Comparative analysis of mitochondrial DNA datasets indicates that Cylicostephanus minutus represents a species complex

Comparative phylogenetic and sequence identity analysis of internal transcribed spacer 2 and cytochrome c oxidase subunit I as DNA barcode markers for the most common equine Strongylidae species

Morphologically, 64 strongylid species have been described in equines. Co-infections are common, with up to 29 species reported in a single horse. Morphological identification of these species is time consuming and requires expert knowledge due to their similar appearance. Therefore, non-invasive identification methods are needed. DNA barcoding offers a rapid and reliable tool for species identification and the discovery of cryptic species for these most common parasitic nematodes of equines. In total, 269 cytochrome c oxidase subunit I (COI) gene and 312 internal transcribed spacer 2 (ITS-2) sequences from 27 equine Strongylidae species, including sequences from two uncharacterised species, Coronocyclus sagittatus and Triodontophorus tenuicollis, were generated and combined with COI and ITS-2 sequences data from six Cyathostominae species from previous studies. This study represents a comprehensive DNA barcoding analysis of 22 Cyathostominae and six Strongylinae species using mitochondrial COI gene and ITS-2 sequences. Maximum likelihood phylogenetic trees were constructed and the intra- and interspecific genetic distances for both markers were compared. Analysis revealed complex phylogenetic relationships. Para- and polyphyletic relationships were observed among most genera within Strongylinae and Cyathostominae. This challenges current morphological classifications. Although both markers showed overlapping pairwise identities in intra- and inter-species comparisons, COI had higher discriminatory power than ITS-2. Expanding the COI and ITS-2 reference database, including the first sequences for Coronocyclus sagittatus and Triodontophorus tenuicollis, improve a reliable species identification and advanced studies on Strongylinae and Cyathostominae diversity using barcoding and metabarcoding.

Comparison of two molecular barcodes for the study of equine strongylid communities with amplicon sequencing

Basic knowledge on the biology and epidemiology of equine strongylid species still needs to be improved to contribute to the design of better parasite control strategies. Nemabiome metabarcoding is a convenient tool to quantify and identify species in bulk samples that could overcome the hurdle that cyathostomin morphological identification represents. To date, this approach has relied on the internal transcribed spacer 2 (ITS-2) of the ribosomal RNA gene, with a limited investigation of its predictive performance for cyathostomin communities. Using DNA pools of single cyathostomin worms, this study aimed to provide the first elements to compare performances of the ITS-2 and a cytochrome c oxidase subunit I (COI) barcode newly developed in this study. Barcode predictive abilities were compared across various mock community compositions of two, five and 11 individuals from distinct species. The amplification bias of each barcode was estimated. Results were also compared between various types of biological samples, i.e., eggs, infective larvae or adults. Bioinformatic parameters were chosen to yield the closest representation of the cyathostomin community for each barcode, underscoring the need for communities of known composition for metabarcoding purposes. Overall, the proposed COI barcode was suboptimal relative to the ITS-2 rDNA region, because of PCR amplification biases, reduced sensitivity and higher divergence from the expected community composition. Metabarcoding yielded consistent community composition across the three sample types. However, imperfect correlations were found between relative abundances from infective larvae and other life-stages for Cylicostephanus species using the ITS-2 barcode. While the results remain limited by the considered biological material, they suggest that additional improvements are needed for both the ITS-2 and COI barcodes.

Characterization of the complete mitochondrial genomes of Diplodiscus japonicus and Diplodiscus mehari (Trematoda: Diplodiscidae): Comparison with the members of the superfamily Paramphistomoidea and phylogenetic implication

Diplodiscus japonicus and Diplodiscus mehari (Trematoda: Diplodiscidae) are two important parasites in wood frogs, which have large infection rates and essential importance of ecology, economy and society. In this study, the complete mitochondrial (mt) genomes of D. japonicus and D. mehari were sequenced, then compared with other related trematodes in the superfamily Paramphistomoidea. The complete circular mt sequence of D. japonicus and D. mehari were 14,210 bp and 14,179 bp in length, respectively. Both mt genomes comprised 36 functional subunits, consisting of 12 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and one non-coding region. The mt genes of D. japonicus and D. mehari were transcribed in the same direction, and the gene arrangements were identical to those of Paramphistomoidea trematodes. In the 12 PCGs, GTG was the most common initiation codon, whereas TAG was the most common termination codon. All tRNAs had a typical cloverleaf structure except tRNA Ser1. A comparison with related Paramphistomoidea trematode mt genomes suggested that the cox1 gene of D. mehari was the longest in these trematodes. Phylogenetic analyses revealed that Paramphistomoidea trematodes formed a monophyletic branch, Paramphistomidae and Gastrothylacidae were more closely related than Diplodiscidae. And the further analysis with Pronocephalata branch found that the flukes parasitic in amphibians (frogs) formed one group, and the flukes from ruminants (cattle, sheep, ect) formed another group. Our study demonstrated the importance of sequencing mt genomes of D. japonicus and D. mehari, which will provide significant molecular resources for further studies of Paramphistomoidea taxonomy, population genetics and systematics.

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The complete mt genomes of Diplodiscus japonicus and D. mehari were determined first time.

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There is only one NCR in Diplodiscus japonicus and D. mehari complete mt genomes.

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Phylogenetic analyses revealed two monophyletic groups for the flukes parasitic in amphibians and ruminants.