Comparative genomics and transcriptomics of 4 Paragonimus species provide insights into lung fluke parasitism and pathogenesis

Rosa, Bruce A., Choi, Young-Jun, McNulty, Samantha N., Jung, Hyeim, Martin, John, Agatsuma, Takeshi, Sugiyama, Hiromu, Le, Thanh Hoa, Doanh, Pham Ngoc, Maleewong, Wanchai, Blair, David, Brindley, Paul J., Fischer, Peter, and Mitreva, Makedonka (2020) Comparative genomics and transcriptomics of 4 Paragonimus species provide insights into lung fluke parasitism and pathogenesis. GigaScience, 9 (7). giaa073.

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Background: Paragonimus spp. (lung flukes) are among the most injurious foodborne helminths, infecting ∼23 million people and subjecting ∼292 million to 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 owing to similar pulmonary symptoms, and accordingly, diagnostics are in demand.

Results: We assembled, annotated, and compared draft genomes of 4 prevalent and distinct Paragonimus species: Paragonimus miyazakii, Paragonimus westermani, Paragonimus kellicotti, and Paragonimus heterotremus. Genomes ranged from 697 to 923 Mb, included 12,072–12,853 genes, and were 71.6–90.1% complete according to BUSCO. Orthologous group analysis spanning 21 species (lung, liver, and blood flukes, additional platyhelminths, and hosts) provided insights into lung fluke biology. We identified 256 lung fluke–specific and conserved orthologous groups with consistent transcriptional adult-stage Paragonimus expression profiles and enriched for iron acquisition, immune modulation, and other parasite functions. Previously identified Paragonimus diagnostic antigens were matched to genes, providing an opportunity to optimize and ensure pan-Paragonimus reactivity for diagnostic assays.

Conclusions: This report provides advances in molecular understanding of Paragonimus and underpins future studies into the biology, evolution, and pathogenesis of Paragonimus and related foodborne flukes. We anticipate that these novel genomic and transcriptomic resources will be invaluable for future lung fluke research.

Item ID: 64729
Item Type: Article (Research - C1)
ISSN: 2047-217X
Keywords: lung flukes, Paragonimus, genomics, transcriptomics, diagnostics, paragonimiasis, infectious disease, trematodes
Copyright Information: © The Author(s) 2020. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Funders: National Human Genome Research Institute (NHGRI), National Institute of Allergy and Infectious Diseases (NIAID), National Institute of General Medical Sciences (NIGMS), Thailand Research Fund (TRF)
Projects and Grants: NHGRI award No. U54HG003079, NIAD grant no. AI081803, NIGMS grant no. GM097435, TRF grant no. DPG6280002
Date Deposited: 21 Oct 2020 08:26
FoR Codes: 31 BIOLOGICAL SCIENCES > 3105 Genetics > 310509 Genomics @ 50%
32 BIOMEDICAL AND CLINICAL SCIENCES > 3207 Medical microbiology > 320704 Medical parasitology @ 50%
SEO Codes: 92 HEALTH > 9204 Public Health (excl. Specific Population Health) > 920406 Food Safety @ 25%
92 HEALTH > 9204 Public Health (excl. Specific Population Health) > 920405 Environmental Health @ 25%
97 EXPANDING KNOWLEDGE > 970106 Expanding Knowledge in the Biological Sciences @ 50%
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