Abstract
BackgroundGenetic markers like the nuclear ribosomal RNA (rRNA) genes, internal transcribed spacer regions, mitochondrial protein-coding genes, and genomes have been utilized for molecular identification of parasitic trematodes. However, challenges such as the design of broadly applicable primers for the vast number of species within Digenea and the genetic markers’ ability to provide sufficient species-level resolution limited their utility. This study presented novel and broadly applicable primers using the mitochondrial 12S and 16S rRNA genes for Digenea and aimed to show their suitability as alternative genetic markers for molecular identification of orders Plagiorchiida, Echinostomida, and Strigeida.ResultsOur results revealed that the mitochondrial 12S and 16S rRNA genes are suitable for trematode molecular identification, with sufficient resolution to discriminate closely related species and achieve accurate species identification through phylogenetic placements. Moreover, the robustness of our newly designed primers to amplify medically important parasitic trematodes encompassing three orders was demonstrated through successful amplification. The convenience and applicability of the newly designed primers and adequate genetic variation of the mitochondrial rRNA genes can be useful as complementary markers for trematode molecular-based studies.ConclusionsWe demonstrated that the mitochondrial rRNA genes could be alternative genetic markers robust for trematode molecular identification and potentially helpful for DNA barcoding where our primers can be widely applied across the major Digenea orders. Furthermore, the potential of the mitochondrial rRNA genes for molecular systematics can be explored, enhancing their appeal for trematode molecular-based studies. The novelty of utilizing the mitochondrial rRNA genes and the designed primers in this study can potentially open avenues for species identification, discovery, and systematics in the future.
Highlights
Genetic markers like the nuclear ribosomal RNA genes, internal transcribed spacer regions, mitochondrial protein-coding genes, and genomes have been utilized for molecular identification of parasitic trematodes
Our results indicate that both the 12S and 16S ribosomal RNA (rRNA) genes are suitable for trematode molecular identification, as revealed through accurate taxonomic assignments through phylogenetic placements, genetic distances between closely related species higher than the nuclear DNA genetic markers, and comparable inter-species genetic distances to the mitochondrial c oxidase subunit 1 (COI) gene
The suitability of the mitochondrial rRNA genes for trematode molecular identification was demonstrated through the robustness of the genetic marker and the ability of the developed primers to amplify medically important parasitic trematodes encompassing three orders
Summary
Genetic markers like the nuclear ribosomal RNA (rRNA) genes, internal transcribed spacer regions, mitochondrial protein-coding genes, and genomes have been utilized for molecular identification of parasitic trematodes. Challenges such as the design of broadly applicable primers for the vast number of species within Digenea and the genetic markers’ ability to provide sufficient species-level resolution limited their utility. The small size and soft bodies of adult trematodes, coupled with variations in characters due to morphological plasticity, hinder species identification accuracy [8, 9]. Higher numbers of cryptic species have been reported in trematodes than other groups of helminths, contributing to the complexity involved with morphological-based identification [12]
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