Supporting data for "Comparative genomics and transcriptomics of four Paragonimus species provide insights into lung fluke parasitism and pathogenesis"

<i>Paragonimus spp.</i> (lung flukes) are among the most injurious food-borne helminths, infecting ~23 million people, (~293 million with infection risk). Paragonimiasis is acquired from infected undercooked crustaceans and primarily affects the lungs, but often causes lesions elsewhere including the brain. The disease is easily mistaken for tuberculosis due to similar pulmonary symptoms, and accordingly, diagnostics are in demand.<br> We assembled, annotated, and compared draft genomes of four prevalent and distinct Paragonimus species: <i>P. miyazakii</i> , <i>P. westermani</i> , <i>P. kellicotti</i> and <i>P. heterotremus</i>. Genomes ranged from 697 to 923 Mb, included 12,072 to 12,853 genes, and were 71.6% to 90.1% complete according to BUSCO. Orthologous group (OG) analysis spanning 21 species (lung, liver and blood flukes, additional platyhelminths and hosts) provided insights into lung fluke biology, including identifying 256 lung fluke-specific and conserved OGs enriched for iron acquisition, immune modulation, and other parasite functions. Transcriptome analysis identified consistent adult-stage <i>Paragonimus</i> expression profiles, and previously identified <i>Paragonimus</i> diagnostic antigens were matched to genes, providing an opportunity to optimize and ensure pan-<i>Paragonimus</i>-reactivity for diagnostic assays.<br>This report provides advances in molecular understanding of <i>Paragonimus</i> and underpins future studies into the biology, evolution and pathogenesis of <i>Paragonimus</i> and related food-borne flukes. We anticipate that these novel genomic and transcriptomic resources will be invaluable for future lung fluke research.