Additional file 1 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 1: Fig. S1. Quality of the sequenced PacBio HiFi reads of five Cladosporium fulvum isolates. Fig. S2. The genomes of five Cladosporium fulvum isolates have similar complements of predicted transposable elements (TEs). Fig. S3. The chromosomes of five Cladosporium fulvum isolates are heavily affected by Repeat-Induced Point (RIP) mutations. Fig. S4. Bimodal GC content distribution of five Cladosporium fulvum genomes. Fig. S5. Number of genes encoding carbohydrate-active enzymes (CAZymes) in five Cladosporium fulvum genomes. Fig. S6. Number of genes encoding proteases in five Cladosporium fulvum genomes. Fig. S7. Number of genes encoding cytochrome P450s, transporters, and key enzymes for secondary metabolite biosynthesis (SM) in five Cladosporium fulvum genomes. Fig. S8. Number of genes in five Cladosporium fulvum genomes assigned to different Gene Ontology (GO) terms and EuKaryotic Ortholog Group (KOG) categories. Fig. S9. Overall number of pairwise synteny blocks in pairwise alignments of five Cladosporium fulvum genomes. Fig. S10. Alignment dot plots showing pairwise syntenic regions among Cladosporium fulvum genomes. Fig. S11. Confirmation of large-scale structural variations in the Cladosporium fulvum genomes. Fig. S12. Three large-scale chromosomal structural variations were identified among the five isolates of Cladosporium fulvum. Fig. S13. Comparison of reciprocal translocation events in Cladosporium fulvum and the pine tree pathogen Dothistroma septosporum. Fig. S14. PacBio HiFi reads mapped to the Avr9 locus of Cladosporium fulvum support a non-reciprocal translocation. Fig. S15. The deletion of Avr4E in Cladosporium fulvum likely requires neighboring copies of a Tc1/mariner DNA transposon. Fig. S16. The deletion of Avr5 in Cladosporium fulvum likely requires neighboring copies of a LINE/Tad1 non-LTR retrotransposon. Fig. S17. Most long INDELs in the genome of Cladosporium fulvum are composed of repetitive DNA. Scatter plot showing 1226 INDELs as points. Fig. S18. Cases of tandem gene duplications in the genome of Cladosporium fulvum. Fig. S19. Matching dispensable chromosomes present in different isolates of Cladosporium fulvum exhibit high nucleotide identity. Fig. S20. The left end of the dispensable Chr15 of Cladosporium fulvum is composed of segments from core chromosomes. Fig. S21. Phylogeny of the sequenced Cladosporium fulvum isolates. Fig. S22. Dinucleotide bias in regions of high nucleotide diversity in the genome of Cladosporium fulvum. Fig. S23. Positive correlation between nucleotide diversity of transitions and of transversions in the genome of Cladosporium fulvum. Fig. S24. No differences of repeat family divergence in regions of high and low nucleotide diversity in the Cladosporium fulvum genome. Fig. S25. No differences in GC content of transposable elements copies within regions of low and high diversity of transitions in the genome of Cladosporium fulvum.