Supplemental Files for genotyping the mitochondria and ITS rDNA locus in S. haemaotbium and S. bovis collected in Nigeria

This dataset contains chromatograms in .ab1 format for ITS1–5.8S–ITS2 amplicons generated from Schistosoma haematobium and S. bovis parasites, primarily collected in Nigeria. We used reference profiles representing canonical S. haematobium, S. bovis, and S. curassoni ITS genotypes to classify each individual. ITS fragments (~922 bp) were amplified from the same DNA aliquots used for whole-genome sequencing using primers ETTS1 and ETTS2, visualized on 1% agarose gels, purified with ExoSAP-IT™, and Sanger sequenced (forward and reverse) by Eurofins Genomics. Chromatograms were assembled and manually edited in BioEdit, and heterozygous peaks were called using the Indigo algorithm implemented in the Tracy web platform. The resulting forward and reverse AB1 files were used to assign ITS genotypes and to classify parasites into parental, hybrid, backcross/late-generation, and complex categories based on mitochondrial and ITS two-marker schemes.

In addition to the ITS chromatograms, we provide de novo mitochondrial genome assemblies for each sample with sufficient mitochondrial coverage in FASTA format, a trimmed multiple sequence alignment of these mitogenomes in FASTA format, and the corresponding maximum-likelihood phylogeny in Newick format with bootstrap support values. Briefly, mitochondrial reads were identified by mapping whole-genome data to a reference panel of schistosome mitochondrial genomes, and de novo assemblies were generated with get_organelle_from_reads and scaffolded against the reference panel. The largest contiguous mitochondrial scaffold per sample was aligned, low-confidence regions were trimmed using trimAl with an automated model, and a mitochondrial phylogeny was inferred and support estimated with RAxML-ng.