Molecular identification and phylogenetic analysis of nuclear rDNA sequences among three opisthorchid liver fluke species (Opisthorchiidae: Trematoda)

Kang, Soo Yong; Sultana, Tahera; Loktev, V. B.; Wongratanacheewin, Surasakdi; Sohn, Woon Mok; Eom, Keeseon S.; Park, Joong Ki

doi:10.1016/j.parint.2007.12.007

Cited by 55 publications

(36 citation statements)

References 21 publications

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“…The ninth intron of the paramyosin gene proved to be more variable than the nuclear ITS markers used before (Müller et al 2007a, b;Kang et al 2008). On phylogentic trees, the association of O. viverrini with C. sinensis was shown with high bootstrap support.…”

Section: Itsmentioning

confidence: 94%

“…Two previous studies (Kang et al 2008;Katokhin et al 2008) have provided evidence that O. viverrini, O. felineus, and C. sinensis are closely related. However, the schemes of phylogenetic relationships of these three species obtained in these studies somewhat contradict and none of them had strong bootstrap support.…”

Section: Itsmentioning

confidence: 96%

“…Kang et al (2008) examined ITS1 sequences of these three species and concluded that O. viverrini and O. felineus grouped together but not with a high support. On the contrast, Katokhin et al (2008) used ITS2 and mitochondrial cox1 as phylogenetic markers and came to the conclusion that O. felineus was more closely related to C. sinensis than to O. viverrini.…”

Section: Itsmentioning

confidence: 99%

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A novel nuclear marker, Pm-int9, for phylogenetic studies of Opisthorchis felineus, Opisthorchis viverrini, and Clonorchis sinensis (Opisthorchiidae, Trematoda)

et al. 2009

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Opisthorchis felineus, O. viverrini, and Clonorchis sinensis, the trematodes of the family Opisthorchiidae, are important human parasites. Two previous studies (Kang et al. Parasitol Int 57:191-197, 2008; Katokhin et al. Dokl Biochem Biophys 421:214-217, 2008) have provided evidence using ribosomal and mitochondrial sequences that O. viverrini, O. felineus, and C. sinensis are closely related. We developed a novel nuclear marker, Pm-int9, which included the ninth intron of the paramyosin gene and flanking exon sequences. Samples of O. felineus from four localities of West Siberia, C. sinensis from the Russian Far East, and O. viverrini from Thailand were genotyped by Pm-int9. Little variation was detected in exon sequences, however, intron sequences turned out to be more variable than ribosomal internal transcribed spacers. We can conclude that Pm-int9 is valuable for interspecific variation studies. Phylogenetic analysis based on Pm-int9 revealed that O. viverrini and C. sinensis were closer to each other than either of them to O. felineus, supporting the opinion that C. sinensis should be considered the sister species of Opisthorchis spp.

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Section: Itsmentioning

confidence: 94%

Section: Itsmentioning

confidence: 96%

Section: Itsmentioning

confidence: 99%

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A novel nuclear marker, Pm-int9, for phylogenetic studies of Opisthorchis felineus, Opisthorchis viverrini, and Clonorchis sinensis (Opisthorchiidae, Trematoda)

et al. 2009

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“…The ITS-1 sequence of ancient specimen differed from modern samples due to sequence divergence or polymorphism. Kang et al (2008) reported the molecular identifi cation of fl ukes (Opisthorchis viverrini, O. felineus and Clonorchis sinensis) using PCR-RFLP technique for 18S, ITS-1 and 5.8S rDNA region. Any intra-specifi c polymorphism or cross-reaction was not observed in the restriction pattern of ITS-1 region.…”

Section: Opisthorchiidae (Looss 1899)mentioning

confidence: 99%

A review on the molecular characterization of digenean parasites using molecular markers with special reference to ITS region

et al. 2015

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SummaryThe rDNA region of eukaryotes has the immense potential to resolve the evolutionary and phylogeny problems using molecular markers. As evident from the present review, ITS region data is considered for interpretation of inter and intra-specifi c variations of 136 studies of 33 families including 78 genus and 114 species affecting individuals worldwide. Along with ITS-1 and ITS-2 region in 29 studies 18S region, in 38 studies 28S region and in 43 studies mitochondrial genes (COI and NDI) were also analyzed. Three new genera (Allobilharzia gen. nov., Caulanus gen. nov., and Latuterus gen. nov.) and 49 new species were discovered. Only 47 studies expressed variations at intra-specifi c and inter-specifi c level in complete ITS region, ITS-1 and ITS-2 rDNA sequences due to differences in nucleotide positions. According to the fi ndings ITS region is more reliable and precise marker for demarcation and identifi cation of species in combination of other DNA markers. Major studies were involved around the parasites of families Fasciolidae, Schistosomatidae, Opisthorchidae, Paragonimidae and Paramphistomidae, Clinostomidae, Diplostomidae, Haploporidae, among others infecting humans, farm animals, birds, fi shes, reptiles and amphibians on the clinical basis. In future, molecular and bioinformatics aspects based on genetic variations will lead to explore the untouched areas of trematodes.

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“…PCR-RFLP markers are commonly used and highly repeatable (Meyer et al 1995) for the identification of a variety of species in several phyla (Wolf et al 1999, McDonald et al 2005, Torres 2006, Santaclara et al 2007, Spergser and Rosengarten 2007, FernandezTajes and Méndez 2007, Sowmya et al 2007, Kang et al 2008. Although DNA sequencing and analysis is accurate and authentic, it is costly, time-consuming and not suitable for routine species identification studies.…”

Section: Introductionmentioning

confidence: 99%

DNA barcoding approaches for fishing authentication of exploited grouper species including the endangered and legally protected goliath grouper <i>Epinephelus itajara</i>

et al. 2013

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SUMMARY: Fishing strategies are constantly changing to meet the needs for new or alternative food sources. Consequently, management of fishing activities regarding rates of exploitation is essential, as a number of resources have reached situations of overexploitation. The aim of the present study was to use DNA barcoding from the goliath grouper and other exploited epinephelids in order to provide procedures for DNA authentication to be used as evidence for combating putative illegal fishing. The species studied were Epinephelus adscensionis, Mycteroperca bonaci, Mycteroperca interstitialis, Epinephelus itajara, Mycteroperca venenosa, Epinephelus mystacinus, Dermatolepis inermis, Alphestes afer, Cephalopholis fulva, Mycteroperca acutirostris, Rypticus saponaceus, Mycteroperca marginata and Epinephelus morio. Four of these species are the main epinephelids fished in the Atlantic Ocean. Differential patterns of polymerase chain reaction-restriction fragment length polymorphism were obtained from the species and additional single nucleotide polymorphisms were also detected among the four main epinephelids studied. The procedures proved very efficient and we suggest their applicability to the other fish groups as a way to control illegal capture and retail around the world, especially in cases in which filleting and other forms of de-characterization cause a lack of morpho-anatomical key characters.Keywords: DNA authentication, PCR-RFLPs, SNPs, groupers, goliath grouper, epinephelids. RESUMEN: Autenticación mediante DNA bArcoDiNg de especies de meros legalmente protegidas y en peligro de extinción, sometidas a explotación pesquera, incluyendo el mero Goliat EpiNEphElus itAjArA. -Las estrategias de pesca cambian constantemente para satisfacer las necesidades de fuentes de alimento nuevas o alternativas. En consecuencia, a medida que los recursos alcanzan situaciones de sobreexplotación, resulta esencial establecer procedimientos de inspección de las actividades relacionadas con las tasas de explotación pesquera. El objetivo de este estudio es proponer el uso de la téc-nica de DNA barcoding para establecer la verificación de la identidad del mero Goliat y otros epinefélidos, a fin de utilizarlo como evidencia para combatir la pesca ilegal cuando se sospeche su ocurrencia. Las especies aquí estudiadas fueron Alphestes afer, Cephalopholis fulva, Dermatolepis inermis, Epinephelus adscensionis, E. itajara, E. morio, E. mystacinus, Mycteroperca acutirostris, M. bonaci, M. interstitialis, M. marginata, M. venenosa y Rypticus saponaceus de las cuales cuatro constituyen las más pescadas en el Océano Atlántico. Fueron encontrados patrones diferenciables de PCR-RFLPs para todas las especies y, además, fue posible detectar SNPs adicionales entre las cuatro especies más explotadas. Los procedimientos aquí empleados fueron muy eficaces por lo que sugerimos su aplicabilidad a otros grupos de peces como medida de control de la captura y comercialización ilegal a nivel mundial, particularmente en aquellos casos en los que el filete...

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Molecular identification and phylogenetic analysis of nuclear rDNA sequences among three opisthorchid liver fluke species (Opisthorchiidae: Trematoda)

Cited by 55 publications

References 21 publications

A novel nuclear marker, Pm-int9, for phylogenetic studies of Opisthorchis felineus, Opisthorchis viverrini, and Clonorchis sinensis (Opisthorchiidae, Trematoda)

A novel nuclear marker, Pm-int9, for phylogenetic studies of Opisthorchis felineus, Opisthorchis viverrini, and Clonorchis sinensis (Opisthorchiidae, Trematoda)

A review on the molecular characterization of digenean parasites using molecular markers with special reference to ITS region

DNA barcoding approaches for fishing authentication of exploited grouper species including the endangered and legally protected goliath grouper <i>Epinephelus itajara</i>

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