Additional file 2 of Analysis of five near-complete genome assemblies of the tomato pathogen Cladosporium fulvum uncovers additional accessory chromosomes and structural variations induced by transposable elements effecting the loss of avirulence genes

Additional file 2: Table S1. Cladosporium fulvum isolates for which near-complete genome assemblies were obtained using PacBio HiFi sequencing technology. Table S2. Comparison of the assembled chromosomes of five Cladosporium fulvum isolates. Table S3. Summary of estimated abundance of transposable elements in the genomes of five Cladosporium fulvum isolates. Table S4. Summary of regions of the five Cladosporium fulvum genomes affected by Repeat-Induced Point (RIP) mutations. Table S5. Update of the gene annotations of Cladosporium fulvum isolate Race 5. Table S6. Summary of genes from different functional categories and select sub-categories in five Cladosporium fulvum genomes. Table S7. Genes encoding carbohydrate-active enzymes (CAZymes) in five Cladosporium fulvum genomes. Table S8. Genes encoding proteases in five Cladosporium fulvum genomes. Table S9. Genes encoding cytochromes P450 in five Cladosporium fulvum genomes. Table S10. Genes encoding ABC and MFS transporters in five Cladosporium fulvum genomes. Table S11. Genes encoding key secondary metabolite enzymes in five Cladosporium fulvum genomes. Table S12. Genes encoding secreted proteins in Cladosporium fulvum genomes. Table S13. Genes encoding candidate effector proteins in five Cladosporium fulvum genomes. Table S14. Number of genes in five Cladosporium fulvum genomes assigned to different Gene Ontology (GO) terms and EuKaryotic Ortholog Group (KOG) categories. Table S15. Accessory genes from five Cladosporium fulvum genomes. Table S16. Summary of pairwise synteny blocks in pairwise alignments of five Cladosporium fulvum genomes. Table S17. Number and type of structural variations (SVs) identified in four Cladosporium fulvum genomes. Table S18. Structural variations (INDELs) affecting genes in the genome of Cladosporium fulvum. Table S19. Homologs and expression of predicted genes from the dispensable chromosomes Chr14 and Chr15 of Cladosporium fulvum.