12. Average number of genes predicted to encode for effector, carbohydrate-active enzymes (CAZYmes) and secondary metabolite biosynthetic gene clusters (SMBGCs) of FSSC genomes by chromosome types. Table S13. Multiple mean comparisons of methylation levels among the chromosome type and genome features in F. falciforme Fu3. Table S14. Top 50 enriched biological processes of FSSC pathogen F. falciforme Fu3 and F. keratoplasticum Fu6 during P. sinensis host infection. Table S15. Subset of differentially expressed and upregulated genes of F. falciforme Fu3 during P. sinensis host infection previously known to associate with plant host infection. Table S16. Subset of differentially expressed and upregulated genes of F. keratoplasticum Fu6 during P. sinensis host infection previously known to associate with plant host infection. Table S17. Selected enriched biological processes of co-upregulated genes of F. falciforme Fu3 and F. keratoplasticum Fu6 during P. sinensis host infection. Table S18. Top 50 differentially expressed genes of F. falciforme Fu3 which were co-upregulated with F. keratoplasticum Fu6 (Table S19) during P. sinensis host infection. Table S19. Top 50 differentially expressed genes of F. keratoplasticum Fu6 which were co-upregulated with F. falciforme Fu3 (Table S18) during P. sinensis host infection. Table S20. Selected enriched biological processes of co-downregulated genes of F. falciforme Fu3 and F. keratoplasticum Fu6 during P. sinensis host infection. Table S21. Top 50 differentially expressed genes of F. falciforme Fu3 which were unique to F. keratoplasticum Fu6 (by orthogroup) during P. sinensis host infection. Table S22. Top 50 differentially expressed genes of F. keratoplasticum Fu6 which were unique to F. falciforme Fu3 (by orthogroup) during P. sinensis host infection. Table S23. RNA-seq and read statistics of FSSC-animal infection experiment. Table S24. Upregulated biological processes of P. sinensis host infected by pathogen F. falciforme and F. keratoplasticum. Table S25. Sequencing information of gDNA and RNA for genome assembly and gene annotation. Table S26. All sequenced samples and metadata for inoculation experiment.