Genetic variation among Clonorchis sinensis isolates from different geographic regions in China revealed by sequence analyses of four mitochondrial genes

2011 ◽  
Vol 86 (4) ◽  
pp. 479-484 ◽  
Author(s):  
G.H. Liu ◽  
B. Li ◽  
J.Y. Li ◽  
H.Q. Song ◽  
R.Q. Lin ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Clonorchis Sinensis ◽  
Mtdna Sequences ◽  
Specific Sequence ◽  
Opisthorchis Felineus ◽  
Phylogenetic Studies ◽  
Sequence Variations ◽  
Specific Variation ◽  
Geographic Regions ◽  
Liver Flukes

AbstractThe present study examined sequence variation in four mitochondrial (mt) genes, namely cytochrome c oxidase subunits 1 (cox1) and 2 (cox2), and NADH dehydrogenase subunits 1 and 2 (nad1 and nad2) among Clonorchis sinensis isolates from different endemic regions in China, and their phylogenetic relationships with other zoonotic trematodes were reconstructed. A portion of the cox1 and cox2 genes (pcox1 and pcox2), and nad1 and nad2 genes (pnad1 and pnad2) were amplified separately from individual liver flukes by polymerase chain reaction (PCR) and the amplicons were subjected to sequencing from both directions. The intra-specific sequence variations within C. sinensis were 0–1.6% for pcox1, 0–1.4% for pcox2, 0–0.9% for pnad1 and 0–1.0% for pnad2. Phylogenetic analyses based on the combined sequences of pcox1, pcox2, pnad1 and pnad2 revealed that all the C. sinensis isolates grouped together and were closely related to Opisthorchis felineus. These findings revealed the existence of intra-specific variation in mitochondrial DNA (mtDNA) sequences among C. sinensis isolates from different geographic regions, and demonstrated that mtDNA sequences provide reliable genetic markers for phylogenetic studies of zoonotic trematodes.

Sequence variability in four mitochondrial genes among Bunostomum trigonocephalum isolates from four provinces in China

2012 ◽  
Vol 87 (4) ◽  
pp. 416-421 ◽  
Author(s):  
C.R. Wang ◽  
J.F. Gao ◽  
Q.C. Chang ◽  
F.C. Zou ◽  
Q. Zhao ◽  
...  
Keyword(s):  
Direct Sequencing ◽  
Phylogenetic Analyses ◽  
Mitochondrial Genes ◽  
Sequence Variability ◽  
Specific Sequence ◽  
Sequence Variations ◽  
The Family ◽  
Specific Variation ◽  
Geographic Regions ◽  
Inference Methods

AbstractThe present study examined sequence variability in four mitochondrial genes, namely cytochrome c oxidase subunit (cox1), cytochrome b (cytb) and NADH dehydrogenase subunits 1 and 5 (nad1 and nad5), among Bunostomum trigonocephalum isolates from four different geographic regions in China. Ten B. trigonocephalum samples were collected from each of the four provinces (Heilongjiang, Jilin, Shaanxi and Yunnan), China. A part of the cox1 (pcox1), cytb (pcytb), nad1 and nad5 genes (pnad1 and pnad5) were amplified separately from individual hookworms by polymerase chain reaction (PCR) and were subjected to direct sequencing in order to define sequence variations and their phylogenetic relationships. The intra-specific sequence variations within B. trigonocephalum were 0–1.9% for pcox1, 0–2.0% for pcytb, 0–1.6% for pnad1 and 0–1.7% for pnad5. The A+T contents of the sequences were 69.6–70.4% (pcox1), 71.9–72.7 (pcytb), 70.4–71.1% (pnad1) and 72.0–72.6% (pnad5). However, the inter-specific sequence differences among members of the family Ancylostomatidae were significantly higher, being 12.1–14.2% for pcox1, 13.7–16.0 for cytb, 17.6–19.4 for nad1 and 16.0–21.6 for nad5. Phylogenetic analyses based on the combined partial sequences of cox1, cytb, nad1 and nad5 using three inference methods, namely Bayesian inference (Bayes), maximum likelihood (ML) and maximum parsimony (MP), revealed that all the B. trigonocephalum samples form monophyletic groups, but samples from the same geographical origin did not always cluster together, suggesting that there was no obvious geographical distinction within B. trigonocephalum based on sequences of the four mtDNA genes. These results demonstrated the existence of low-level intra-specific variation in mitochondrial DNA (mtDNA) sequences among B. trigonocephalum isolates from different geographic regions.

scholarly journals The liver fluke Opisthorchis felineus as a group III or group I carcinogen

4open ◽  
2019 ◽  
Vol 2 ◽  
pp. 23 ◽  
Author(s):  
Mariya Yurievna Pakharukova ◽  
José Manuel Correia da Costa ◽  
Viatcheslav Alekseevitch Mordvinov
Keyword(s):  
Risk Factors ◽  
Russian Federation ◽  
Liver Fluke ◽  
Clonorchis Sinensis ◽  
Opisthorchis Felineus ◽  
Group Iii ◽  
Group I ◽  
Carcinogenic Potential ◽  
The Russian Federation ◽  
Liver Flukes

Opisthorchiasis caused by the liver fluke Opisthorchis felineus is one of the most common helminthic infections in the Russian Federation. The largest area affected by opisthorchiasis felinea occupies almost the entire territory of Western Siberia and extends to northern Kazakhstan and a part of the Ural region. Natural endemic regions of opisthorchiasis also exist in the European part of Russia, and in the regions of Western and Eastern Europe. According to the official statistics of the Russian Federation, up to 40 000 patients with opisthorchiasis are registered annually in the country. Opisthorchiasis felinea affects the hepatobiliary system and causes serious liver disorders, including cancer of the biliary tract. Other parasitoses, opisthorchiasis viverrini and clonorchiasis, are widespread in the Southeast Asia and China. The causative agents of these diseases, liver flukes O. viverrini and Clonorchis sinensis, are officially recognized as Group 1 biological carcinogens and are classified as the main risk factors for cholangiocarcinoma. O. felineus is included in Group 3 of biological carcinogens and is not officially considered carcinogenic to humans. Studies on the carcinogenic potential of this liver fluke and the epidemiology of cholangiocarcinoma in the Russian Federation have started in earnest quite recently. Nevertheless, we have some evidence that infection with O. felineus leads to a precancerous state of the bile duct epithelium. This state, combined with additional risk factors, poses a real risk of cholangiocarcinoma. In our opinion, taking into consideration the accumulated facts, the classification of the carcinogenic potential of O. felineus requires revision. In this review, we focus on the relevant characteristics of the biology and epidemiology of this helminth as well as experimental data on opisthorchiasis felinea; this information might clarify the carcinogenicity of O. felineus to humans.

The complete mitochondrial genomes of the liver flukes Opisthorchis felineus and Clonorchis sinensis (Trematoda)

2010 ◽  
Vol 59 (1) ◽  
pp. 100-103 ◽  
Author(s):  
Sergei V. Shekhovtsov ◽  
Alexei V. Katokhin ◽  
Nikolai A. Kolchanov ◽  
Viatcheslav A. Mordvinov
Keyword(s):  
Clonorchis Sinensis ◽  
Mitochondrial Genomes ◽  
Opisthorchis Felineus ◽  
Liver Flukes ◽  
Complete Mitochondrial Genomes

The zoonotic, fish-borne liver flukes Clonorchis sinensis, Opisthorchis felineus and Opisthorchis viverrini

2013 ◽  
Vol 43 (12-13) ◽  
pp. 1031-1046 ◽  
Author(s):  
Trevor N. Petney ◽  
Ross H. Andrews ◽  
Weerachai Saijuntha ◽  
Alexandra Wenz-Mücke ◽  
Paiboon Sithithaworn
Keyword(s):  
Clonorchis Sinensis ◽  
Opisthorchis Viverrini ◽  
Opisthorchis Felineus ◽  
Liver Flukes

Sequence variation in two mitochondrial DNA regions and internal transcribed spacer among isolates of the nematode Oesophagostomum asperum originating from goats in Hunan Province, China

2014 ◽  
Vol 90 (1) ◽  
pp. 1-6 ◽  
Author(s):  
F. Li ◽  
T. Hu ◽  
N.C. Duan ◽  
W.Y. Li ◽  
Q. Teng ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Analyses ◽  
Its Rdna ◽  
Hunan Province ◽  
Nuclear Ribosomal Dna ◽  
Specific Sequence ◽  
5.8S Rdna ◽  
Rdna Sequences ◽  
Specific Variation

AbstractThe present study examined sequence variability in two mitochondrial DNA (mtDNA) regions, namely cytochrome c oxidase subunit 1 (cox1) and NADH dehydrogenase subunit 1 (nad1), and internal transcribed spacer (ITS) of nuclear ribosomal DNA (rDNA) among Oesophagostomum asperum isolates from goats in Hunan Province, China. A portion of the cox1 (pcox1), nad1 (pnad1) genes and the ITS (ITS1+5.8S rDNA+ITS2) rDNA were amplified by polymerase chain reaction (PCR) separately from adult O. asperum individuals and the representative amplicons were subjected to sequencing from both directions. The lengths of pcox1, pnad1 and ITS rDNA were 366 bp, 681 bp and 785 bp, respectively. The A+T contents of gene sequences were 71.5–72% for pcox1, 73.7–74.2% for pnad1 and 58–58.8% for ITS rDNA. Intra-specific sequence variations within O. asperum were 0–1.6% for pcox1, 0–1.9% for pnad1 and 0–1.7% for ITS rDNA, while inter-specific sequence differences among members of the genus Oesophagostomum were significantly higher, being 11.1–12.5%, 13.3–17.7% and 8.5–18.6% for pcox1, pnad1 and ITS rDNA, respectively. Phylogenetic analyses using combined sequences of pcox1 and pnad1, with three different computational algorithms (Bayesian inference, maximum likelihood and maximum parsimony), revealed distinct groups with high statistical support. These findings demonstrated the existence of intra-specific variation in mtDNA and rDNA sequences among O. asperum isolates from goats in Hunan Province, China, and have implications for studying molecular epidemiology and population genetics of O. asperum.

scholarly journals Conflicting phylogenetic signals in plastomes of the tribe Laureae (Lauraceae)

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10155
Author(s):  
Tian-Wen Xiao ◽  
Yong Xu ◽  
Lu Jin ◽  
Tong-Jian Liu ◽  
Hai-Fei Yan ◽  
...  
Keyword(s):  
Phylogenetic Signal ◽  
Phylogenetic Analyses ◽  
Critical Role ◽  
Gene Tree ◽  
Tree Topology ◽  
Intergenic Spacers ◽  
Coding Regions ◽  
Phylogenetic Studies ◽  
Specific Variation ◽  
Gene Tree Discordance

Background Gene tree discordance is common in phylogenetic analyses. Many phylogenetic studies have excluded non-coding regions of the plastome without evaluating their impact on tree topology. In general, plastid loci have often been treated as a single unit, and tree discordance among these loci has seldom been examined. Using samples of Laureae (Lauraceae) plastomes, we explored plastome variation among the tribe, examined the influence of non-coding regions on tree topology, and quantified intra-plastome conflict. Results We found that the plastomes of Laureae have low inter-specific variation and are highly similar in structure, size, and gene content. Laureae was divided into three groups, subclades I, II and III. The inclusion of non-coding regions changed the phylogenetic relationship among the three subclades. Topologies based on coding and non-coding regions were largely congruent except for the relationship among subclades I, II and III. By measuring the distribution of phylogenetic signal across loci that supported different topologies, we found that nine loci (two coding regions, two introns and five intergenic spacers) played a critical role at the contentious node. Conclusions Our results suggest that subclade III and subclade II are successively sister to subclade I. Conflicting phylogenetic signals exist between coding and non-coding regions of Laureae plastomes. Our study highlights the importance of evaluating the influence of non-coding regions on tree topology and emphasizes the necessity of examining discordance among different plastid loci in phylogenetic studies.

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

2009 ◽  
Vol 106 (1) ◽  
pp. 293-297 ◽  
Author(s):  
Sergei V. Shekhovtsov ◽  
Alexei V. Katokhin ◽  
Konstantin V. Romanov ◽  
Vladimir V. Besprozvannykh ◽  
Konstantin P. Fedorov ◽  
...  
Keyword(s):  
Clonorchis Sinensis ◽  
Opisthorchis Viverrini ◽  
Nuclear Marker ◽  
Opisthorchis Felineus ◽  
Phylogenetic Studies

Never seen before? Opisthorchiasis and Clonorchiasis

2018 ◽  
Vol 56 (12) ◽  
pp. 1513-1520 ◽  
Author(s):  
Christoph Dietrich ◽  
Nathan Atkinson ◽  
W. Lee ◽  
Kerstin Kling ◽  
Andreas Neumayr ◽  
...  
Keyword(s):  
South Asia ◽  
Liver Fluke ◽  
Clonorchis Sinensis ◽  
Human Migration ◽  
Current Therapy ◽  
Parasitic Diseases ◽  
Imaging Features ◽  
Opisthorchis Felineus ◽  
Therapy Options ◽  
Liver Flukes

AbstractParasitic diseases are relatively rarely diagnosed and treated in Europe. Therefore, European clinicians are not familiar with their clinical and imaging features. In an era of increased human migration, it is fundamental for clinicians to be able to identify such diseases. We have recently described the features of cystic echinococcosis, schistosomiasis, fascioliasis and ascariasis. Here, we report on the clinical and imaging features as well as on the current therapy options of infections by the small liver flukes: Clonorchis sinensis, Opisthorchis viverrini (Southeast Asian liver fluke) and Opisthorchis felineus (cat liver fluke) and other Opisthorchis species prevalent in South Asia.

Adult Opisthorchis felineus major protein fractions deduced from transcripts: Comparison with liver flukes Opisthorchis viverrini and Clonorchis sinensis

2013 ◽  
Vol 135 (2) ◽  
pp. 297-306 ◽  
Author(s):  
Mikhail Pomaznoy ◽  
Sergey Tatkov ◽  
Alexey Katokhin ◽  
Dmitry Afonnikov ◽  
Vladimir Babenko ◽  
...  
Keyword(s):  
Clonorchis Sinensis ◽  
Opisthorchis Viverrini ◽  
Protein Fractions ◽  
Major Protein ◽  
Opisthorchis Felineus ◽  
Liver Flukes

scholarly journals Genetic data of the ITS1-5.8S rDNA sequences of small liver flukes (Opisthorchiidae) from cats in Northern Vietnam

2020 ◽  
Vol 17 (4) ◽  
pp. 621-628
Author(s):  
Nguyen Manh Hung ◽  
Loan Thi Ho ◽  
Yulia V. Tatonova
Keyword(s):  
Nucleotide Diversity ◽  
Phylogenetic Analyses ◽  
Clonorchis Sinensis ◽  
Nuclear Ribosomal Dna ◽  
Neighbor Joining ◽  
5.8S Rdna ◽  
Northern Vietnam ◽  
Rdna Sequences ◽  
Its1 Rdna ◽  
Liver Flukes

Domestic cats and humans are favorite final hosts for some hepatic trematodes of Opisthorchiidae. The present study examined the sequence variation in the nuclear ribosomal DNA (rDNA) region, including the internal transcribed spacer (ITS1) and the 5.8S gene, of two human opisthorchiid species Clonorchis sinensis (Cobbold, 1875) Looss, 1907 and Opisthorchis viverrini (Poirier, 1886) Stiles & Hassal, 1896, in cats sampled in Northern Vietnam. The length of 30 partial ITS1‒5.8S rDNA sequences of C. sinensis from different hosts and localities varied from 761 to 766 bp. The results showed completely identity for all investigated 5.8S rDNA sequences of C. sinensis. In contrast, the variations were revealed in the complete ITS1 sequences of C. sinensis. Three polymorphic sites, indel and new sites with intragenomic polymorphism were detected. The length of the complete ITS1 rDNA region ranged from 656 to 661 bp. There are no substitutions downstream of the 5 bp insertion, and the different ratio of nucleotide in polymorphic sites with presence/absence of insertion leads to the existence of 6 genotypes in the investigated samples. The major genotype was obtained in 70% of sequences, other genotypes were presented by 1, 2 or 3 sequences. Nucleotide diversity in whole sample of C. sinensis was 0.00122 ± 0.00073. Partial sequences of ITS1‒5.8S rDNA of O. viverrini were 745 bp in length, and no difference was observed. Phylogenetic analyses by neighbor joining phylogram inferred from ITS1‒5.8S rDNA of 3 sequences of O. viverrini and 30 sequences of C. sinensis were formed two separately monophyletic clades.  

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