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

Ivashko, Y I; Semenchenko, Alexander A.; Solodovnik, Daria A.; Atopkin, D. M.

doi:10.1017/s0022149x22000438

Cited by 3 publications

(7 citation statements)

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“…also reported in previous studies using the mtDNA genome (Atopkin et al, 2021;An et al, 2022;Ivashko et al, 2022). However, this was not consistent with those of a previous study using ITS2 for phylogenies, which demonstrated a close genetic affinity of Notocotylidae with Bucephalidae (of the order Strigeidida), rather than with Paramphistomidae and Gastrothylacidae (Xu et al, 2021).…”

Section: Conflict Of Interest Nonecontrasting

confidence: 82%

The complete mitochondrial genome of Ogmocotyle ailuri: gene content, composition and rearrangement and phylogenetic implications

et al. 2023

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Trematodes of the genus Ogmocotyle are intestinal flukes that can infect a variety of definitive hosts, resulting in significant economic losses worldwide. However, there are few studies on molecular data of these trematodes. In this study, the mitochondrial (mt) genome of Ogmocotyle ailuri isolated from red panda (Ailurus fulgens) was determined and compared with those from Pronocephalata to investigate the mt genome content, genetic distance, gene rearrangements and phylogeny. The complete mt genome of O.ailuri is a typical closed circular molecule of 14,642 base pairs, comprising 12 proteincoding genes, 22 transfer RNA genes, two ribosomal RNA genes, and two noncoding regions. All genes are transcribed in the same direction. In addition, 23 intergenic spacers and two locations with gene overlaps were determined. Sequence identities and sliding window analysis indicated that cox1 is the most conserved gene among 12 PCGs in O. ailuri mt genome. The sequenced mt genomes of the 48 Plagiorchiida trematodes showed five types of gene arrangement based on all mt genome genes, with the gene arrangement of O. ailuri being type I. Phylogenetic analysis using concatenated amino acid sequences of 12 protein-coding genes revealed that O. ailuri was closer to Ogmocotyle sikae than to Notocotylus intestinalis. These data enhance the Ogmocotyle mt genome database and provide molecular resources for further studies of Pronocephalata taxonomy, population genetics, and systematics.

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Section: Conflict Of Interest Nonecontrasting

confidence: 82%

The complete mitochondrial genome of Ogmocotyle ailuri: gene content, composition and rearrangement and phylogenetic implications

et al. 2023

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“…The third clade comprised 47 species from 18 families, representing seven suborders. The topology of this subclade completely agreed with the previous phylogenetic reconstructions of Digenea (Ivashko et al 2022). The suborder Xiphidiata Olson, Cribb, Tkach, Bray & Littlewood, 2003 was polyphyletic and appeared as two independent groups.…”

Section: Resultssupporting

confidence: 88%

“…On the one hand, this result supports the taxonomic status of Azygiidae as a separate order within Digenea, which largely agrees with the previous results by Wu et al (2020) that showed a basal position of Azygiidae relative to other Digenea, except Schistosomatidae. On the other hand, our results do not confirm the hypothesis, advanced in our previous studies, about the consistency between phylogenetic relationships and gene rearrangement within mitochondrial genomes of Schistosomatidae and other trematodes (Atopkin et al 2021;Ivashko et al 2022). In particular, the basal position of Azygiidae relative to other trematodes and the emergence of Cyathocotyle prussica and Clinostomum complanatum within a single clade with Schistosomatidae are evidence against this hypothesis.…”

Section: Systematics and Phylogenetic Relationships Of Azygiidaecontrasting

confidence: 99%

“…and Brachycladium goliath ) and Opisthorchiata. These differences between the BI and ML tree topologies were also reported in previous studies (Atopkin et al 2021; Ivashko et al 2022).

Figure 6. Phylogenetic relationships of Azygia robusta and other digenetic trematodes reconstructed by the Maximum Likelihood (ML) algorithm on the basis of alignment of protein sequences containing 2280 amino acids, available after Gblock processing.…”

Section: Resultssupporting

confidence: 83%

“…and Brachycladium goliath) and Opisthorchiata. These differences between the BI and ML tree topologies were also reported in previous studies (Atopkin et al 2021;Ivashko et al 2022).…”

Section: Phylogenetic Analysissupporting

confidence: 84%

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A report on the complete mitochondrial genome of the trematode Azygia robusta Odhner, 1911, its new definitive host from the Russian Far East, and unexpected phylogeny of Azygiidae within Digenea, as inferred from mitogenome sequences

Atopkin,

Semenchenko,

Solodovnik

et al. 2023

J. Helminthol.

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New data on the complete mitochondrial genome of Azygia robusta (Azygiidae) were obtained by the next-generation sequencing (NGS) approach. The mitochondrial DNA (mtDNA) of A. robusta had a length of 13 857 bp and included 12 protein-coding genes, two ribosomal genes, 22 transfer RNA genes, and two non-coding regions. The nucleotide sequences of the complete mitochondrial genomes of two A. robusta specimens differed from each other by 0.12 ± 0.03%. Six of 12 protein-coding genes demonstrated intraspecific variation. The difference between the nucleotide sequences of the complete mitochondrial genomes of A. robusta and Azygia hwangtsiyui was 26.95 ± 0.35%; the interspecific variation of protein-coding genes between A. robusta and A. hwangtsiyui ranged from 20.5 ± 0.9% (cox1) to 30.7 ± 1.2% (nad5). The observed gene arrangement in the mtDNA sequence of A. robusta was identical to that of A. hwangtsiyui. Codon usage and amino acid frequencies were highly similar between A. robusta and A. hwangtsiyui. The results of phylogenetic analyses based on mtDNA protein-coding regions showed that A. robusta is closely related to A. hwangtsiyui (belonging to the same suborder, Azygiida) that formed a distinct early-diverging branch relative to all other Digenea. A preliminary morphological analysis of paratypes of the two azygiid specimens studied showed visible morphological differences between them. The specimen extracted from Sakhalin taimen (Parahucho perryi) was most similar to A. robusta. Thus, we here provide the first record of a new definitive host, P. perryi, for A. robusta and also molecular characteristics of the trematode specimens.

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Complete mitochondrial genome and phylogenetic analysis of Dollfustrema vaneyi (Trematoda: Bucephalidae)

Hu,

Ye,

Zou

et al. 2024

BMC Genomics

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Background The Bucephalidae is a large family of digenean trematodes but most previous analyses of its phylogenetic position have relied on a single mitochondrial gene or morphological features. Mitochondrial genomes (mitogenomes) remain unavailable for the entire family. To address this, we sequenced the complete mitogenome of Dollfustrema vaneyi and analyzed the phylogenetic relationships with other trematodes. Results The circular genome of Dollfustrema vaneyi spanned 14,959 bp and contained 12 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a major non-coding region. We used concatenated amino acid and nucleotide sequences of all 36 genes for phylogenetic analyses, conducted using MrBayes, IQ-TREE and PhyloBayes. We identified pronounced topological instability across different analyses. The addition of recently sequenced two mitogenomes for the Aspidogastrea subclass along with the use of a site-heterogeneous model stabilized the topology, particularly the positions of Azygiidae and Bucephalidae. The stabilized results indicated that Azygiidae was the closest lineage to Bucephalidae in the available dataset, and together, they clustered at the base of the Plagiorchiida. Conclusions Our study provides the first comprehensive description and annotation of the mitochondrial genome for the Bucephalidae family. The results indicate a close phylogenetic relationship between Azygiidae and Bucephalidae, and reveal their basal placement within the order Plagiorchiida. Furthermore, the inclusion of Aspidogastrea mitogenomes and the site-heterogeneous model significantly improved the topological stability. These data will provide key molecular resources for future taxonomic and phylogenetic studies of the family Bucephalidae. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-024-10740-1.

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Characterization of complete mitochondrial genome and ribosomal operon forCarassotrema koreanumPark, 1938 (Digenea: Haploporidae) by means of next-generation sequencing data

Cited by 3 publications

References 53 publications

The complete mitochondrial genome of Ogmocotyle ailuri: gene content, composition and rearrangement and phylogenetic implications

The complete mitochondrial genome of Ogmocotyle ailuri: gene content, composition and rearrangement and phylogenetic implications

A report on the complete mitochondrial genome of the trematode Azygia robusta Odhner, 1911, its new definitive host from the Russian Far East, and unexpected phylogeny of Azygiidae within Digenea, as inferred from mitogenome sequences

Complete mitochondrial genome and phylogenetic analysis of Dollfustrema vaneyi (Trematoda: Bucephalidae)

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