Mitochondrial genome refinement and comparative phylogenetics of Parastrongyloides trichosuri (KNP strain; Nematoda: Strongyloididae) from South Africa

Whole-genome Illumina paired-end reads (ERS056619; 2x100 bp) of Parastrongyloides trichosuri were downloaded from the SRA. Reads were quality-trimmed with Trimmomatic v0.39 using a Phred score cutoff of 33. De novo assembly was performed with GetOrganelle toolkit v1.7.7.1, employing a customized seed/label databases of Nematoda RefSeq mitogenomes (Taxonomy ID: 6231). The resulting assembly was confirmed in Bandage v0.8.1. Annotation was generated by MITOS2 (genetic code 5, Invertebrate Mitochondrial) and manually curated. tRNA-Glu and atp6 genes not detected by MITOS2 were recovered through BLAST searches against Rfam v15 (Strongyloididae sequences). Furthermore, cox3 and nad3 were manually annotated based on open reading frame (ORF) completeness and validated through detailed analysis of transmembrane topology. Gene order, protein-coding ORFs, and tRNA annotations were cross-validated against related Strongyloididae mitogenomes. Tandem repeats in the non-coding region were identified using Tandem Repeats Finder v4.09.1. The complete mitochondrial genome of P. trichosuri is 13,809 bp in length and has been deposited in the Zenodo repository (DOI: 10.5281/zenodo.17350726).