Cross-subgenus hybridization between and informs on parasite genomic compatibility and transcriptomic adaptation.

parasites can enter a cryptic sexual reproductive cycle generating hybrid genotypes that can lead to unpredictable clinical outcomes and transmission cycles. Despite the importance of hybrids in epidemiology, the mechanisms involved in their formation - including the impact of parental genetic distance - remain poorly understood. We report the generation of a hybrid between and two species from sister phylogenetic clades circulating across Southern Italy, providing evidence of genomic compatibility. Whole-Genome Sequencing indicates that, while the hybrid is largely tetraploid, its genome is not just the sum of its parental content. RNA-seq analysis of the hybrid transcriptome uncovers significant differences in the abundance of orthologous transcripts expressed from both parental genomes, driven by either parent-specific gene copy number variations or differential mRNA turnover. These results demonstrate that, beyond genomic restructuring, post-transcriptional regulation may serve as an additional mechanism shaping viable hybrid phenotypes, potentially enhancing parasite adaptability and fitness.