Sequencing and characterization of the complete mitochondrial genome from the pancreatic fluke Eurytrema pancreaticum (Trematoda: Dicrocoeliidae)

Chang, Qiao‐Cheng; Li, Guohua; Gao, Jinliang; Xu, Zheng; Zhang, Yan; Duan, Hong; Yue, Dongmei; Fu, Xue; Su, Xin; Gao, Yuan; Wang, Chun-Ren

doi:10.1016/j.gene.2015.09.081

Cited by 32 publications

(18 citation statements)

References 41 publications

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“…The position of the Dicrocoeliidae clade as well as the internal branch topology within the Dicrocoeliidae were identical in the phylogenies based on the nucleotide and amino acid sequence alignments. The general tree topology and positions of included families were consistent with previous studies based on mitogenome sequences [19,20,55]. The phylogenetic tree supported the monophyly of all families represented in the analysis by more than a single mt genome.…”

Section: Phylogeny Of the Dicrocoeliidae Based On Mt Genome Sequencessupporting

confidence: 87%

“…Hypoderaeum conoideum (Trematoda: Echinostomatidae) [52] and Khawia sinensis (Cestoda: Caryophyllidea) [53]. The secondary structures of tRNAs were similar to those in the corresponding genes in E. pancreaticum [20]; all tRNAs except for trnS1 (AGN) and trnS2 (UCN), could be folded into the typical cloverleaf secondary structure. Similar to other dicrocoeliids, the two ribosomal RNA genes (rrnL and rrnS) in the species examined in our study, were located between trnT and cox2 for each species.…”

Section: Transfer and Ribosomal Rna Genesmentioning

confidence: 96%

“…Degenerate primer pairs were designed based on relatively conserved regions of the mtDNA sequences of D. chinensis, D. dendriticum [19] and E. pancreaticum [20] and used to amplify the mitogenomes of three dicrocoelids (Additional file 2: Table S1…”

Section: Long-pcr-based Sequencing Of Mt Genomesmentioning

confidence: 99%

“…Mitochondrial genomes have been proven to be a useful source of genetic markers for taxonomic identification, studies of inter-and intra-specific variation as well as systematics and phylogenetic analysis of trematodes at different taxonomic levels including members of the Dicrocoeliidae [19,20]. Although molecular phylogenetic analyses based on complete mt genomes from multiple taxa within the Dicrocoeliidae are not yet available, mt genomes of three dicrocoeliids, Dicrocoelium chinensis, D. dendriticum and Eurytrema pancreaticum (all parasitic in mammals) have been published recently [19,20]. In the present study, the complete mt genome of Lyperosomum longicauda Rudolphi, 1809 (the typespecies of the genus) and nearly complete mitogenomes of Brachydistomum sp.…”

Section: Introductionmentioning

confidence: 99%

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Molecular phylogenetics and mitogenomics of three avian dicrocoeliids (Digenea: Dicrocoeliidae) and comparison with mammalian dicrocoeliids

et al. 2020

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Background: The Dicrocoeliidae are digenetic trematodes mostly parasitic in the bile ducts and gall bladder of various avian and mammalian hosts. Until recently their systematics was based on morphological data only. Due to the high morphological uniformity across multiple dicrocoeliid taxa and insufficient knowledge of relative systematic value of traditionally used morphological characters, their taxonomy has always been unstable. Therefore, DNA sequence data provide a critical independent source of characters for phylogenetic inference and improvement of the system. Methods: We examined the phylogenetic affinities of three avian dicrocoeliids representing the genera Brachylecithum, Brachydistomum and Lyperosomum, using partial sequences of the nuclear large ribosomal subunit (28S) RNA gene. We also sequenced the complete or nearly complete mitogenomes of these three isolates and conducted a comparative mitogenomic analysis with the previously available mitogenomes from three mammalian dicrocoeliids (from 2 different genera) and examined the phylogenetic position of the family Dicrocoeliidae within the order Plagiorchiida based on concatenated nucleotide sequences of all mitochondrial genes (except trnG and trnE). Results: Combined nucleotide diversity, Kimura-2-parameter distance, non-synonymous/synonymous substitutions ratio and average sequence identity analyses consistently demonstrated that cox1, cytb, nad1 and two rRNAs were the most conserved and atp6, nad5, nad3 and nad2 were the most variable genes across dicrocoeliid mitogenomes. Phylogenetic analyses based on mtDNA sequences did not support the close relatedness of the Paragonimidae and Dicrocoeliidae and suggested non-monophyly of the Gorgoderoidea as currently recognized. Conclusions: Our results show that fast-evolving mitochondrial genes atp6, nad5 and nad3 would be better markers than slow-evolving genes cox1 and nad1 for species discrimination and population level studies in the Dicrocoeliidae.

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Section: Phylogeny Of the Dicrocoeliidae Based On Mt Genome Sequencessupporting

confidence: 87%

Section: Transfer and Ribosomal Rna Genesmentioning

confidence: 96%

Section: Long-pcr-based Sequencing Of Mt Genomesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Molecular phylogenetics and mitogenomics of three avian dicrocoeliids (Digenea: Dicrocoeliidae) and comparison with mammalian dicrocoeliids

et al. 2020

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“…The mt genome of A. hwangtsiyui has 22 intergenic spacers ranging from 1 to 15 bp and contains two overlapping nucleotides ranging from 1 to 40 bp (Table 1). Noteworthily, a 40 bp overlap between the nad4 and nad4L genes exists in the A. hwangtsiyui mitogenome, which is consistent with most helminths such as Eurytrema pancreaticum Janson, 1889 (Chang et al 2016), Hypoderaeum conoideum (Bloch, 1782) (Yang et al 2015), but shorter than that of Schistosoma mekongi Voge, Bruckner & Bruce, 1978 (64 bp;Littlewood et al 2006). The nucleotide contents of T, C, A, G, in A. hwangtsiyui mitogenome are 42.8%, 12.0%, 16.8%, and 28.5%, respectively ( Table 2).…”

Section: General Traits Of the Azygia Hwangtsiyui Mitogenomesupporting

confidence: 52%

Characterization and comparative analysis of the complete mitochondrial genome of Azygia hwangtsiyui Tsin, 1933 (Digenea), the first for a member of the family Azygiidae

Wu¹,

Gao²,

Cheng³

et al. 2020

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Azygia hwangtsiyui (Trematoda, Azygiidae), a neglected parasite of predatory fishes, is little-known in terms of its molecular epidemiology, population ecology and phylogenetic study. In the present study, the complete mitochondrial genome of A. hwangtsiyui was sequenced and characterized: it is a 13,973 bp circular DNA molecule and encodes 36 genes (12 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes) as well as two non-coding regions. The A+T content of the A. hwangtsiyui mitogenome is 59.6% and displays a remarkable bias in nucleotide composition with a negative AT skew (–0.437) and a positive GC skew (0.408). Phylogenetic analysis based on concatenated amino acid sequences of twelve protein-coding genes reveals that A. hwangtsiyui is placed in a separate clade, suggesting that it has no close relationship with any other trematode family. This is the first characterization of the A. hwangtsiyui mitogenome, and the first reported mitogenome of the family Azygiidae. These novel datasets of the A. hwangtsiyui mt genome represent a meaningful resource for the development of mitochondrial markers for the identification, diagnostics, taxonomy, homology and phylogenetic relationships of trematodes.

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Characterization of the Complete Mitochondrial Genome of Pleurogenoides japonicus (Digenea, Pleurogenidae): Comparison With the Members of Microphalloidea and Phylogenetic Implications

Gao,

Ma,

Hou

et al. 2024

Ecology and Evolution

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Pleurogenoides japonicus (Trematoda: Microphalloidea) is an important parasite in wood frogs with high infection rates and significant ecological, economic, and societal importance. The scarcity of molecular data for these parasites severely limits population genetics and phylogenetic studies. In the present study, for the first time, we determined and described the entire mitochondrial (mt) genome of P. japonicus as the first representative of the family Pleurogenidae. The entire mt genome of P. japonicus was circular, with 15,043 bp (GenBank accession number OR900118), containing 36 genes, comprising 12 protein‐coding genes (cox1–3, nad1–6, nad4L, cytb, and atp6), two ribosomal RNA genes, 22 transfer RNA genes, and two non‐coding regions. There were 23 intergenic spacers, ranging from 2 to 162 bp, and only one 40 bp overlap between nad4L and nad4 genes in the P. japonicus mt genome. The nucleotide composition of P. japonicus mt genome exhibited a strong AT bias with a 63.75% A + T content, while the AT‐ and GC‐skews were − 0.435 and 0.407, respectively. Comparative analysis demonstrated that the P. japonicus mt genome shared the most common characteristics with Microphalloidea trematodes, and the cox1 gene was the longest and most conserved gene in Microphalloidea trematodes. The gene arrangements of Xiphidiata trematodes were of the same order based on protein‐coding genes and rRNA genes, except for tRNA. More than two gene arrangement types exist in Echinostomata and Xiphidiata, and the gene rearrangement events mainly occurred in “trnE‐trnG” and “trnG‐trnE”. Phylogenetic analysis suggested that trematodes of the family Pleurogenidae clustered more with Prosthogonimidae than Eucotylidae. The mt genome data of P. japonicus provide an accurate genetic marker for further studies of Xiphidiata trematodes.

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Sequencing and characterization of the complete mitochondrial genome from the pancreatic fluke Eurytrema pancreaticum (Trematoda: Dicrocoeliidae)

Cited by 32 publications

References 41 publications

Molecular phylogenetics and mitogenomics of three avian dicrocoeliids (Digenea: Dicrocoeliidae) and comparison with mammalian dicrocoeliids

Molecular phylogenetics and mitogenomics of three avian dicrocoeliids (Digenea: Dicrocoeliidae) and comparison with mammalian dicrocoeliids

Characterization and comparative analysis of the complete mitochondrial genome of Azygia hwangtsiyui Tsin, 1933 (Digenea), the first for a member of the family Azygiidae

Characterization of the Complete Mitochondrial Genome of Pleurogenoides japonicus (Digenea, Pleurogenidae): Comparison With the Members of Microphalloidea and Phylogenetic Implications

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