Supplementary files for the comparative analysis of five near-complete genomes of Cladosporium fulvum

Description of the files

expression_values

• gene_tpms.txt: 5-column table containing the expression values in transcripts per million (TPM) of genes from Cladosporium fulvum isolate Race 0WU. Columns 1 to 3 show the TPM values for genes using RNA seq data of C. fulvum Race 0WU-Solanum lycopersicum cv. Heinz interaction at 4, 8, and 12 dpi, respectively (NCBI accessions SRR1171035, SRR1171040, SRR1171043). The last column shows the TPM values for genes using RNA seq data of C. fulvum Race 0WU grown in vitro in potato-dextrose broth (SRR1171044).

nucleotide_diversity

All three files are 3-column tables, each line is a 20 kb window in the genome of C. fulvum Race 0WU. The last column indicates the nucleotide diversity per site within the 20 kb window calculated based on SNPs from whole-genome alignments using the genomes of C. fulvum Race 5, Race 4, Race 2 4 5 9 11 IPO, and Race 2 5 9 11 mapped to the genome of Race 0WU.

• merged_syri_SNPs_gt_dedup_pi.txt: 3-column table showing nucleotide diversity per site within 20 kb windows. All SNPs were considered.
• merged_syri_SNPs_gt_dedup_pi_ts.txt: 3-column table showing nucleotide diversity per site within 20 kb windows. Only transition substitutions were considered, i.e., (A<->G or C<->T).
• merged_syri_SNPs_gt_dedup_pi_tv.txt: 3-column table showing nucleotide diversity per site within 20 kb windows. Only transversion substitutions were considered, i.e., (A<->C, A<->T, C<->G, or G<->T).

orthogroups

• N0.tsv: 8-column table showing the hierarchical orthogroups (HOGs) generated with OrthoFinder for genes from C. fulvum isolates Race 0WU (CLAFUR0), Race 4 (CLAFUR4), Race 5 (CLAFUR5), Race 2 4 5 9 11 IPO (CLAFUW4), and Race 2 5 9 11 (CLAFUW7).

repeat_files

• XX-families.fa: fasta files containing the repetitive DNA libraries of C. fulvum Race 0WU (R0), Race 4 (R4), Race 5 (R5), 2 4 5 9 11 IPO (W4), and 2 5 9 11 (W7). These libraries were produced with RepeatModeler v2
• XX.fasta.out.gff: GFF files generated with RepeatMasker using the custom repetitive DNA libraries of C. fulvum Race 0WU (R0), Race 4 (R4), Race 5 (R5), 2 4 5 9 11 IPO (W4), and 2 5 9 11 (W7).

RIP

• XX_RIPped_windows.txt: 7-column tables generated with RIPPer. These tables shows values of the RIP indices product substrate, and composite, as well as the GC content of 1 kb windows in the genomes of C. fulvum Race 0WU (R0), Race 4 (R4), Race 5 (R5), 2 4 5 9 11 IPO (W4), and 2 5 9 11 (W7).

vcf_files

• XX_syri_SNPs.vcf: VCF files containing the SNPs obtained with SyRI by aligning the genomes of C. fulvum isolates Race 4 (R4), Race 5 (R5), 2 4 5 9 11 IPO (W4), 2 5 9 11 (W7) against Race 0WU (R0) as reference.
• merged_syri_SNPs.vcf: VCF file of all SNPs merged with bcftools. This VCF file hsa the SNP genotypes of C. fulvum isolates Race 4 (R4), Race 5 (R5), 2 4 5 9 11 IPO (W4), 2 5 9 11 (W7) using Race 0WU (R0) as reference.
• merged_survivor_variants.vcf: VCF file containing the structural variants merged with SURVIVOR.
• R0_XX_variants.vcf: VCF files containing the structural variants obtained with SVIM based on whole-genome alignments of isolates Race 4 (R4), Race 5 (R5), 2 4 5 9 11 IPO (W4), 2 5 9 11 (W7) against Race 0WU (R0) as reference.