Abstract
The complete mitochondrial genome (mitogenome or mtDNA) of the trematode Echinostoma malayanum Leiper, 1911 was fully determined and annotated. The circular mtDNA molecule comprised 12 protein-coding genes (PCGs) (cox1 − 3, cob, nad1 − 6, nad4L, atp6), two mitoribosomal RNAs (MRGs) (16S or rrnL and 12S or rrnS), and 22 transfer RNAs (tRNAs or trn), and a non-coding region (NCR) rich in long and short tandem repeats (5.5 LRUs/336 bp/each and 7.5 SRUs/207 bp/each). The atp8 gene is absent and the 3′ end of nad4L overlaps the 5′ end of nad4 by 40 bp. Special DHU-arm missing tRNAs for Serine were found for both tRNASer1(AGN) and tRNASer2(UCN). Codons of TTT (for phenylalanine), TTG (for leucine), and GTT (for valine) were the most, and CGC (for Arginine) was the least frequently used. A similar usage pattern was seen in base composition, AT and GC skewness for PCGs, MRGs, and mtDNA* (coding cox3 to nad5) in E. malayanum and Echinostomatidae. The nucleotide use is characterized by (T > G > A > C) for PCGs/mtDNA*, and by (T > G ≈ A > C) for MRGs. E. malayanum exhibited the lowest genetic distance (0.53%) to Artyfechinostomum sufrartyfex, relatively high to the Echinostoma congeners (13.20–13.99%), higher to Hypoderaeum conoideum (16.18%), and the highest to interfamilial Echinochasmidae (26.62%); Cyclocoelidae (30.24%); and Himasthlidae (25.36%). Topology indicated the monophyletic position between E. malayanum/A. sufrartyfex and the group of Echinostoma caproni, Echinostoma paraensei, Echinostoma miyagawai, and Echinostoma revolutum, rendering Hypoderaeum conoideum and unidentified Echinostoma species paraphyletic. The strictly closed genomic/taxonomic/phylogenetic features (including base composition, skewness, codon usage/bias, genetic distance, and topo-position) reinforced Echinostoma malayanum to retake its generic validity within the Artyfechinostomum genus.
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We express our thanks to colleagues and technicians for contribution to our laboratory work.
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This research is funded by Vietnam National Foundation for Science and Technology Development (NAFOSTED) under grant number 108.02–2020.07 (PI: Thanh Hoa Le).
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Conceptualization: Thanh Hoa Le. Methodology: Linh Thi Khanh Pham, Thanh Hoa Le. Formal analysis and investigation: Linh Thi Khanh Pham, Thanh Hoa Le, Weerachai Saijuntha. Writing—original draft preparation: Linh Thi Khanh Pham, Thanh Hoa Le. Writing — review and editing: Thanh Hoa Le, Scott P. Lawton. Funding acquisition: Thanh Hoa Le. Resources: Linh Thi Khanh Pham; Weerachai Saijuntha. Supervision: Thanh Hoa Le, Scott P. Lawton, Weerachai Saijuntha. This study represents a part of the biological doctoral dissertation of Linh Thi Khanh Pham at the University of Science and Technology of Hanoi. All authors read and approved the final manuscript.
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Figure S1.
An Echinostoma malayanum adult worm recovered from the intestines of experimental hamsters fed on cysts containing metacercariae collected from the freshwater snail Indoplanorbis exustus (stained sample). The worm has the shape of elongated, bluntly rounded ends, a horseshoe-shaped collar with collar spines, and branched testes arranged high in the posterior half. The globular ovary is anterior to the testes. (PPTX 1512 KB)
Figure S2.
Schematic drawings of predicted structure models of 22 transfer RNAs in the mitogenome of Echinostoma malayanum. Each tRNA gene (here abbreviated as trn) is named according to the one-letter amino acid abbreviation, with the exception of those specifying Serine, tRNASer1(AGN) and in tRNASer2(UCN), where DHU-arms are missing, instead, replaced by a loop. (PPT 205 KB)
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Pham, L.T.K., Saijuntha, W., Lawton, S.P. et al. Mitophylogenomics of the zoonotic fluke Echinostoma malayanum confirms it as a member of the genus Artyfechinostomum Lane, 1915 and illustrates the complexity of Echinostomatidae systematics. Parasitol Res 121, 899–913 (2022). https://doi.org/10.1007/s00436-022-07449-z
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DOI: https://doi.org/10.1007/s00436-022-07449-z