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The complete mitogenome of the Asian lung fluke Paragonimus skrjabini miyazakii and its implications for the family Paragonimidae (Trematoda: Platyhelminthes)

Published online by Cambridge University Press:  23 August 2022

Thanh Hoa Le Open the ORCID record for Thanh Hoa Le [Opens in a new window] ,
Khue Thi Nguyen ,
Linh Thi Khanh Pham ,
Huong Thi Thanh Doan ,
Takeshi Agatsuma  and
David Blair Open the ORCID record for David Blair [Opens in a new window]
Thanh Hoa Le*
Affiliation:
Immunology Department, Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), 18. Hoang Quoc Viet Rd., Cau Giay, Hanoi, Vietnam Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), 18. Hoang Quoc Viet Rd., Cau Giay, Hanoi, Vietnam
Khue Thi Nguyen
Affiliation:
Immunology Department, Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), 18. Hoang Quoc Viet Rd., Cau Giay, Hanoi, Vietnam
Linh Thi Khanh Pham
Affiliation:
Immunology Department, Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), 18. Hoang Quoc Viet Rd., Cau Giay, Hanoi, Vietnam
Huong Thi Thanh Doan
Affiliation:
Immunology Department, Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), 18. Hoang Quoc Viet Rd., Cau Giay, Hanoi, Vietnam Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), 18. Hoang Quoc Viet Rd., Cau Giay, Hanoi, Vietnam
Takeshi Agatsuma
Affiliation:
Department of Environmental Health Sciences, Kochi Medical School, Kohasu, Oko-cho 185-1, Nankoku, Kochi, 783-8505, Japan
David Blair*
Affiliation:
College of Marine and Environmental Sciences, James Cook University, Townsville, Queensland 4811, Australia
*
Author for correspondence: Thanh Hoa Le, E-mail: imibtvn@gmail.com; David Blair, E-mail: davidblair49@gmail.com
Author for correspondence: Thanh Hoa Le, E-mail: imibtvn@gmail.com; David Blair, E-mail: davidblair49@gmail.com
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Abstract

The complete circular mitogenome of Paragonimus skrjabini miyazakii (Platyhelminthes: Paragonimidae) from Japan, obtained by PacBio long-read sequencing, was 17 591 bp and contained 12 protein-coding genes (PCGs), 2 mitoribosomal RNA and 22 transfer RNA genes. The atp8 gene was absent, and there was a 40 bp overlap between nad4L and nad4. The long non-coding region (4.3 kb) included distinct types of long and short repeat units. The pattern of base usage for PCGs and the mtDNA coding region overall in Asian and American Paragonimus species (P. s. miyazakii, P. heterotremus, P. ohirai and P. kellicotti) and the Indian form of P. westermani was T > G > A > C. On the other hand, East-Asian P. westermani used T > G > C > A. Five Asian and American Paragonimus species and P. westermani had TTT/Phe, TTG/Leu and GTT/Val as the most frequently used codons, whereas the least-used codons were different in each species and between regional forms of P. westermani. The phylogenetic tree reconstructed from a concatenated alignment of amino acids of 12 PCGs from 36 strains/26 species/5 families of trematodes confirmed that the Paragonimidae is monophyletic, with 100% nodal support. Paragonimus skrjabini miyazakii was resolved as a sister to P. heterotremus. The P. westermani clade was clearly separate from remaining congeners. The latter clade was comprised of 2 subclades, one of the East-Asian and the other of the Indian Type 1 samples. Additional mitogenomes in the Paragonimidae are needed for genomic characterization and are useful for diagnostics, identification and genetic/ phylogenetic/ epidemiological/ evolutionary studies of the Paragonimidae.

Keywords

MitogenomeParagonimidaeParagonimus skrjabini miyazakiiphylogenetic analysisrepeat unitsskewness valueTroglotremata
Type
Research Article
Information
Parasitology , Volume 149 , Issue 13 , November 2022 , pp. 1709 - 1719
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Copyright © The Author(s), 2022. Published by Cambridge University Press

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References

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