Assemblies_and_data.zip

All datasets used for the phylogenomics, Virulency factors, mitochondria metabolism, and LRT
assembly_and_annotations directory contains: full genome assembly of the C. proliferans (assembly.fasta); predicted proteins (predicted_proteins.aa); predicted coding DNA sequences (predicted_CDS.codingseq); files with the position of genes on the contains in gff (C_proliferans.gff) and gff3 (C_proliferans.gff3) formats; functional annotations of predicted genes (annotations.xlsx).
LRT director contains: an excel spreadsheet with the summary of the Likelihood ratio test (LRT_CHI-square-0.01-df1-alpha-6.635.xlsx).
mitochondrial_metabolism directory contains: subdirectory "initial_fasta" with all the candidate sequences from preliminary datasets; subdirectory "trees" with all final trees in newick format.
phylogenomics directory contains: archive file that contains everything for making a PhyloFisher database for all taxa used in this study (Crypto_PF_DB.tar.gz); alignment used for construction of the phylogenomic tree (CryptoConcat_178_genes.fasta), the partition file (partitions.txt), and the maximum likelihood tree (RAxML_bipartitions.CryptoConcat_178_genes_1000_PMSF_boots.tre); subdirectory "initial_fasta" with all the candidate sequences from preliminary datasets.
syntent directory contains: synetny files generated by the GENESPACE with the following columns: 1-8: annotation positions of the query genes columns 9-16: annotation positions of the target genes column 17: bit score from the blast file col 18 (sameOg): logical, query and target in same orthogroup col 19 (noAnchor): logical, should this hit never be an anchor col 20 (isAnchor): logical, is this hit a syntenic anchor col 21 (regID): character, large region ID of syntenic hits col 22 (blkID): character, blockID of syntenic hits.
virulency_factros directory contains: three subdirectories: “initial_fasta”, “aln”, and “trees” respectively. The “initial_fasta” directory contains all the candidate sequences from the preliminary datasets. The “aln” directory comprises of all the aligments used for the construction of the trees in newick format, which can be found in “trees” subdirectory.