Supplementary data for the analysis of five near-complete genome assemblies of the tomato pathogen Cladosporium fulvum
Creators: name: Zaccaron, Alex
name: Stergiopoulos, Ioannis
Publisher: name: Zenodo
Year: 2023

description: This repository has supplementary files associated with the comparative analyses of five near-complete genome assemblies of the tomato pathogen <em>Cladosporium fulvum</em>. Other 11 isolates were also sequenced and included in some of the analyses. In the files, isolate names are often replaced with their IDs, as shown in the table below <strong>Isolate name</strong> <strong>ID</strong> Race 5 R5 0WU R0 Race 4 R4 2 4 5 9 11 IPO W4 2 4 9 11 W7 IPO 2 4 5 9 (60787) W8 IPO 2 4 8 9 11 Polen W9 2 5 9 W10 IPO 249 France W12 Can 38 W13 IMI Argent 358077 W14 Turk 1a W15 18-A6 W18 2.5 W20 CF-Nangol CF-Nangol CF301 CF301 <strong>nucleotide_diversity</strong>: This folder has files that show the calculate nucleotide diversity of genes and windows across the genome Cfulvum_0WU_genes_pi.txt: a two-column file with the gene ID (locus tag) and its estimate nucleotide diversity per site (pi) of genes from isolate 0WU based on SNPs identified with the 16 isolates. merged_syri_SNPs_gt_dedup_pi_ts.txt: a four-column table with sliding window coordinates (window size = 20 kb) and the estimate nucleotide diversity per site (pi) within each window. Only transition substitutions were considered to calculate pi. Values of pi were calculated based on whole-genome alignments of the near-complete genomes of C. fulvum isolates Race 5, 0WU, Race 4, 2 4 5 9 11 IPO, and 2 4 9 11, using the genome of isolate 0WU as reference. merged_syri_SNPs_gt_dedup_pi_tv.txt: a four-column table with sliding window coordinates (window size = 20 kb) and the estimate nucleotide diversity per site (pi) within each window. Only transversion substitutions were considered to calculate pi. Values of pi were calculated based on whole-genome alignments of the near-complete genomes of C. fulvum isolates Race 5, 0WU, Race 4, 2 4 5 9 11 IPO, and 2 4 9 11, using the genome of isolate 0WU as reference. <strong>orthologs</strong>: This folder has the orthologs genes N0.tsv: output of OrthoFinder with genes from isolate Race 5, 0WU, Race 4, 2 4 5 9 11 IPO, and 2 5 9 11 organized into hierarchical orthogroups. <strong>phylogeny</strong>: This folder has the phylogenetic tree RAxML_bestTree.snptree: SNP-based phylogenetic tree of 16 C. fulvum isolates constructed with 40,378 SNPs with RAxML. <strong>polymorphisms</strong>: This folder has the VCF files of polymorphisms identified R4_syri.vcf.gz: a VCF file with polymorphisms identified with SyRI after whole-genome alignment performed with NUCmer between isolate Race 4 (query) and 0WU (reference). R5_syri.vcf.gz: a VCF file with polymorphisms identified with SyRI after whole-genome alignment performed with NUCmer between isolate Race 5 (query) and 0WU (reference). W4_syri.vcf.gz: a VCF file with polymorphisms identified with SyRI after whole-genome alignment performed with NUCmer between isolate 2 4 5 9 11 IPO (query) and 0WU (reference). W7_syri.vcf.gz: a VCF file with polymorphisms identified with SyRI after whole-genome alignment performed with NUCmer between isolate 2 4 9 11 (query) and 0WU (reference). variants_filt_INDELs.recode.ann.vcf.gz: A VCF file with short INDELs identified after mapping whole-genome sequencing reads from 15 isolates to the reference genome of C. fulvum 0WU. INDELs are already filtered by quality (Q &gt; 30) and their impact annotated with SnpEff. variants_filt_SNPs.recode.ann.vcf.gz: A VCF file with SNPs identified after mapping whole-genome sequencing reads from 15 isolates to the reference genome of C. fulvum 0WU. SNPs are already filtered by quality (Q &gt; 30) and their impact annotated with SnpEff. <strong>repeats</strong>: This folder has the repetitive DNA annotation (GFF) and repetitive DNA libraries. GCA_020509005.2_Cfulv_R5_v5_genomic.fna.out.gff: a GFF file with the repetitive DNA annotation of isolate Race 5 produced by RepatMasker using custom de novo repeat library obtained with RepeatModeler v2. PB655_01_Race0.bp.p_ctg_sorted_edited.fasta.out.gff: a GFF file with the repetitive DNA annotation of isolate 0WU produced by RepatMasker using custom de novo repeat library obtained with RepeatModeler v2. PB655_02_Race4.bp.p_ctg_sorted_edited.fasta.out.gff: a GFF file with the repetitive DNA annotation of isolate Race 4 produced by RepatMasker using custom de novo repeat library obtained with RepeatModeler v2. PB655_03_W4_chr2_8_fixed_edited.fasta.out.gff: a GFF file with the repetitive DNA annotation of isolate 2 4 5 9 11 IPO produced by RepatMasker using custom de novo repeat library obtained with RepeatModeler v2. PB655_04_W7.bp.p_ctg_sorted_edited.fasta.out.gff: a GFF file with the repetitive DNA annotation of isolate 2 4 9 11 produced by RepatMasker using custom de novo repeat library obtained with RepeatModeler v2. R0-families.fa: fasta file with the repetitive DNA library of isolate 0WU. R4-families.fa: fasta file with the repetitive DNA library of isolate Race 4. R5-families.fa: fasta file with the repetitive DNA library of isolate Race 5. W4-families.fa: fasta file with the repetitive DNA library of isolate 2 4 5 9 11 IPO. W7-families.fa: fasta file with the repetitive DNA library of isolate 2 4 9 11.