The complete mitochondrial genome of <i>Paragonimus ohirai</i> (Paragonimidae: Trematoda: Platyhelminthes) and its comparison with <i>P. westermani</i> congeners and other trematodes

Le, Thanh Hoa; Nguyen, Khue Thi; Nguyen, Nga; Doan, Huong Thi Thanh; Agatsuma, Takeshi; Blair, David

doi:10.7717/peerj.7031

Cited by 24 publications

(30 citation statements)

References 72 publications

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“…The sizes and A+T contents of the two rRNA genes for P. commutatum are almost similar to those of other digeneans sequenced to date, such as that of Clonorchis sinensis , Paragonimus ohirai and Uvitellina sp. (Cai et al, 2012; Le et al, 2019; Suleman et al, 2019a).…”

Section: Resultsmentioning

confidence: 99%

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The Complete Mitochondrial Genome of the Caecal Fluke of Poultry, Postharmostomum commutatum, as the First Representative from the Superfamily Brachylaimoidea

Jin

2019

Front. Genet.

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Postharmostomum commutatum (Platyhelminthes: Brachylaimoidea), a parasite of the caeca of poultry, has been frequently reported from many countries and regions, including China. However, the molecular epidemiology, population genetics and phylogenetics of this parasite are poorly understood. In the present study, we determined and characterized the complete mitochondrial (mt) genome of P. commutatum, as the first representative from the superfamily Brachylaimoidea. The mt genome of P. commutatum is a circular DNA molecule of 13,799 bp in size and encodes the complete set of 36 genes (12 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes) as well as a typical control region. The mt genome of P. commutatum presents a clear bias in nucleotide composition with a negative AT-skew on average (−0.306) and a positive GC-skew on average (0.466). Phylogenetic analyses showed that P. commutatum (superfamily Brachylaimoidea) and other ten members of the order Diplostomida were recovered as sister groups of the order Plagiorchiida, indicating that the order Diplostomida is paraphyletic. This is the first mt genome of any member of the superfamily Brachylaimoidea and should represent a rich source of genetic markers for molecular epidemiological, population genetic and phylogenetic studies of parasitic flukes of socio-economic importance in poultry.

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Section: Resultsmentioning

confidence: 99%

“…The mt genome sequences of flukes contain usually two non-coding regions (NC) of significant size difference (Yan et al, 2013; Le et al, 2019; Suleman et al, 2019b). However, In P. commutatum mt genome, there is only one NC ( Table 2 and Figure 1 ).…”

Section: Resultsmentioning

confidence: 99%

The Complete Mitochondrial Genome of the Caecal Fluke of Poultry, Postharmostomum commutatum, as the First Representative from the Superfamily Brachylaimoidea

Jin

2019

Front. Genet.

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“…The first, initial specific primer pairs (ERE1F/ERE2R; ERE3F/ERE4R; ERE5F/ERE6R) designed based on the conserved nucleotide sequences aligned by those E. revolutum- mt sequences, cox 1, nad 1, rrn S (12S), respectively, available in GenBank and others, namely platyhelminth-universal primers (TRECOBF; TRECOBR; GLYF; GLYR) previously described in Le et al . (2019) were used. They were paired to bind on the target regions for amplification of long PCR of 4.0–7.5 kb or short of <4.0 kb overlapping fragments.…”

Section: Methodsmentioning

confidence: 99%

“…The ribosomal 16S ( rrn L) and 12S ( rrn S) RNA genes were recognized as described in Le et al . (2019) in the region located between tRNA Thr ( trn T) and cox 2 separated by tRNA Cys ( trn C), respectively.…”

Section: Methodsmentioning

confidence: 99%

Comparative mitogenomics of the zoonotic parasite Echinostoma revolutum resolves taxonomic relationships within the ‘E. revolutum’ species group and the Echinostomata (Platyhelminthes: Digenea)

Pham

Doan

et al. 2020

Parasitology

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The complete mitochondrial sequence of 17,030 bp was obtained from Echinostoma revolutum and characterized with those of previously reported members of the superfamily Echinostomatoidea, i.e. six echinostomatids, one echinochasmid, five fasciolids, one himasthlid, and two cyclocoelids. Relationship within suborders and between superfamilies, such as Echinostomata, Pronocephalata, Troglotremata, Opisthorchiata, and Xiphiditata, are also considered. It contained 12 protein-coding, two ribosomal RNA, 22 transfer RNA genes and a tandem repetitive consisting non-coding region (NCR). The gene order, one way-positive transcription, the absence of atp8 and the overlapped region by 40 bp between nad4L and nad4 genes were similar as in common trematodes. The NCR located between tRNAGlu (trnE) and cox3 contained 11 long (LRUs) and short repeat units (SRUs) (seven LRUs of 317 bp, four SRUs of 207 bp each), and an internal spacer sequence between LRU7 and SRU4 specifying high-level polymorphism. Special DHU-arm missing tRNAs for Serine were found for both tRNAS1(AGN) and tRNAS2(UCN). Echinostoma revolutum indicated the lowest divergence rate to E. miyagawai and the highest to Tracheophilus cymbius and Echinochasmus japonicus. The usage of ATG/GTG start and TAG/TAA stop codons, the AT composition bias, the negative AT-skewness, and the most for Phe/Leu/Val and the least for Arg/Asn/Asp codons were noted. Topology indicated the monophyletic position of E. revolutum to E. miyagawai. Monophyly of Echinostomatidae and Fasciolidae was clearly solved with respect to Echinochasmidae, Himasthlidae, and Cyclocoelidae which were rendered paraphyletic in the suborder Echinostomata.

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“…This progress is starting to have a major positive impact in many areas of parasitology, both fundamental and applied. For instance, exploring the mitochondrial genomes has enabled systematic (taxonomic and phylogenetic) and population genetic investigations of helminths (flatworms and roundworms) [2][3][4][5][6]. Such genomes provide a rich source of markers for such investigations and are particularly applicable to systematic investigations of species of flatworms (platyhelminths) [7], because the mitochondrial genes are usually considerably less variable in sequence than for many roundworm (nematode) species [8][9][10][11].…”

Section: Introductionmentioning

confidence: 99%

First record of a tandem-repeat region within the mitochondrial genome of Clonorchis sinensis using a long-read sequencing approach

et al. 2020

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Background Mitochondrial genomes provide useful genetic markers for systematic and population genetic studies of parasitic helminths. Although many such genome sequences have been published and deposited in public databases, there is evidence that some of them are incomplete relating to an inability of conventional techniques to reliably sequence non-coding (repetitive) regions. In the present study, we characterise the complete mitochondrial genome-including the long, non-coding region-of the carcinogenic Chinese liver fluke, Clonorchis sinensis, using long-read sequencing. Methods The mitochondrial genome was sequenced from total high molecular-weight genomic DNA isolated from a pool of 100 adult worms of C. sinensis using the MinION sequencing platform (Oxford Nanopore Technologies), and assembled and annotated using an informatic approach. Results From > 93,500 long-reads, we assembled a 18,304 bp-mitochondrial genome for C. sinensis. Within this genome we identified a novel non-coding region of 4,549 bp containing six tandem-repetitive units of 719-809 bp each. Given that genomic DNA from pooled worms was used for sequencing, some variability in length/sequence in this tandem-repetitive region was detectable, reflecting population variation. Conclusions For C. sinensis, we report the complete mitochondrial genome, which includes a long (> 4.5 kb) tandem-repetitive region. The discovery of this non-coding region using a nanopore-PLOS NEGLECTED TROPICAL DISEASES

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The complete mitochondrial genome of Paragonimus ohirai (Paragonimidae: Trematoda: Platyhelminthes) and its comparison with P. westermani congeners and other trematodes

Cited by 24 publications

References 72 publications

The Complete Mitochondrial Genome of the Caecal Fluke of Poultry, Postharmostomum commutatum, as the First Representative from the Superfamily Brachylaimoidea

The Complete Mitochondrial Genome of the Caecal Fluke of Poultry, Postharmostomum commutatum, as the First Representative from the Superfamily Brachylaimoidea

Comparative mitogenomics of the zoonotic parasite Echinostoma revolutum resolves taxonomic relationships within the ‘E. revolutum’ species group and the Echinostomata (Platyhelminthes: Digenea)

First record of a tandem-repeat region within the mitochondrial genome of Clonorchis sinensis using a long-read sequencing approach

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