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Characterization of complete mitochondrial genome and ribosomal operon for Carassotrema koreanum Park, 1938 (Digenea: Haploporidae) by means of next-generation sequencing data

Published online by Cambridge University Press:  27 July 2022

Y.I. Ivashko ,
A.A. Semenchenko ,
D.A. Solodovnik  and
D.M. Atopkin Open the ORCID record for D.M. Atopkin [Opens in a new window]
Y.I. Ivashko
Affiliation:
Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the RAS, Vladivostok, Russia
A.A. Semenchenko
Affiliation:
Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the RAS, Vladivostok, Russia
D.A. Solodovnik
Affiliation:
Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the RAS, Vladivostok, Russia
D.M. Atopkin*
Affiliation:
Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the RAS, Vladivostok, Russia Department of Cell Biology and Genetics, Far Eastern Federal University, Vladivostok, Russia
*
Author for correspondence: D.M. Atopkin, E-mail: atop82@gmail.com
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Abstract

We obtained new data on the complete mitochondrial DNA (mtDNA) and the ribosomal operon of the trematode Carassotrema koreanum (Digenea: Haploporata: Haploporidae), an intestinal parasite of Carassius auratus, using next-generation sequencing. The mtDNA of C. koreanum contained 13,965 bp, including 12 protein-coding genes, two ribosomal genes, 22 transport RNA (tRNA) genes and a non-coding region. The ribosomal operon of C. koreanum was 10,644 bp in length, including ETS1 (1449 bp), 18S ribosomal RNA (rRNA) gene (1988 bp), ITS1 ribosomal DNA (rDNA) (558 bp), 5.8S rRNA gene (157 bp), ITS2 rDNA (274 bp), 28S rRNA gene (4152 bp) and ETS2 (2066 bp). Phylogenetic analysis based on mtDNA protein-coding regions showed that C. koreanum was closely related to Parasaccocoelium mugili, a species from the same suborder Haploporata. Bayesian phylogenetic tree topology was the most reliable and confirmed the validity of the Haploporata. The results of sequence cluster analysis based on codon usage bias demonstrated some agreement with the results of the phylogenetic analysis. In particular, Schistosoma spp. were differentiated from the other members of Digenea and the members of Pronocephalata were localized within the same cluster. Carassotrema koreanum and P. mugili fell within different clusters. The grouping of C. koreanum and P. mugili within the same cluster was obtained on the basis of frequencies of 13 specified codons, of which three codon pairs were degenerate. A similarity was found between two haploporid species and two Dicrocoelium spp. in the presence of TTG start codon of the mitochondrial nad5 gene. Our results confirmed the taxonomical status of the Haploporata identified in the previous studies and revealed some characteristic features of the codon usage in its representatives.

Keywords

CarassotremaHaploporidaemitochondrial DNAWaretrematinae
Type
Research Paper
Information
Journal of Helminthology , Volume 96 , 2022 , e54
Copyright
Copyright © The Author(s), 2022. Published by Cambridge University Press

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