Processed comparative transcriptomic, functional annotation, orthology and transcriptome-derived SNP data for Philasterides dicentrarchi isolates B1, C1 and I1

This dataset contains processed data and analysis outputs from a comparative transcriptomic study of three isolates of the scuticociliate parasite Philasterides dicentrarchi: B1, C1 and I1. The deposited material includes: • de novo Trinity transcriptome assemblies;• representative coding sequences and corresponding protein sequences;• protein sequences translated using the ciliate nuclear genetic code (NCBI translation table 6);• functional annotation and KEGG/Kofam-derived comparative tables;• definitive OrthoFinder orthology results;• transcriptome-derived SNP calls and supporting quality-control data;• representative-locus sequence alignments;• source data and scripts used to generate the deposited results. The representative dataset comprises 63,765 coding sequences and 63,765 corresponding proteins: 21,269 from isolate B1, 21,744 from isolate C1 and 20,752 from isolate I1. Each representative coding sequence was validated by translation using NCBI genetic code 6 and exact comparison with its corresponding definitive protein sequence. The definitive orthology analysis identified 19,402 orthogroups. A total of 56,681 proteins were assigned to orthogroups, corresponding to 88.9% of the representative protein dataset. The analysis identified 14,954 orthogroups shared by the three isolates, including 13,280 single-copy core orthogroups, and 85 isolate-specific orthogroups. Transcriptome-derived sequence variants were identified by mapping RNA-seq reads from isolates B1, C1 and I1 against the cleaned I1 genome assembly. These variants represent variation detected within expressed and callable regions and should not be interpreted as a complete survey of whole-genome or population-level genetic diversity. The representative locus analysed in detail corresponds to contig k141_48303 and orthogroup OG0011550. Three B1-specific substitutions were identified at positions 529, 533 and 654. The substitutions at positions 529 and 533 were synonymous, whereas the substitution at position 654 resulted in a predicted phenylalanine-to-tyrosine amino-acid change. Raw RNA-seq reads are deposited separately in the NCBI Sequence Read Archive under BioProject accession PRJNA1506660 and are therefore not duplicated in this Zenodo dataset.