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Lyngdoh D, Sharma S, Roy B, Tandon V, Zas P. Secondary Structure Analysis of Fasciola from Semi-wild Ruminants of Northeast India. Acta Parasitol 2024; 69:599-608. [PMID: 38261242 DOI: 10.1007/s11686-023-00777-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 12/07/2023] [Indexed: 01/24/2024]
Abstract
PURPOSE The objective of this study is to study the secondary structure analysis of Fasciola flukes from a rare mithun host from Manipur. Fascioliasis, a neglected tropical trematodiasis, is poorly studied in India and is widely believed to be predominantly caused by F. gigantica. Through this study, we want to assess the flukes from the rare semi-wild ruminants of Northeast India. This study is important as the mithun population is semi-wild and its population is declining in Manipur. METHODS Sample collected from the difficult and challenging terrain of Northeast India. The sample was collected from mithun and observed under the microscope. DNA was isolated, sequenced, and analyzed using various bioinformatics tools. The secondary structure analysis of the Internal Transcribed Spacer 2 (ITS2) region was also performed. RESULTS The secondary structure species tree corroborated the Bayesian inference and, hence, strengthened the phylogeny reconstructed. The annotated ITS2 sequence and RNA secondary of the Manipur isolate displayed the typical four-helix or four-domain model. Helix III reveals the presence of the UGGU motif with other deviations like UGG and GGU. CONCLUSION This is an in-depth analysis of the secondary structure of Fasciola species. The present study has demonstrated the usefulness of ITS2 and its secondary structures for characterizing parasites. The information on fascioliasis in the mithun's population presents itself useful with regards to their conservation strategy as their populations in both Manipur and Nagaland are dwindling.
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Affiliation(s)
- Damanbha Lyngdoh
- Department of Zoology, St. Anthony's College, Shillong, 793001, Meghalaya, India.
| | - Sunil Sharma
- Biotech Hub, St. Edmund's College, Shillong, 793003, Meghalaya, India
| | - Bishnupada Roy
- Department of Zoology, North Eastern Hill University, Shillong, 793022, Meghalaya, India
| | - Veena Tandon
- NASI Senior Scientist Platinum Jubilee Fellow, Mahanagar, Uttar Pradesh, Lucknow, 226006, India
| | - Philayung Zas
- Department of Zoology, William Carey University, Shillong, 793019, Meghalaya, India
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Shumenko PG, Tatonova YV. Assessing the population structure of trematode Metagonimus suifunensis using three mitochondrial markers. Parasitol Res 2022; 121:915-923. [PMID: 35133488 DOI: 10.1007/s00436-022-07456-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 01/26/2022] [Indexed: 11/27/2022]
Abstract
In this work, for the first time, the genetic variability of the Metagonimus suifunensis population in the Russian southern Far East was estimated based on the full-length sequences of the nad1 gene of mitochondrial DNA. In addition, for a sample of the same size, the sequences of cox1 and cytb genes, previously used for population studies for M. suifunensis, were reanalysed. Three markers were combined to a common sequence, and the obtained data were studied. Despite the higher level of variability, nad1 and cox1 mtDNA genes did not reveal subdivisions within the population. The combined dataset made it possible to determine that the sample from the Odyr River was the centre of the species' range formation and clarified the continental migration route of the parasite from south to north. According to the data obtained, it was presumed that piscivorous birds participate in the life cycle of the parasite. The subdivision within population revealed that using all three mitochondrial markers is consistent with the features of differentiation within populations of related species, but the reasons for its formation remain unclear due to the insufficient amount of data and the use of different markers in studies of different species.
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Affiliation(s)
- Polina G Shumenko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch, Russian Academy of Sciences, 100-letiya Street, 159, Vladivostok, 690022, Russia
| | - Yulia V Tatonova
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch, Russian Academy of Sciences, 100-letiya Street, 159, Vladivostok, 690022, Russia. .,School of Biomedicine, Far Eastern Federal University, Sukhanova Street, 8, Vladivostok, 690091, Russia.
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Trevisan B, Jacob Machado D, Lahr DJG, Marques FPL. Comparative Characterization of Mitogenomes From Five Orders of Cestodes (Eucestoda: Tapeworms). Front Genet 2022; 12:788871. [PMID: 35003223 PMCID: PMC8727539 DOI: 10.3389/fgene.2021.788871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/23/2021] [Indexed: 12/26/2022] Open
Abstract
The recognized potential of using mitogenomics in phylogenetics and the more accessible use of high-throughput sequencing (HTS) offer an opportunity to investigate groups of neglected organisms. Here, we leveraged HTS to execute the most comprehensive documentation of mitogenomes for cestodes based on the number of terminals sequenced. We adopted modern approaches to obtain the complete mitogenome sequences of 86 specimens representing five orders of cestodes (three reported for the first time: Phyllobothriidea, “Tetraphyllidea” and Trypanorhyncha). These complete mitogenomes represent an increase of 41% of the mitogenomes available for cestodes (61–147) and an addition of 33% in the representativeness of the cestode orders. The complete mitochondrial genomes are conserved, circular, encoded in the same strand, and transcribed in the same direction, following the pattern observed previously for tapeworms. Their length varies from 13,369 to 13,795 bp, containing 36 genes in total. Except for the Trypanorhyncha specimen, the gene order of the other four cestode orders sequenced here suggests that it could be a synapomorphy for the acetabulate group (with a reversion for taenids). Our results also suggest that no single gene can tell all the evolutionary history contained in the mitogenome. Therefore, cestodes phylogenies based on a single mitochondrial marker may fail to capture their evolutionary history. We predict that such phylogenies would be improved if conducted under a total evidence framework. The characterization of the new mitochondrial genomes is the first step to provide a valuable resource for future studies on the evolutionary relationships of these groups of parasites.
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Affiliation(s)
- Bruna Trevisan
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Denis Jacob Machado
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Daniel J G Lahr
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Fernando P L Marques
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
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Catalano S, Léger E, Fall CB, Borlase A, Diop SD, Berger D, Webster BL, Faye B, Diouf ND, Rollinson D, Sène M, Bâ K, Webster JP. Multihost Transmission of Schistosoma mansoni in Senegal, 2015-2018. Emerg Infect Dis 2021; 26:1234-1242. [PMID: 32441625 PMCID: PMC7258455 DOI: 10.3201/eid2606.200107] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
In West Africa, Schistosoma spp. are capable of infecting multiple definitive hosts, a lifecycle feature that may complicate schistosomiasis control. We characterized the evolutionary relationships among multiple Schistosoma mansoni isolates collected from snails (intermediate hosts), humans (definitive hosts), and rodents (definitive hosts) in Senegal. On a local scale, diagnosis of S. mansoni infection ranged 3.8%-44.8% in school-aged children, 1.7%-52.6% in Mastomys huberti mice, and 1.8%-7.1% in Biomphalaria pfeifferi snails. Our phylogenetic framework confirmed the presence of multiple S. mansoni lineages that could infect both humans and rodents; divergence times of these lineages varied (0.13-0.02 million years ago). We propose that extensive movement of persons across West Africa might have contributed to the establishment of these various multihost S. mansoni clades. High S. mansoni prevalence in rodents at transmission sites frequented by humans further highlights the implications that alternative hosts could have on future public health interventions.
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Tang Y, Zhang X, Ma Y, Zheng X. Descriptive study of the mitogenome of the diamondback squid (
Thysanoteuthis rhombus
Troschel, 1857) and the evolution of mitogenome arrangement in oceanic squids. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yan Tang
- Institute of Evolution and Marine Biodiversity Ocean University of China Qingdao China
- Key Laboratory of Mariculture Ocean University of China Qingdao China
| | - Xiaoying Zhang
- Institute of Evolution and Marine Biodiversity Ocean University of China Qingdao China
- Key Laboratory of Mariculture Ocean University of China Qingdao China
| | - Yuanyuan Ma
- Institute of Evolution and Marine Biodiversity Ocean University of China Qingdao China
- Key Laboratory of Mariculture Ocean University of China Qingdao China
| | - Xiaodong Zheng
- Institute of Evolution and Marine Biodiversity Ocean University of China Qingdao China
- Key Laboratory of Mariculture Ocean University of China Qingdao China
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Assessing the suitability of mitochondrial and nuclear DNA genetic markers for molecular systematics and species identification of helminths. Parasit Vectors 2021; 14:233. [PMID: 33933158 PMCID: PMC8088577 DOI: 10.1186/s13071-021-04737-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 04/21/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genetic markers are employed widely in molecular studies, and their utility depends on the degree of sequence variation, which dictates the type of application for which they are suited. Consequently, the suitability of a genetic marker for any specific application is complicated by its properties and usage across studies. To provide a yardstick for future users, in this study we assess the suitability of genetic markers for molecular systematics and species identification in helminths and provide an estimate of the cut-off genetic distances per taxonomic level. METHODS We assessed four classes of genetic markers, namely nuclear ribosomal internal transcribed spacers, nuclear rRNA, mitochondrial rRNA and mitochondrial protein-coding genes, based on certain properties that are important for species identification and molecular systematics. For molecular identification, these properties are inter-species sequence variation; length of reference sequences; easy alignment of sequences; and easy to design universal primers. For molecular systematics, the properties are: average genetic distance from order/suborder to species level; the number of monophyletic clades at the order/suborder level; length of reference sequences; easy alignment of sequences; easy to design universal primers; and absence of nucleotide substitution saturation. Estimation of the cut-off genetic distances was performed using the 'K-means' clustering algorithm. RESULTS The nuclear rRNA genes exhibited the lowest sequence variation, whereas the mitochondrial genes exhibited relatively higher variation across the three groups of helminths. Also, the nuclear and mitochondrial rRNA genes were the best possible genetic markers for helminth molecular systematics, whereas the mitochondrial protein-coding and rRNA genes were suitable for molecular identification. We also revealed that a general gauge of genetic distances might not be adequate, using evidence from the wide range of genetic distances among nematodes. CONCLUSION This study assessed the suitability of DNA genetic markers for application in molecular systematics and molecular identification of helminths. We provide a novel way of analyzing genetic distances to generate suitable cut-off values for each taxonomic level using the 'K-means' clustering algorithm. The estimated cut-off genetic distance values, together with the summary of the utility and limitations of each class of genetic markers, are useful information that can benefit researchers conducting molecular studies on helminths.
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Kamel B, Laidemitt MR, Lu L, Babbitt C, Weinbaum OL, Mkoji GM, Loker ES. Detecting and identifying Schistosoma infections in snails and aquatic habitats: A systematic review. PLoS Negl Trop Dis 2021; 15:e0009175. [PMID: 33760814 PMCID: PMC8021170 DOI: 10.1371/journal.pntd.0009175] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 04/05/2021] [Accepted: 01/26/2021] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND We were tasked by the World Health Organization (WHO) to address the following question: What techniques should be used to diagnose Schistosoma infections in snails and in the water in potential transmission sites? Our goal was to review and evaluate the available literature and provide recommendations and insights for the development of WHO's Guidelines Development Group for schistosomiasis control and elimination. METHODOLOGY We searched several databases using strings of search terms, searched bibliographies of pertinent papers, and contacted investigators who have made contributions to this field. Our search covered from 1970 to Sept 2020. All papers were considered in a PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) framework, and retained papers were grouped by technique and subjected to our GRADE (Grading of Recommendations, Assessment, Development and Evaluations) evidence assessment profile determined in consultation with WHO. We also considered issues of sensitivity, specificity, coverage, cost, robustness, support needs, schistosome species discrimination, and relevant detection limits. PRINCIPAL FINDINGS Our PRISMA process began with the perusal of 949 articles, of which 158 were retained for data extraction and evaluation. We identified 25 different techniques and for each applied a GRADE assessment considering limitations, inconsistency, imprecision, indirectness, and publication bias. We also provide advantages and disadvantages for each category of techniques. CONCLUSIONS Our GRADE analysis returned an assessment of moderate quality of evidence for environmental DNA (eDNA), qPCR and LAMP (Loop-mediated isothermal amplification). No single ideal diagnostic approach has yet been developed, but considerable recent progress has been made. We note a growing trend to use eDNA techniques to permit more efficient and replicable sampling. qPCR-based protocols for follow-up detection offer a versatile, mature, sensitive, and specific platform for diagnosis though centralized facilities will be required to favor standardization. Droplet digital PCR (ddPCR) can play a complementary role if inhibitors are a concern, or more sensitivity or quantification is needed. Snail collection, followed by shedding, is encouraged to provide specimens for sequence verifications of snails or schistosomes. LAMP or other isothermal detection techniques offer the prospect of less expensive and more distributed network of analysis but may face standardization and verification challenges related to actual sequences amplified. Ability to detect schistosome infections in snails or in the water is needed if control and elimination programs hope to succeed. Any diagnostic techniques used need to be regularly verified by the acquisition of DNA sequences to confirm that the detected targets are of the expected species. Further improvements may be necessary to identify the ideal schistosome or snail sequences to target for amplification. More field testing and standardization will be essential for long-term success.
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Affiliation(s)
- Bishoy Kamel
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM, United States of America
| | - Martina R. Laidemitt
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM, United States of America
- Parasitology Division, Museum of Southwestern Biology, Department of Biology, University of New Mexico, Albuquerque, NM, United States of America
| | - Lijun Lu
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM, United States of America
- Parasitology Division, Museum of Southwestern Biology, Department of Biology, University of New Mexico, Albuquerque, NM, United States of America
| | - Caitlin Babbitt
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM, United States of America
- Parasitology Division, Museum of Southwestern Biology, Department of Biology, University of New Mexico, Albuquerque, NM, United States of America
| | - Ola Liota Weinbaum
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM, United States of America
| | - Gerald M. Mkoji
- Center for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya
| | - Eric S. Loker
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM, United States of America
- Parasitology Division, Museum of Southwestern Biology, Department of Biology, University of New Mexico, Albuquerque, NM, United States of America
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Xu G, Zhu P, Zhu W, Ma B, Li X, Li W. Characterization of the complete mitochondrial genome of Notocotylus sp. (Trematoda, Notocotylidae) and its phylogenetic implications. Parasitol Res 2021; 120:1291-1301. [PMID: 33559042 DOI: 10.1007/s00436-021-07075-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 01/28/2021] [Indexed: 01/20/2023]
Abstract
The parasite genus Notocotylus comprises at least 50 species colonizing mainly aquatic birds and to a lesser extent some mammals, particularly rodents. Here trematode specimens isolated from a wild black swan were characterized and identified to belong to the genus Notocotylus via morphological and molecular analyses. Phylogenetic position of the isolate among other trematodes was determined based on the ribosomal internal transcribed spacer (ITS) 1 and 2. The complete mitochondrial (mt) genome of the isolate was amplified, sequenced, assembled, analyzed, and annotated. The isolate has an AT-rich mt genome (14,317 bp in length) that comprises 12 protein-coding genes (PCGs), 22 transfer RNA genes, and two ribosomal RNA genes. The Notocotylus isolate identified in this study has relatively high mt genome sequence identity and identical gene content and arrangement to a known Notocotylidae species, Ogmocotyle sikae. The isolate formed a genetic clade with O. sikae in phylogenetic analysis of the concatenated PCG amino acid sequences. Compared to the ITS, the trematode mt genome appears more informative for resolving high-level phylogenies. To the best of our knowledge, this is the first study exploring the complete mt genome for the genus Notocotylus, and it offers a novel genomic resource that has important implications for trematode phylogenetics.
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Affiliation(s)
- Guoliang Xu
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China.,Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Peng Zhu
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Weining Zhu
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Bo Ma
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Xiaoyun Li
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Wei Li
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China.
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Landeryou T, Kett SM, Ropiquet A, Wildeboer D, Lawton SP. Characterization of the complete mitochondrial genome of Diplostomum baeri. Parasitol Int 2020; 79:102166. [DOI: 10.1016/j.parint.2020.102166] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 10/24/2022]
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Palevich N, Maclean PH, Choi YJ, Mitreva M. Characterization of the Complete Mitochondrial Genomes of Two Sibling Species of Parasitic Roundworms, Haemonchus contortus and Teladorsagia circumcincta. Front Genet 2020; 11:573395. [PMID: 33133162 PMCID: PMC7578395 DOI: 10.3389/fgene.2020.573395] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/18/2020] [Indexed: 12/20/2022] Open
Abstract
Haemonchus contortus and Teladorsagia circumcincta are among the two most pathogenic internal parasitic nematodes infecting small ruminants, such as sheep and goats, and are a global animal health issue. Accurate identification and delineation of Haemonchidae species is essential for development of diagnostic and control strategies with high resolution for Trichostrongyloidea infection in ruminants. Here, we describe in detail and compare the complete mitochondrial (mt) genomes of the New Zealand H. contortus and T. circumcincta field strains to improve our understanding of species- and strain-level evolution in these closely related roundworms. In the present study, we performed extensive comparative bioinformatics analyses on the recently sequenced complete mt genomes of the New Zealand H. contortus NZ_Hco_NP and T. circumcincta NZ_Teci_NP field strains. Amino acid sequences inferred from individual genes of each of the two mt genomes were compared, concatenated and subjected to phylogenetic analysis using Bayesian inference (BI), Maximum Likelihood (ML), and Maximum Parsimony (MP). The AT-rich mt genomes of H. contortus NZ_Hco_NP and T. circumcincta NZ_Teci_NP are 14,001 bp (A+T content of 77.4%) and 14,081 bp (A+T content of 77.3%) in size, respectively. All 36 of the typical nematode mt genes are transcribed in the forward direction in both species and comprise of 12 protein-encoding genes (PCGs), 2 ribosomal RNA (rrn) genes, and 22 transfer RNA (trn) genes. The secondary structures for the 22 trn genes and two rrn genes differ between H. contortus NZ_Hco_NP and T. circumcincta NZ_Teci_NP, however the gene arrangements of both are consistent with other Trichostrongylidea sequenced to date. Comparative analyses of the complete mitochondrial nucleotide sequences, PCGs, A+T rich and non-coding repeat regions of H. contortus NZ_Hco_NP and T. circumcincta NZ_Teci_NP further reinforces the high levels of diversity and gene flow observed among Trichostrongylidea, and supports their potential as ideal markers for strain-level identification from different hosts and geographical regions with high resolution for future studies. The complete mt genomes of H. contortus NZ_Hco_NP and T. circumcincta NZ_Teci_NP presented here provide useful novel markers for further studies of the meta-population connectivity and the genetic mechanisms driving evolution in nematode species.
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Affiliation(s)
- Nikola Palevich
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Paul H. Maclean
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Young-Jun Choi
- McDonnell Genome Institute and Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States
| | - Makedonka Mitreva
- McDonnell Genome Institute and Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States
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Ceruso M, Mascolo C, De Luca P, Venuti I, Smaldone G, Biffali E, Anastasio A, Pepe T, Sordino P. A Rapid Method for the Identification of Fresh and Processed Pagellus erythrinus Species against Frauds. Foods 2020; 9:E1397. [PMID: 33023115 PMCID: PMC7600753 DOI: 10.3390/foods9101397] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 09/28/2020] [Accepted: 09/30/2020] [Indexed: 11/16/2022] Open
Abstract
The commercialization of porgies or seabreams of the family Sparidae has greatly increased in the last decade, and some valuable species have become subject to seafood substitution. DNA regions currently used for fish species identification in fresh and processed products belong to the mitochondrial (mt) genes cytochrome b (Cytb), cytochrome c oxidase I (COI), 16S and 12S. However, these markers amplify for fragments with lower divergence within and between some species, failing to provide informative barcodes. We adopted comparative mitogenomics, through the analysis of complete mtDNA sequences, as a compatible approach toward studying new barcoding markers. The intent is to develop a specific and rapid assay for the identification of the common pandora Pagellus erythrinus, a sparid species frequently subject to fraudulent replacement. The genetic diversity analysis (Hamming distance, p-genetic distance, gene-by-gene sequence variability) between 16 sparid mtDNA genomes highlighted the discriminating potential of a 291 bp NAD2 gene fragment. A pair of species-specific primers were successfully designed and tested by end-point and real-time PCR, achieving amplification only in P. erythrinus among several fish species. The use of the NAD2 barcoding marker provides a rapid presence/absence method for the identification of P. erythrinus.
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Affiliation(s)
- Marina Ceruso
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via F. Delpino, n.1, 80137 Naples, Italy; (M.C.); (C.M.); (I.V.); (A.A.)
| | - Celestina Mascolo
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via F. Delpino, n.1, 80137 Naples, Italy; (M.C.); (C.M.); (I.V.); (A.A.)
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy;
| | - Pasquale De Luca
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (P.D.L.); (E.B.)
| | - Iolanda Venuti
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via F. Delpino, n.1, 80137 Naples, Italy; (M.C.); (C.M.); (I.V.); (A.A.)
| | - Giorgio Smaldone
- Department Agricultural Sciences, University of Naples Federico II, via Università, n.100, Portici, 80055 Naples, Italy;
| | - Elio Biffali
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (P.D.L.); (E.B.)
| | - Aniello Anastasio
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via F. Delpino, n.1, 80137 Naples, Italy; (M.C.); (C.M.); (I.V.); (A.A.)
| | - Tiziana Pepe
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via F. Delpino, n.1, 80137 Naples, Italy; (M.C.); (C.M.); (I.V.); (A.A.)
| | - Paolo Sordino
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy;
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Kinkar L, Young ND, Sohn WM, Stroehlein AJ, Korhonen PK, Gasser RB. First record of a tandem-repeat region within the mitochondrial genome of Clonorchis sinensis using a long-read sequencing approach. PLoS Negl Trop Dis 2020; 14:e0008552. [PMID: 32845881 PMCID: PMC7449408 DOI: 10.1371/journal.pntd.0008552] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/01/2020] [Indexed: 12/14/2022] Open
Abstract
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-sequencing/informatic approach now paves the way to investigating the nature and extent of length/sequence variation in this region within and among individual worms, both within and among C. sinensis populations, and to exploring whether this region has a functional role in the regulation of replication and transcription, akin to the mitochondrial control region in mammals. Although applied to C. sinensis, the technological approach established here should be broadly applicable to characterise complex tandem-repetitive or homo-polymeric regions in the mitochondrial genomes of a wide range of taxa. In the present study, we characterised the complete mitochondrial genome of Clonorchis sinensis—a carcinogenic liver fluke. To do this, we sequenced from total genomic DNA from multiple adult worms using a new method (Oxford Nanopore technology) to obtain data for long stretches of DNA, and then assembled these data to construct a mitochondrial genome of 18,304 bp, containing a > 4.5 kb-long tandem-repetitive region—not previously detected in this species. The results demonstrate that this method is effective at sequencing long and complex non-coding elements—not achievable using conventional techniques. The discovery of this long tandem-repetitive region in C. sinensis provides an opportunity to now explore its origin(s) and length/sequence diversity in populations of this species, and also to characterise its function(s). The technological approach employed here should have broad applicability to characterise previously-elusive non-coding mitochondrial genomic regions in a wide range of taxa.
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Affiliation(s)
- Liina Kinkar
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Neil D. Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
- * E-mail: (NDY); (RBG)
| | - Woon-Mok Sohn
- Department of Parasitology and Tropical Medicine, and Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju, Korea
| | - Andreas J. Stroehlein
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Pasi K. Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Robin B. Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
- * E-mail: (NDY); (RBG)
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13
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Klein AH, Ballard KR, Storey KB, Motti CA, Zhao M, Cummins SF. Multi-omics investigations within the Phylum Mollusca, Class Gastropoda: from ecological application to breakthrough phylogenomic studies. Brief Funct Genomics 2020; 18:377-394. [PMID: 31609407 DOI: 10.1093/bfgp/elz017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 07/06/2019] [Accepted: 07/15/2019] [Indexed: 12/22/2022] Open
Abstract
Gastropods are the largest and most diverse class of mollusc and include species that are well studied within the areas of taxonomy, aquaculture, biomineralization, ecology, microbiome and health. Gastropod research has been expanding since the mid-2000s, largely due to large-scale data integration from next-generation sequencing and mass spectrometry in which transcripts, proteins and metabolites can be readily explored systematically. Correspondingly, the huge data added a great deal of complexity for data organization, visualization and interpretation. Here, we reviewed the recent advances involving gastropod omics ('gastropodomics') research from hundreds of publications and online genomics databases. By summarizing the current publicly available data, we present an insight for the design of useful data integrating tools and strategies for comparative omics studies in the future. Additionally, we discuss the future of omics applications in aquaculture, natural pharmaceutical biodiscovery and pest management, as well as to monitor the impact of environmental stressors.
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Affiliation(s)
- Anne H Klein
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Kaylene R Ballard
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Kenneth B Storey
- Institute of Biochemistry & Department of Biology, Carleton University, Ottawa, ON, Canada K1S 5B6
| | - Cherie A Motti
- Australian Institute of Marine Science (AIMS), Cape Ferguson, Townsville Queensland 4810, Australia
| | - Min Zhao
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Scott F Cummins
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
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14
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Abstract
While disease and outbreaks are mainly clonal for bacteria and other asexually reproducing organisms, sexual reproduction in schistosomes and other helminths usually results in unique individuals. For sexually reproducing organisms, the traits conserved in clones will instead be conserved in the group of organisms that tends to breed together, the population. While the same tools are applied to characterize DNA, how results are interpreted can be quite different at times (see another article in this collection, http://www.asmscience.org/content/journal/microbiolspec/10.1128/microbiolspec.AME-0002-2018). It is difficult to know what the real effect any control program has on the parasite population without assessing the health of this population, how they respond to the control measure, and how they recover, if they do. This review, part of the Microbiology Spectrum Curated Collection: Advances in Molecular Epidemiology of Infectious Diseases, concentrates on one approach using pooled samples to study schistosome populations and shows how this and other approaches have contributed to our understanding of this parasite family's biology and epidemiology. *This article is part of a curated collection.
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Jones BP, Norman BF, Borrett HE, Attwood SW, Mondal MMH, Walker AJ, Webster JP, Rajapakse RPVJ, Lawton SP. Divergence across mitochondrial genomes of sympatric members of the Schistosoma indicum group and clues into the evolution of Schistosoma spindale. Sci Rep 2020; 10:2480. [PMID: 32051431 PMCID: PMC7015907 DOI: 10.1038/s41598-020-57736-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 01/07/2020] [Indexed: 11/21/2022] Open
Abstract
Schistosoma spindale and Schistosoma indicum are ruminant-infecting trematodes of the Schistosoma indicum group that are widespread across Southeast Asia. Though neglected, these parasites can cause major pathology and mortality to livestock leading to significant welfare and socio-economic issues, predominantly amongst poor subsistence farmers and their families. Here we used mitogenomic analysis to determine the relationships between these two sympatric species of schistosome and to characterise S. spindale diversity in order to identify possible cryptic speciation. The mitochondrial genomes of S. spindale and S. indicum were assembled and genetic analyses revealed high levels of diversity within the S. indicum group. Evidence of functional changes in mitochondrial genes indicated adaptation to environmental change associated with speciation events in S. spindale around 2.5 million years ago. We discuss our results in terms of their theoretical and applied implications.
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Affiliation(s)
- Ben P Jones
- Molecular Parasitology Laboratory, School of Life Sciences, Pharmacy & Chemistry, Kingston University London, Kingston Upon Thames, Surrey, KT1 2EE, UK
| | - Billie F Norman
- Molecular Parasitology Laboratory, School of Life Sciences, Pharmacy & Chemistry, Kingston University London, Kingston Upon Thames, Surrey, KT1 2EE, UK
| | - Hannah E Borrett
- Molecular Parasitology Laboratory, School of Life Sciences, Pharmacy & Chemistry, Kingston University London, Kingston Upon Thames, Surrey, KT1 2EE, UK
| | - Stephen W Attwood
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Mohammed M H Mondal
- Department of Parasitology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Anthony J Walker
- Molecular Parasitology Laboratory, School of Life Sciences, Pharmacy & Chemistry, Kingston University London, Kingston Upon Thames, Surrey, KT1 2EE, UK
| | - Joanne P Webster
- Centre for Emerging, Endemic and Exotic Diseases, Department of Pathobiology and Population Sciences, The Royal Veterinary College, University of London, Hatfield, Hertfordshire, AL9 7TA, United Kingdom
| | - R P V Jayanthe Rajapakse
- Faculty of Veterinary Medicine and Animal Science, Department of Veterinary Pathobiology, University of Peradeniya, Peradeniya, 20400, Sri Lanka
| | - Scott P Lawton
- Molecular Parasitology Laboratory, School of Life Sciences, Pharmacy & Chemistry, Kingston University London, Kingston Upon Thames, Surrey, KT1 2EE, UK.
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Trevisan B, Alcantara DM, Machado DJ, Marques FP, Lahr DJ. Genome skimming is a low-cost and robust strategy to assemble complete mitochondrial genomes from ethanol preserved specimens in biodiversity studies. PeerJ 2019; 7:e7543. [PMID: 31565556 PMCID: PMC6746217 DOI: 10.7717/peerj.7543] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 07/24/2019] [Indexed: 12/17/2022] Open
Abstract
Global loss of biodiversity is an ongoing process that concerns both local and global authorities. Studies of biodiversity mainly involve traditional methods using morphological characters and molecular protocols. However, conventional methods are a time consuming and resource demanding task. The development of high-throughput sequencing (HTS) techniques has reshaped the way we explore biodiversity and opened a path to new questions and novel empirical approaches. With the emergence of HTS, sequencing the complete mitochondrial genome became more accessible, and the number of genome sequences published has increased exponentially during the last decades. Despite the current state of knowledge about the potential of mitogenomics in phylogenetics, this is still a relatively under-explored area for a multitude of taxonomic groups, especially for those without commercial relevance, non-models organisms and with preserved DNA. Here we take the first step to assemble and annotate the genomes from HTS data using a new protocol of genome skimming which will offer an opportunity to extend the field of mitogenomics to under-studied organisms. We extracted genomic DNA from specimens preserved in ethanol. We used Nextera XT DNA to prepare indexed paired-end libraries since it is a powerful tool for working with diverse samples, requiring a low amount of input DNA. We sequenced the samples in two different Illumina platform (MiSeq or NextSeq 550). We trimmed raw reads, filtered and had their quality tested accordingly. We performed the assembly using a baiting and iterative mapping strategy, and the annotated the putative mitochondrion through a semi-automatic procedure. We applied the contiguity index to access the completeness of each new mitogenome. Our results reveal the efficiency of the proposed method to recover the whole mitogenomes of preserved DNA from non-model organisms even if there are gene rearrangement in the specimens. Our findings suggest the potential of combining the adequate platform and library to the genome skimming as an innovative approach, which opens a new range of possibilities of its use to obtain molecular data from organisms with different levels of preservation.
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Affiliation(s)
- Bruna Trevisan
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Daniel M.C. Alcantara
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Denis Jacob Machado
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
- Department of Bioinformatics and Genomics / College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, NC, United States of America
| | - Fernando P.L. Marques
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Daniel J.G. Lahr
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
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18
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Le TH, Nguyen KT, Nguyen NTB, Doan HTT, Agatsuma T, Blair D. The complete mitochondrial genome of Paragonimus ohirai (Paragonimidae: Trematoda: Platyhelminthes) and its comparison with P. westermani congeners and other trematodes. PeerJ 2019; 7:e7031. [PMID: 31259095 PMCID: PMC6589331 DOI: 10.7717/peerj.7031] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 04/27/2019] [Indexed: 11/20/2022] Open
Abstract
We present the complete mitochondrial genome of Paragonimus ohirai Miyazaki, 1939 and compare its features with those of previously reported mitochondrial genomes of the pathogenic lung-fluke, Paragonimus westermani, and other members of the genus. The circular mitochondrial DNA molecule of the single fully sequenced individual of P. ohirai was 14,818 bp in length, containing 12 protein-coding, two ribosomal RNA and 22 transfer RNA genes. As is common among trematodes, an atp8 gene was absent from the mitogenome of P. ohirai and the 5' end of nad4 overlapped with the 3' end of nad4L by 40 bp. Paragonimusohirai and four forms/strains of P. westermani from South Korea and India, exhibited remarkably different base compositions and hence codon usage in protein-coding genes. In the fully sequenced P. ohirai individual, the non-coding region started with two long identical repeats (292 bp each), separated by tRNAGlu . These were followed by an array of six short tandem repeats (STR), 117 bp each. Numbers of the short tandem repeats varied among P. ohirai individuals. A phylogenetic tree inferred from concatenated mitochondrial protein sequences of 50 strains encompassing 42 species of trematodes belonging to 14 families identified a monophyletic Paragonimidae in the class Trematoda. Characterization of additional mitogenomes in the genus Paragonimus will be useful for biomedical studies and development of molecular tools and mitochondrial markers for diagnostic, identification, hybridization and phylogenetic/epidemiological/evolutionary studies.
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Affiliation(s)
- Thanh Hoa Le
- Immunology Department, Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
- Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Khue Thi Nguyen
- Immunology Department, Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Nga Thi Bich Nguyen
- Immunology Department, Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Huong Thi Thanh Doan
- Immunology Department, Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
- Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Takeshi Agatsuma
- Department of Environmental Medicine, Kochi Medical School, Kochi University, Oko, Nankoku City, Kochi, Japan
| | - David Blair
- College of Science and Engineering, James Cook University, Townsville, Australia
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19
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Tang Y, Zheng X, Zhong H, Li Q. Phylogenetics and comparative analysis of the mitochondrial genomes of three violet‐ringed octopuses. ZOOL SCR 2019. [DOI: 10.1111/zsc.12359] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yan Tang
- Key Laboratory of Mariculture Ocean University of China Qingdao China
- Institute of Evolution and Marine Biodiversity Ocean University of China Qingdao China
| | - Xiaodong Zheng
- Key Laboratory of Mariculture Ocean University of China Qingdao China
- Institute of Evolution and Marine Biodiversity Ocean University of China Qingdao China
| | - Hong Zhong
- Shenzhen BGTX Foods Co., Ltd. Shenzhen China
| | - Qi Li
- Key Laboratory of Mariculture Ocean University of China Qingdao China
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20
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Testing the higher-level phylogenetic classification of Digenea (Platyhelminthes, Trematoda) based on nuclear rDNA sequences before entering the age of the 'next-generation' Tree of Life. J Helminthol 2019; 93:260-276. [PMID: 30973318 DOI: 10.1017/s0022149x19000191] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Digenea Carus, 1863 represent a highly diverse group of parasitic platyhelminths that infect all major vertebrate groups as definitive hosts. Morphology is the cornerstone of digenean systematics, but molecular markers have been instrumental in searching for a stable classification system of the subclass and in establishing more accurate species limits. The first comprehensive molecular phylogenetic tree of Digenea published in 2003 used two nuclear rRNA genes (ssrDNA = 18S rDNA and lsrDNA = 28S rDNA) and was based on 163 taxa representing 77 nominal families, resulting in a widely accepted phylogenetic classification. The genetic library for the 28S rRNA gene has increased steadily over the last 15 years because this marker possesses a strong phylogenetic signal to resolve sister-group relationships among species and to infer phylogenetic relationships at higher levels of the taxonomic hierarchy. Here, we have updated the database of 18S and 28S rRNA genes until December 2017, we have added newly generated 28S rDNA sequences and we have reassessed phylogenetic relationships to test the current higher-level classification of digeneans (at the subordinal and subfamilial levels). The new dataset consisted of 1077 digenean taxa allocated to 106 nominal families for 28S and 419 taxa in 98 families for 18S. Overall, the results were consistent with previous higher-level classification schemes, and most superfamilies and suborders were recovered as monophyletic assemblages. With the advancement of next-generation sequencing (NGS) technologies, new phylogenetic hypotheses from complete mitochondrial genomes have been proposed, although their power to resolve deep levels of trees remains controversial. Since data from NGS methods are replacing other widely used markers for phylogenetic analyses, it is timely to reassess the phylogenetic relationships of digeneans with conventional nuclear rRNA genes, and to use the new analysis to test the performance of genomic information gathered from NGS, e.g. mitogenomes, to infer higher-level relationships of this group of parasitic platyhelminths.
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Chapman PA, Cribb TH, Flint M, Traub RJ, Blair D, Kyaw-Tanner MT, Mills PC. Spirorchiidiasis in marine turtles: the current state of knowledge. DISEASES OF AQUATIC ORGANISMS 2019; 133:217-245. [PMID: 31187736 DOI: 10.3354/dao03348] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Blood flukes of the family Spirorchiidae are important disease agents in marine turtles. The family is near cosmopolitan in distribution. Twenty-nine marine species across 10 genera are currently recognized, but taxonomic problems remain and it is likely that more species will be discovered. Spirorchiids infect the circulatory system, where they and their eggs cause a range of inflammatory lesions. Infection is sometimes implicated in the death of the turtle. In some regions, prevalence in stranded turtles is close to 100%. Knowledge of life cycles, important for control and epidemiological studies, has proven elusive until recently, when the first intermediate host identifications were made. Recent molecular studies of eggs and adult worms indicate that a considerable level of intrageneric and intraspecific diversity exists. The characterization of this diversity is likely to be of importance in exploring parasite taxonomy and ecology, unravelling life cycles, identifying the differential pathogenicity of genotypes and species, and developing antemortem diagnostic tools, all of which are major priorities for future spirorchiid research. Diagnosis to date has been reliant on copromicroscopy or necropsy, which both have significant limitations. The current lack of reliable antemortem diagnostic options is a roadblock to determining the true prevalence and epidemiology of spirorchiidiasis and the development of effective treatment regimes.
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Affiliation(s)
- Phoebe A Chapman
- Veterinary-Marine Animal Research, Teaching and Investigation, School of Veterinary Science, The University of Queensland, Gatton, Queensland 4343, Australia
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Comparative genomics and phylogenomics of Trichostrongyloidea mitochondria reveal insights for molecular diagnosis and evolutionary biology of nematode worms. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Li WX, Zhang D, Boyce K, Xi BW, Zou H, Wu SG, Li M, Wang GT. The complete mitochondrial DNA of three monozoic tapeworms in the Caryophyllidea: a mitogenomic perspective on the phylogeny of eucestodes. Parasit Vectors 2017; 10:314. [PMID: 28655342 PMCID: PMC5488446 DOI: 10.1186/s13071-017-2245-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 06/12/2017] [Indexed: 11/20/2022] Open
Abstract
Background External segmentation and internal proglottization are important evolutionary characters of the Eucestoda. The monozoic caryophyllideans are considered the earliest diverging eucestodes based on partial mitochondrial genes and nuclear rDNA sequences, yet, there are currently no complete mitogenomes available. We have therefore sequenced the complete mitogenomes of three caryophyllideans, as well as the polyzoic Schyzocotyle acheilognathi, explored the phylogenetic relationships of eucestodes and compared the gene arrangements between unsegmented and segmented cestodes. Results The circular mitogenome of Atractolytocestus huronensis was 15,130 bp, the longest sequence of all the available cestodes, 14,620 bp for Khawia sinensis, 14,011 bp for Breviscolex orientalis and 14,046 bp for Schyzocotyle acheilognathi. The A-T content of the three caryophyllideans was found to be lower than any other published mitogenome. Highly repetitive regions were detected among the non-coding regions (NCRs) of the four cestode species. The evolutionary relationship determined between the five orders (Caryophyllidea, Diphyllobothriidea, Bothriocephalidea, Proteocephalidea and Cyclophyllidea) is consistent with that expected from morphology and the large fragments of mtDNA when reconstructed using all 36 genes. Examination of the 54 mitogenomes from these five orders, revealed a unique arrangement for each order except for the Cyclophyllidea which had two types that were identical to that of the Diphyllobothriidea and the Proteocephalidea. When comparing gene order between the unsegmented and segmented cestodes, the segmented cestodes were found to have the lower similarities due to a long distance transposition event. All rearrangement events between the four arrangement categories took place at the junction of rrnS-tRNAArg (P1) where NCRs are common. Conclusions Highly repetitive regions are detected among NCRs of the four cestode species. A long distance transposition event is inferred between the unsegmented and segmented cestodes. Gene arrangements of Taeniidae and the rest of the families in the Cyclophyllidea are found be identical to those of the sister order Proteocephalidea and the relatively basal order Diphyllobothriidea, respectively. Electronic supplementary material The online version of this article (doi:10.1186/s13071-017-2245-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wen X Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Dong Zhang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kellyanne Boyce
- South Devon College University Centre, Long Road, Paignton, TQ4 7EJ, UK
| | - Bing W Xi
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Shan G Wu
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Ming Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Gui T Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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Li Y, Yin M, Wu Q, McManus DP, Blair D, Li H, Xu B, Mo X, Feng Z, Hu W. Genetic diversity and selection of three nuclear genes in Schistosoma japonicum populations. Parasit Vectors 2017; 10:87. [PMID: 28212676 PMCID: PMC5316221 DOI: 10.1186/s13071-017-2033-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 02/11/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The blood fluke, Schistosoma japonicum still causes severe disease in China, the Philippines and Indonesia. Although there have been some studies the molecular epidemiology of this persistent and harmful parasite, few have explored the possibility and implications of selection in S. japonicum populations. METHODS We analyzed diversity and looked for evidence of selection at three nuclear genes (SjIpp2, SjFabp and SjT22.6) in 13 S. japonicum populations. RESULTS SjT22.6 was found to exhibit high nucleotide diversity and was under positive selection in the mountainous region of mainland China. As a tegumental protein, its secondary and tertiary structure differed between S. japonicum strains from the mountainous and lakes regions. In contrast, SjIpp2 and SjFabp had relatively low levels of nucleotide diversity and did not show significant departure from neutrality. CONCLUSIONS As a tegument-associated antigen-encoding gene of S. japonicum, SjT22.6 has high nucleotide diversity and appears to be under positive selection in the mountainous region of mainland China.
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Affiliation(s)
- Yaqi Li
- School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China
| | - Mingbo Yin
- School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China
| | - Qunfeng Wu
- School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China
| | - Donald P. McManus
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Brisbane, QLD 4029 Australia
| | - David Blair
- College of Science and Engineering, James Cook University, Townsville, QLD 4811 Australia
| | - Hongyan Li
- School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China
| | - Bin Xu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 207 Rui Jin Er Road, Shanghai, 200025 China
| | - Xiaojin Mo
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 207 Rui Jin Er Road, Shanghai, 200025 China
| | - Zheng Feng
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 207 Rui Jin Er Road, Shanghai, 200025 China
| | - Wei Hu
- School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 207 Rui Jin Er Road, Shanghai, 200025 China
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Guo A. Moniezia benedeni and Moniezia expansa are distinct cestode species based on complete mitochondrial genomes. Acta Trop 2017; 166:287-292. [PMID: 27923556 DOI: 10.1016/j.actatropica.2016.11.032] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 10/07/2016] [Accepted: 11/24/2016] [Indexed: 01/18/2023]
Abstract
Moniezia spp. parasitize the intestines of ruminants, causing monieziasis. In this study, the complete mitochondrial (mt) genomes of M. benedeni and M. expansa have been determined, characterized and employed to test the hypothesis that M. benedeni and M. expansa are distinct species by phylogenetic analysis based on the concatenated amino acid sequences derived from 12 protein-coding genes, inferred with Bayesian and Maximum-likelihood methods. The complete mt genomes of M. benedeni and M. expansa were 13,958bp and 13,934bp in size, respectively. Nucleotide sequence identity between the two mt genomes was 83.4%. Each of the two circular mt genomes encodes 36 genes including two ribosomal RNA genes, 22 transfer RNA genes and 12 protein-coding genes, which are transcribed from the same direction. The gene orders of the two mt genomes are identical to those of Anoplocephala spp. (Anoplocephalidae), Hymenolepis spp. (Hymenolepididae) and Dipylidium caninum (Dipylidiidae), but distinct from the species of the Taeniidae family. Phylogenetic analysis confirmed that M. benedeni and M. expansa are taxonomically valid species and have a sister relationship, regardless of the analytical method employed. Furthermore, comparing the cox1 gene sequences of Moniezia spp. from the NCBI deposited sequences and the ones obtained in the present study revealed that the nucleotide sequence differences were 12.5% for M. benedeni and 6.2% for M. expansa, respectively, suggesting the existence of cryptic species in these parasites. The complete mt genome sequences reported herein will be valuable in further studies of diagnoses, molecular ecology and population genetics of Moniezia spp. of socio-economic importance.
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Le TH, Nguyen NTB, Nguyen KT, Doan HTT, Dung DT, Blair D. A complete mitochondrial genome from Echinochasmus japonicus supports the elevation of Echinochasminae Odhner, 1910 to family rank (Trematoda: Platyhelminthes). INFECTION GENETICS AND EVOLUTION 2016; 45:369-377. [DOI: 10.1016/j.meegid.2016.09.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 09/28/2016] [Accepted: 09/30/2016] [Indexed: 10/20/2022]
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Chu H, Li C, Guo X, Zhang H, Luo P, Wu Z, Wang G, Zhao T. The phylogenetic relationships of known mosquito (Diptera: Culicidae) mitogenomes. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 29:31-35. [PMID: 27731651 DOI: 10.1080/24701394.2016.1233533] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The known mosquito mitogenomes, containing a total of 34 species, which belong to five genera, were collected from GenBank, and the practicality and effectiveness of the variation in the complete mitochondrial DNA genome and portions of mitochondrial COI gene were assessed to reconstruct the phylogeny of mosquitoes. Phylogenetic trees were reconstructed on the basis of parsimony, maximum likelihood, and Bayesian (BI) methods. It is concluded that: (1) Both mitogenomes and COI gene support the monophly of following taxa: Subgenus Nyssorhynchus, Subgenus Cellia, Anopheles albitarsis complex, Anopheles gambiae complex, and Anopheles punctulatus group; (2) Genus Aedes is not monophyletic relative to Ochlerotatus vigilax; (3) The mitogenome results indicate a close relationship between Anopheles epiroticus and Anopheles gambiae complex, Anopheles dirus complex and Anopheles punctulatus group, respectively; (4) The Bayesian posterior probability (BPP) within phylogenetic tree reconstructed by mitogenomes is higher than COI tree. The results show that phylogenetic relationships reconstructed using the mitogenomes were more similar to those based on morphological data.
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Affiliation(s)
- Hongliang Chu
- a State Key Laboratory of Pathogen and Biosecurity, Department of Vector Biology and Control, Institute of Microbiology and Epidemiology, Beijing, China.,b Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Chunxiao Li
- a State Key Laboratory of Pathogen and Biosecurity, Department of Vector Biology and Control, Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaoxia Guo
- a State Key Laboratory of Pathogen and Biosecurity, Department of Vector Biology and Control, Institute of Microbiology and Epidemiology, Beijing, China
| | - Hengduan Zhang
- a State Key Laboratory of Pathogen and Biosecurity, Department of Vector Biology and Control, Institute of Microbiology and Epidemiology, Beijing, China
| | - Peng Luo
- c Zhejiang Entry-exit Inspection and Quarantine Bureau, Hangzhou, China
| | - Zhonghua Wu
- c Zhejiang Entry-exit Inspection and Quarantine Bureau, Hangzhou, China
| | - Gang Wang
- c Zhejiang Entry-exit Inspection and Quarantine Bureau, Hangzhou, China
| | - Tongyan Zhao
- a State Key Laboratory of Pathogen and Biosecurity, Department of Vector Biology and Control, Institute of Microbiology and Epidemiology, Beijing, China
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Peña Cantero ÁL, Sentandreu V. Phylogenetic relationships of endemic Antarctic species of Staurotheca Allman, 1888 (Cnidaria, Hydrozoa). Polar Biol 2016. [DOI: 10.1007/s00300-016-1954-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Lu L, Zhang SM, Mutuku MW, Mkoji GM, Loker ES. Relative compatibility of Schistosoma mansoni with Biomphalaria sudanica and B. pfeifferi from Kenya as assessed by PCR amplification of the S. mansoni ND5 gene in conjunction with traditional methods. Parasit Vectors 2016; 9:166. [PMID: 27000855 PMCID: PMC4802880 DOI: 10.1186/s13071-016-1457-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 03/16/2016] [Indexed: 12/02/2022] Open
Abstract
Background Schistosoma mansoni is hosted by several species of Biomphalaria spp. snails in Africa. We were interested in determining if there were differences in compatibility of S. mansoni with Biomphalaria sudanica from Lake Victoria, or with B. pfeifferi from streams and smaller water bodies in Kenya. Does this parasite develop with equal efficiency in both snail species, and does this have implications for transmission in different habitat types? Methods Primers for PCR amplification of the S. mansoni ND5 gene were designed and tested for sensitivity and specificity. We exposed laboratory-reared B. sudanica and field-derived B. pfeifferi to single miracidium infections and at 1, 2, 4, 8, 16 and 24 days post-exposure (dpe), snails were extracted for the PCR assay. Snails were also shed for cercariae and/or dissected prior to extraction. Additionally, B. sudanica and B. pfeifferi were collected from field locations and tested with the PCR assay. Results The ND5 PCR assay was sensitive (>0.1 fg S. mansoni genomic DNA) and allowed S. mansoni to be differentiated from other relevant schistosome species or snails. The number of PCR positive snails at 1–4 dpe was higher for B. pfeifferi than for B. sudanica, but not significantly so (P = 0.052). From 8–24 dpe, more B. pfeifferi harbored successfully developing parasites (positive by both dissection and PCR) than did B. sudanica (P = 0.008). At 40 dpe, more B. pfeifferi than B. sudanica shed cercariae or harbored dissection positive/PCR positive infections (P < 0.001). Both immature and failed (dissection negative but PCR positive) S. mansoni infections could also be detected in naturally infected snails of both species. Conclusions The PCR assay detected S. mansoni infections in snails exposed to one miracidium for one day. Both B. sudanica and B. pfeifferi supported full development of S. mansoni, but B. pfeifferi was more compatible, with significantly more dissection positive/PCR positive or shedding infections, and significantly fewer failed infections (dissection negative/PCR positive). This highlights the relatively lower compatibility of B. sudanica with S. mansoni, and suggests the factors responsible for incompatibility and how they might affect transmission of S. mansoni in habitats like Lake Victoria deserve additional study.
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Affiliation(s)
- Lijun Lu
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, 87131, USA.
| | - Si-Ming Zhang
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, 87131, USA
| | - Martin W Mutuku
- Center for Biotechnology Research and Development, Kenya Medical Research Institute (KEMRI), P.O Box 54840-00200, Nairobi, Kenya
| | - Gerald M Mkoji
- Center for Biotechnology Research and Development, Kenya Medical Research Institute (KEMRI), P.O Box 54840-00200, Nairobi, Kenya
| | - Eric S Loker
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, 87131, USA.,Parasitology Division, Museum of Southwestern Biology, University of New Mexico, Albuquerque, 87131, USA
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Blasco-Costa I, Cutmore SC, Miller TL, Nolan MJ. Molecular approaches to trematode systematics: ‘best practice’ and implications for future study. Syst Parasitol 2016; 93:295-306. [DOI: 10.1007/s11230-016-9631-2] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 01/09/2016] [Indexed: 11/29/2022]
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Guo A. The complete mitochondrial genome of Anoplocephala perfoliata, the first representative for the family Anoplocephalidae. Parasit Vectors 2015; 8:549. [PMID: 26490141 PMCID: PMC4618346 DOI: 10.1186/s13071-015-1172-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 10/15/2015] [Indexed: 12/02/2022] Open
Abstract
Background Mitochondrial (mt) genome sequences are widely used to understand phylogenetic relationships among parasites. However, no complete mt genome sequence is available in the family Anoplocephalidae to date. This study sequenced and annotated the complete mt genome of Anoplocephala perfoliata (Anoplocephalidae), and investigated its phylogenetic relationships with other species from the families Hymenolepididae, Dipylidiidae and Taeniidae of the order Cyclophyllidea using the amino acid sequences of the 12 proteins in their mt genomes. Methods The complete mt genome of A. perfoliata was amplified by Long-range PCR, sequenced using primer walking and annotated by comparing with those of other cestodes. Its phylogenetic relationship with the species from the families Hymenolepididae, Dipylidiidae and Taeniidae was inferred using the 12 protein sequences based on Maximum likelihood and Bayesian methods. Results The complete circular mt genome sequence for A. perfoliata is 14,459 bp in size, and includes 12 protein-coding genes, 2 rRNA genes and 22 tRNA genes. The mt gene arrangement of A. perfoliata is identical to those of previously reported Hymenolepis diminuta (Hymenolepididae) and Dipylidium caninum (Dipylidiidae), but slightly different from those of other taeniids due to an order switch between tRNA(S2) and tRNA(L1). The phylogenetic analyses showed that the Dipylidiidae was more closely related to Anoplocephalidae and Hymenolepididae than to Taeniidae. The relationship among the four families obtained by Maximum likelihood and Bayesian inferences based on predicted amino acid sequences of protein-coding genes is consistent with that based on their mt gene arrangement similarities. Conclusions This study determined the first mt genome for the family Anoplocephalidae, providing rich sources for selecting useful molecular markers for ecological and phylogenetic studies. Analyses on mt genome sequences of the four families of cestodes provide novel insights into their phylogenetic relationships. Of couse, more taxon sampling is necessary for future phylogenetic studies of these cestodes using mt genome sequences. Electronic supplementary material The online version of this article (doi:10.1186/s13071-015-1172-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aijiang Guo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu Province, People's Republic of China. .,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, Jiangsu Province, People's Republic of China.
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Attwood SW, Ibaraki M, Saitoh Y, Nihei N, Janies DA. Comparative Phylogenetic Studies on Schistosoma japonicum and Its Snail Intermediate Host Oncomelania hupensis: Origins, Dispersal and Coevolution. PLoS Negl Trop Dis 2015; 9:e0003935. [PMID: 26230619 PMCID: PMC4521948 DOI: 10.1371/journal.pntd.0003935] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 06/26/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Schistosoma japonicum causes major public health problems in China and the Philippines; this parasite, which is transmitted by freshwater snails of the species Oncomelania hupensis, causes the disease intestinal schistosomiasis in humans and cattle. Researchers working on Schistosoma in Africa have described the relationship between the parasites and their snail intermediate hosts as coevolved or even as an evolutionary arms race. In the present study this hypothesis of coevolution is evaluated for S. japonicum and O. hupensis. The origins and radiation of the snails and the parasite across China, and the taxonomic validity of the sub-species of O. hupensis, are also assessed. METHODOLOGY/PRINCIPAL FINDINGS The findings provide no evidence for coevolution between S. japonicum and O. hupensis, and the phylogeographical analysis suggests a heterochronous radiation of the parasites and snails in response to different palaeogeographical and climatic triggers. The results are consistent with a hypothesis of East to West colonisation of China by Oncomelania with a re-invasion of Japan by O. hupensis from China. The Taiwan population of S. japonicum appears to be recently established in comparison with mainland Chinese populations. CONCLUSIONS/SIGNIFICANCE The snail and parasite populations of the western mountain region of China (Yunnan and Sichuan) appear to have been isolated from Southeast Asian populations since the Pleistocene; this has implications for road and rail links being constructed in the region, which will breach biogeographical barriers between China and Southeast Asia. The results also have implications for the spread of S. japonicum. In the absence of coevolution, the parasite may more readily colonise new snail populations to which it is not locally adapted, or even new intermediate host species; this can facilitate its dispersal into new areas. Additional work is required to assess further the risk of spread of S. japonicum.
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Affiliation(s)
- Stephen W. Attwood
- State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, People's Republic of China
- Department of Life Sciences, The Natural History Museum, London, United Kingdom
| | - Motomu Ibaraki
- School of Earth Sciences, The Ohio State University, Columbus, Ohio, United States of America
| | - Yasuhide Saitoh
- Department of Environmental Parasitology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Naoko Nihei
- Laboratory of Parasitology, School of Veterinary Medicine, Azabu University, Sagamihara, Japan
- Department of Medical Entomology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Daniel A. Janies
- Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
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Brabec J, Kostadinova A, Scholz T, Littlewood DTJ. Complete mitochondrial genomes and nuclear ribosomal RNA operons of two species of Diplostomum (Platyhelminthes: Trematoda): a molecular resource for taxonomy and molecular epidemiology of important fish pathogens. Parasit Vectors 2015; 8:336. [PMID: 26084797 PMCID: PMC4477422 DOI: 10.1186/s13071-015-0949-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 06/11/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The genus Diplostomum (Platyhelminthes: Trematoda: Diplostomidae) is a diverse group of freshwater parasites with complex life-cycles and global distribution. The larval stages are important pathogens causing eye fluke disease implicated in substantial impacts on natural fish populations and losses in aquaculture. However, the problematic species delimitation and difficulties in the identification of larval stages hamper the assessment of the distributional and host ranges of Diplostomum spp. and their transmission ecology. METHODS Total genomic DNA was isolated from adult worms and shotgun sequenced using Illumina MiSeq technology. Mitochondrial (mt) genomes and nuclear ribosomal RNA (rRNA) operons were assembled using established bioinformatic tools and fully annotated. Mt protein-coding genes and nuclear rRNA genes were subjected to phylogenetic analysis by maximum likelihood and the resulting topologies compared. RESULTS We characterised novel complete mt genomes and nuclear rRNA operons of two closely related species, Diplostomum spathaceum and D. pseudospathaceum. Comparative mt genome assessment revealed that the cox1 gene and its 'barcode' region used for molecular identification are the most conserved regions; instead, nad4 and nad5 genes were identified as most promising molecular diagnostic markers. Using the novel data, we provide the first genome wide estimation of the phylogenetic relationships of the order Diplostomida, one of the two fundamental lineages of the Digenea. Analyses of the mitogenomic data invariably recovered the Diplostomidae as a sister lineage of the order Plagiorchiida rather than as a basal lineage of the Diplostomida as inferred in rDNA phylogenies; this was concordant with the mt gene order of Diplostomum spp. exhibiting closer match to the conserved gene order of the Plagiorchiida. CONCLUSIONS Complete sequences of the mt genome and rRNA operon of two species of Diplostomum provide a valuable resource for novel genetic markers for species delineation and large-scale molecular epidemiology and disease ecology studies based on the most accessible life-cycle stages of eye flukes.
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Affiliation(s)
- Jan Brabec
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences and Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic.
| | - Aneta Kostadinova
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences and Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic.
| | - Tomáš Scholz
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences and Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic.
| | - D Timothy J Littlewood
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, UK.
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Li J, Chen F, Sugiyama H, Blair D, Lin RQ, Zhu XQ. A specific indel marker for the Philippines Schistosoma japonicum revealed by analysis of mitochondrial genome sequences. Parasitol Res 2015; 114:2697-704. [PMID: 25899327 DOI: 10.1007/s00436-015-4475-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 04/08/2015] [Indexed: 10/23/2022]
Abstract
In the present study, near-complete mitochondrial (mt) genome sequences for Schistosoma japonicum from different regions in the Philippines and Japan were amplified and sequenced. Comparisons among S. japonicum from the Philippines, Japan, and China revealed a geographically based length difference in mt genomes, but the mt genomic organization and gene arrangement were the same. Sequence differences among samples from the Philippines and all samples from the three endemic areas were 0.57-2.12 and 0.76-3.85 %, respectively. The most variable part of the mt genome was the non-coding region. In the coding portion of the genome, protein-coding genes varied more than rRNA genes and tRNAs. The near-complete mt genome sequences for Philippine specimens were identical in length (14,091 bp) which was 4 bp longer than those of S. japonicum samples from Japan and China. This indel provides a unique genetic marker for S. japonicum samples from the Philippines. Phylogenetic analyses based on the concatenated amino acids of 12 protein-coding genes showed that samples of S. japonicum clustered according to their geographical origins. The identified mitochondrial indel marker will be useful for tracing the source of S. japonicum infection in humans and animals in Southeast Asia.
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Affiliation(s)
- Juan Li
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong Province, People's Republic of China
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Levels of sparganum infections and phylogenetic analysis of the tapeworm Spirometra erinaceieuropaei sparganum in wild frogs from Henan Province in central China. J Helminthol 2014; 89:433-8. [DOI: 10.1017/s0022149x14000248] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
AbstractSparganosis is a serious food-borne parasitic zoonosis caused by infection with Spirometra spargana. The prevalence of sparganum infection in wild frogs (Rana nigromaculata, R. limmochari, R. temporaria and Bufo gargarizans) was investigated in Henan Province of central China during 2008–2012. Of 3482 caught wild frogs, 565 (16.23%) were found to be infected with plerocercoids (spargana) of the genus Spirometra. Spargana were found in 14.85% (320/2155) of R. nigromaculata, 20.82% (233/1119) of R. limmochari and 10.91% (12/110) of R. temporaria frogs. However, no sparganum was found in B. gargarizans. To investigate the phylogenetic position of collected spargana, three mitochondrial DNA (mtDNA) regions, namely cytochrome c oxidase subunits 1 and 3 (cox1 and cox3), and NADH dehydrogenase subunit 4 (nad4), were amplified, sequenced and analysed. Sequences of cox1, cox3 and pnad4 were 417, 390 and 578 bp in length, respectively. The base composition of cox1, cox3 and pnad4 were generally AT rich with a mean of 63.5%, 68.3% and 67% AT, respectively. Phylogenetic analysis showed that all the sparganum isolates in Henan Province represented Spirometra erinaceieuropaei and were a well-supported clade. These findings demonstrated clearly the usefulness of the three mtDNA sequences for molecular identification and population genetics studies of S. erinaceieuropaei spargana of human and animal health significance.
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Jabbar A, Beveridge I, Mohandas N, Chilton NB, Littlewood DTJ, Jex AR, Gasser RB. Analyses of mitochondrial amino acid sequence datasets support the proposal that specimens of Hypodontus macropi from three species of macropodid hosts represent distinct species. BMC Evol Biol 2013; 13:259. [PMID: 24261823 PMCID: PMC4222732 DOI: 10.1186/1471-2148-13-259] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 11/19/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Hypodontus macropi is a common intestinal nematode of a range of kangaroos and wallabies (macropodid marsupials). Based on previous multilocus enzyme electrophoresis (MEE) and nuclear ribosomal DNA sequence data sets, H. macropi has been proposed to be complex of species. To test this proposal using independent molecular data, we sequenced the whole mitochondrial (mt) genomes of individuals of H. macropi from three different species of hosts (Macropus robustus robustus, Thylogale billardierii and Macropus [Wallabia] bicolor) as well as that of Macropicola ocydromi (a related nematode), and undertook a comparative analysis of the amino acid sequence datasets derived from these genomes. RESULTS The mt genomes sequenced by next-generation (454) technology from H. macropi from the three host species varied from 13,634 bp to 13,699 bp in size. Pairwise comparisons of the amino acid sequences predicted from these three mt genomes revealed differences of 5.8% to 18%. Phylogenetic analysis of the amino acid sequence data sets using Bayesian Inference (BI) showed that H. macropi from the three different host species formed distinct, well-supported clades. In addition, sliding window analysis of the mt genomes defined variable regions for future population genetic studies of H. macropi in different macropodid hosts and geographical regions around Australia. CONCLUSIONS The present analyses of inferred mt protein sequence datasets clearly supported the hypothesis that H. macropi from M. robustus robustus, M. bicolor and T. billardierii represent distinct species.
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Affiliation(s)
- Abdul Jabbar
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Melbourne, Victoria 3010, Australia.
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Webster BL, Culverwell CL, Khamis IS, Mohammed KA, Rollinson D, Stothard JR. DNA barcoding of Schistosoma haematobium on Zanzibar reveals substantial genetic diversity and two major phylogenetic groups. Acta Trop 2013; 128:206-17. [PMID: 22721826 DOI: 10.1016/j.actatropica.2012.06.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 05/31/2012] [Accepted: 06/08/2012] [Indexed: 11/26/2022]
Abstract
To shed light on the genetic diversity of Schistosoma haematobium on Zanzibar a DNA barcoding study was performed on parasite material isolated from different time-points 4 years apart. Substantive sequence variation was found within the mitochondrial cytochrome oxidase subunit I (cox1) and the NADH-dehydrogenase subunit 1 (nad1) with 27 and 22 unique haplotypes identified respectively and 38 when both gene regions were considered. Upon phylogenetic analysis and comparison with other S. haematobium isolates, haplotypes or barcode types partitioned into two discrete major groups, designated Group 1 and Group 2. Whilst Group 1 isolates were recovered from both Zanzibar and the African mainland, Group 2 isolates were exclusive to Zanzibar. A mixture of Group 1 and 2 parasites were recovered from individual children with no child shedding parasites of a single group haplotype alone. Whilst changes in general levels of genetic diversity between the two parasite isolation time-points were observed, no obvious change in genetic diversity was detected, despite large-scale drug distribution of praziquantel during the intervening period and there was no biased of Group 1 or 2 parasites persisting at the different time-points. To assist in future genetic screening of schistosome larval stages e.g. eggs, miracidia or cercariae, two new DNA-typing assays based on group-specific PCR primers and SNaPshot™ probes have been developed to distinguish Group 1 and 2 haplotypes.
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Webster BL, Webster JP, Gouvras AN, Garba A, Lamine MS, Diaw OT, Seye MM, Tchuem Tchuenté LA, Simoonga C, Mubila L, Mwanga JR, Lwambo NJ, Kabatereine NB, Lange CN, Kariuki C, Mkoji GM, Rollinson D, Stothard JR. DNA 'barcoding' of Schistosoma mansoni across sub-Saharan Africa supports substantial within locality diversity and geographical separation of genotypes. Acta Trop 2013; 128:250-60. [PMID: 22935316 DOI: 10.1016/j.actatropica.2012.08.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 08/08/2012] [Accepted: 08/10/2012] [Indexed: 11/25/2022]
Abstract
Schistosoma mansoni is a widespread human helminth and causes intestinal schistosomiasis in 54 countries, mainly across Africa but also in Madagascar, the Arabian Peninsula and the neotropics. The geographical range of this parasite relies on the distribution of certain species of freshwater pulmonate snails of the genus Biomphalaria. Whilst S. mansoni is known to exhibit high population diversity the true extent of this diversity is still to be fully elucidated as sampling of this taxon progressively accrues. Here a DNA 'barcoding' approach is taken using sequence analysis of a 450bp region within the mitochondrial cox1 gene to assess the genetic diversity within a large number of S. mansoni larval stages collected from their natural human hosts across sub-Saharan Africa. Five hundred and sixty one individual parasite samples were examined from 22 localities and 14 countries. Considerable within-species diversity was found with 120 unique haplotypes splitting geographically into five discrete lineages. The highest diversity was found in East Africa with samples forming three of the five lineages. Less diversity was found in the Far and Central Western regions of Africa with haplotypes from the New World showing a close affinity to the Far Western African S. mansoni populations supporting the hypothesis of a colonisation of South America via the West African slave trade. The data are discussed in relation to parasite diversity and disease epidemiology.
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Cantacessi C, Seddon JM, Miller TL, Leow CY, Thomas L, Mason L, Willis C, Walker G, Loukas A, Gasser RB, Jones MK, Hofmann A. A genome-wide analysis of annexins from parasitic organisms and their vectors. Sci Rep 2013; 3:2893. [PMID: 24113121 PMCID: PMC3795353 DOI: 10.1038/srep02893] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 09/20/2013] [Indexed: 11/14/2022] Open
Abstract
In this study, we conduct an in-depth analysis of annexin proteins from a diverse range of invertebrate taxa, including the major groups that contain the parasites and vector organisms that are harmful to humans and domestic animals. Using structure-based amino acid sequence alignments and phylogenetic analyses, we present a classification for this protein group and assign names to sequences with ambiguous annotations in public databases. Our analyses reveal six distinct annexin clades, and the mapping of genes encoding annexins to the genome of the human blood fluke Schistosoma mansoni supports the hypothesis of gene duplication as a major evolutionary event in annexin genesis. This study illuminates annexin diversity from a novel perspective using contemporary phylogenetic hypotheses of eukaryote evolution, and will aid the consolidation of annexin protein identities in public databases and provide a foundation for future functional analysis and characterisation of these proteins in parasites of socioeconomic importance.
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Affiliation(s)
- Cinzia Cantacessi
- 1] Centre for Biodiscovery and Molecular Development of Therapeutics, Queensland Tropical Health Alliance, James Cook University, Cairns, Queensland, Australia [2]
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Lobo J, Costa PM, Teixeira MAL, Ferreira MSG, Costa MH, Costa FO. Enhanced primers for amplification of DNA barcodes from a broad range of marine metazoans. BMC Ecol 2013; 13:34. [PMID: 24020880 PMCID: PMC3846737 DOI: 10.1186/1472-6785-13-34] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 09/03/2013] [Indexed: 11/22/2022] Open
Abstract
Background Building reference libraries of DNA barcodes is relatively straightforward when specifically designed primers are available to amplify the COI-5P region from a relatively narrow taxonomic group (e.g. single class or single order). DNA barcoding marine communities have been comparatively harder to accomplish due to the broad taxonomic diversity and lack of consistently efficient primers. Although some of the so-called “universal” primers have been relatively successful, they still fail to amplify COI-5P of many marine animal groups, while displaying random success even among species within each group. Here we propose a new pair of primers designed to enhance amplification of the COI-5P region in a wide range of marine organisms. Results Amplification tests conducted on a wide range of marine animal taxa, rendered possible the first–time sequencing of DNA barcodes from eight separated phyla (Annelida, Arthropoda, Chordata, Cnidaria, Echinodermata, Mollusca, Nemertea and Platyhelminthes), comprising a total of 14 classes, 28 orders, 57 families, 68 genus and 76 species. Conclusions These primers demonstrated to be highly cost-effective, which is of key importance for DNA barcoding procedures, such as for building comprehensive DNA barcode libraries of marine communities, where the processing of a large numbers of specimens from a wide variety of marine taxa is compulsory.
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Affiliation(s)
- Jorge Lobo
- IMAR-Instituto do Mar, Departamento de Ciências e Engenharia do Ambiente, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, 2829-516 Monte de Caparica, Portugal.
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Yan HB, Wang XY, Lou ZZ, Li L, Blair D, Yin H, Cai JZ, Dai XL, Lei MT, Zhu XQ, Cai XP, Jia WZ. The mitochondrial genome of Paramphistomum cervi (Digenea), the first representative for the family Paramphistomidae. PLoS One 2013; 8:e71300. [PMID: 23990943 PMCID: PMC3750040 DOI: 10.1371/journal.pone.0071300] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 06/26/2013] [Indexed: 11/27/2022] Open
Abstract
We determined the complete mitochondrial DNA (mtDNA) sequence of a fluke, Paramphistomum cervi (Digenea: Paramphistomidae). This genome (14,014 bp) is slightly larger than that of Clonorchis sinensis (13,875 bp), but smaller than those of other digenean species. The mt genome of P. cervi contains 12 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 2 non-coding regions (NCRs), a complement consistent with those of other digeneans. The arrangement of protein-coding and ribosomal RNA genes in the P. cervi mitochondrial genome is identical to that of other digeneans except for a group of Schistosoma species that exhibit a derived arrangement. The positions of some transfer RNA genes differ. Bayesian phylogenetic analyses, based on concatenated nucleotide sequences and amino-acid sequences of the 12 protein-coding genes, placed P. cervi within the Order Plagiorchiida, but relationships depicted within that order were not quite as expected from previous studies. The complete mtDNA sequence of P. cervi provides important genetic markers for diagnostics, ecological and evolutionary studies of digeneans.
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Affiliation(s)
- Hong-Bin Yan
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Key Laboratory of Veterinary Public Health of Agriculture Ministry, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, PR China
| | - Xing-Ye Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Key Laboratory of Veterinary Public Health of Agriculture Ministry, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, PR China
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shanxi Province, PR China
| | - Zhong-Zi Lou
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Key Laboratory of Veterinary Public Health of Agriculture Ministry, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, PR China
| | - Li Li
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Key Laboratory of Veterinary Public Health of Agriculture Ministry, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, PR China
| | - David Blair
- School of Marine and Tropical Biology, James Cook University, Queensland, Australia
| | - Hong Yin
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Key Laboratory of Veterinary Public Health of Agriculture Ministry, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, PR China
| | - Jin-Zhong Cai
- Laboratory of Plateau Veterinary Parasitology, Veterinary Research Institute, Qinghai Academy of Animal Science and Veterinary Medicine, Xining, Qinghai Province, PR China
| | - Xue-Ling Dai
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Key Laboratory of Veterinary Public Health of Agriculture Ministry, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, PR China
| | - Meng-Tong Lei
- Laboratory of Plateau Veterinary Parasitology, Veterinary Research Institute, Qinghai Academy of Animal Science and Veterinary Medicine, Xining, Qinghai Province, PR China
| | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Key Laboratory of Veterinary Public Health of Agriculture Ministry, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, PR China
| | - Xue-Peng Cai
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Key Laboratory of Veterinary Public Health of Agriculture Ministry, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, PR China
- * E-mail: (WZJ); (XPC)
| | - Wan-Zhong Jia
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Key Laboratory of Veterinary Public Health of Agriculture Ministry, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, PR China
- * E-mail: (WZJ); (XPC)
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Moszczynska A, Locke SA, McLaughlin JD, Marcogliese DJ, Crease TJ. Development of primers for the mitochondrial cytochrome c oxidase I gene in digenetic trematodes (Platyhelminthes) illustrates the challenge of barcoding parasitic helminths. Mol Ecol Resour 2013; 9 Suppl s1:75-82. [PMID: 21564967 DOI: 10.1111/j.1755-0998.2009.02634.x] [Citation(s) in RCA: 180] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The phylum Platyhelminthes is a diverse group of flatworms that includes parasites with serious impacts on human health, animal husbandry, aquaculture and wildlife management. Here we present degenerate primers for the barcode region of the mitochondrial cytochrome c oxidase I (COI) gene in flatworms. Although amplicons were obtained from a wide taxonomic range in the Cestoda and Trematoda, COI fragments from many taxa in these classes did not amplify. Primers specific to trematodes in the family Diplostomidae were also developed. Amplification success was much higher with diplostomid-specific primers and sequences were obtained from 504 of 585 specimens of Diplostomum and Tylodelphys. Sequences from the barcode region resolved all specimens to the species level, with mean divergence between congeners of 19% (3.9-25%). Because many of our specimens were small, we initially amplified part of the nuclear small subunit ribosomal (r) RNA gene to evaluate the quality and quantity of DNA in our specimens. Short sequences (~380 nt) of this gene were recovered from most specimens and can be used to distinguish specimens at the family level and often the generic level. We suggest that rRNA genes could be used to screen samples of completely unknown taxonomy, after which specific COI primers could be used to obtain species-level identifications.
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Affiliation(s)
- Anna Moszczynska
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada N1G 2W1, Department of Neurosciences, University of Toledo, Toledo, OH 43614-2598, USA
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Chen F, Li J, Sugiyama H, Zhou DH, Song HQ, Zhao GH, Zhu XQ. Genetic variability among Schistosoma japonicum isolates from the Philippines, Japan and China revealed by sequence analysis of three mitochondrial genes. ACTA ACUST UNITED AC 2013; 26:35-40. [DOI: 10.3109/19401736.2013.814110] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Fen Chen
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, PR China,
- Department of Basic Medicine, Xiangnan University, Chenzhou, Hunan Province, PR China,
| | - Juan Li
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, PR China,
- Department of Parasitology, Institute of Veterinary Medicine, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, PR China,
| | - Hiromu Sugiyama
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan,
| | - Dong-Hui Zhou
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, PR China,
| | - Hui-Qun Song
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, PR China,
| | - Guang-Hui Zhao
- Department of Parasitology, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province, PR China, and
| | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, PR China,
- Department of Parasitology, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province, PR China
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Brusentsov II, Katokhin AV, Brusentsova IV, Shekhovtsov SV, Borovikov SN, Goncharenko GG, Lider LA, Romashov BV, Rusinek OT, Shibitov SK, Suleymanov MM, Yevtushenko AV, Mordvinov VA. Low genetic diversity in wide-spread Eurasian liver fluke Opisthorchis felineus suggests special demographic history of this trematode species. PLoS One 2013; 8:e62453. [PMID: 23634228 PMCID: PMC3636034 DOI: 10.1371/journal.pone.0062453] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 03/21/2013] [Indexed: 01/09/2023] Open
Abstract
Opisthorchis felineus or Siberian liver fluke is a trematode parasite (Opisthorchiidae) that infects the hepato-biliary system of humans and other mammals. Despite its public health significance, this wide-spread Eurasian species is one of the most poorly studied human liver flukes and nothing is known about its population genetic structure and demographic history. In this paper, we attempt to fill this gap for the first time and to explore the genetic diversity in O. felineus populations from Eastern Europe (Ukraine, European part of Russia), Northern Asia (Siberia) and Central Asia (Northern Kazakhstan). Analysis of marker DNA fragments from O. felineus mitochondrial cytochrome c oxidase subunit 1 and 3 (cox1, cox3) and nuclear rDNA internal transcribed spacer 1 (ITS1) sequences revealed that genetic diversity is very low across the large geographic range of this species. Microevolutionary processes in populations of trematodes may well be influenced by their peculiar biology. Nevertheless, we suggest that lack of population genetics structure observed in O. felineus can be primarily explained by the Pleistocene glacial events and subsequent sudden population growth from a very limited group of founders. Rapid range expansion of O. felineus through Asian and European territories after severe bottleneck points to a high dispersal potential of this trematode species.
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Affiliation(s)
- Ilja I. Brusentsov
- Laboratory of Molecular Mechanisms of Pathological Processes, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexey V. Katokhin
- Laboratory of Molecular Mechanisms of Pathological Processes, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Irina V. Brusentsova
- Laboratory of Molecular Mechanisms of Pathological Processes, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Sergei V. Shekhovtsov
- Laboratory of Molecular Biotechnology, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Sergei N. Borovikov
- Department of Animal Biotechnology, S.Seifullin Kazakh Agrotechnical University, Astana, Republic of Kazakhstan
| | | | - Lyudmila A. Lider
- Department of Veterinary Medicine, S.Seifullin Kazakh Agrotechnical University, Astana, Republic of Kazakhstan
| | - Boris V. Romashov
- Scientific Department, Voronezh State Biosphere Reserve, Voronezh, Russia
| | - Olga T. Rusinek
- Department of Parasitology, The Baikal Museum at the Irkutsk Scientific Center, Siberian Branch, Russian Academy of Sciences, Listvyanka, Irkutsk, Russia
| | - Samat K. Shibitov
- Department of Epizootological Problems, All-Russian K.I. Skryabin Institute of Helminthology, Moscow, Russia
| | - Marat M. Suleymanov
- Laboratory of Molecular Mechanisms of Pathological Processes, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Andrey V. Yevtushenko
- Department of Parasitology Ichthyopathology and Arachnology, National Scientific Center “Institute of Experimental and Clinical Veterinary Medicine”, Kharkov, Ukraine
| | - Viatcheslav A. Mordvinov
- Laboratory of Molecular Mechanisms of Pathological Processes, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
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A perfect time to harness advanced molecular technologies to explore the fundamental biology of Toxocara species. Vet Parasitol 2013; 193:353-64. [DOI: 10.1016/j.vetpar.2012.12.031] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abstract
Invertebrates comprise approximately 34 phyla, while vertebrates represent one subphylum and insects a (very large) class. Thus, the clades excepting vertebrates and insects encompass almost all of animal diversity. Consequently, the barcoding challenge in invertebrates is that of barcoding animals in general. While standard extraction, cleaning, PCR methods, and universal primers work for many taxa, taxon-specific challenges arise because of the shear genetic and biochemical diversity present across the kingdom, and because problems arising as a result of this diversity, and solutions to them, are still poorly characterized for many metazoan clades. The objective of this chapter is to emphasize general approaches, and give practical advice for overcoming the diverse challenges that may be encountered across animal taxa, but we stop short of providing an exhaustive inventory. Rather, we encourage researchers, especially those working on poorly studied taxa, to carefully consider methodological issues presented below, when standard approaches perform poorly.
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Affiliation(s)
- Nathaniel Evans
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
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New frontiers in schistosoma genomics and transcriptomics. J Parasitol Res 2012; 2012:849132. [PMID: 23227308 PMCID: PMC3512318 DOI: 10.1155/2012/849132] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 10/16/2012] [Indexed: 12/11/2022] Open
Abstract
Schistosomes are digenean blood flukes of aves and mammals comprising 23 species. Some species are causative agents of human schistosomiasis, the second major neglected disease affecting over 230 million people worldwide. Modern technologies including the sequencing and characterization of nucleic acids and proteins have allowed large-scale analyses of parasites and hosts, opening new frontiers in biological research with potential biomedical and biotechnological applications. Nuclear genomes of the three most socioeconomically important species (S. haematobium, S. japonicum, and S. mansoni) have been sequenced and are under intense investigation. Mitochondrial genomes of six Schistosoma species have also been completely sequenced and analysed from an evolutionary perspective. Furthermore, DNA barcoding of mitochondrial sequences is used for biodiversity assessment of schistosomes. Despite the efforts in the characterization of Schistosoma genomes and transcriptomes, many questions regarding the biology and evolution of this important taxon remain unanswered. This paper aims to discuss some advances in the schistosome research with emphasis on genomics and transcriptomics. It also aims to discuss the main challenges of the current research and to point out some future directions in schistosome studies.
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Zhao GH, Li J, Blair D, Li XY, Elsheikha HM, Lin RQ, Zou FC, Zhu XQ. Biotechnological advances in the diagnosis, species differentiation and phylogenetic analysis of Schistosoma spp. Biotechnol Adv 2012; 30:1381-9. [DOI: 10.1016/j.biotechadv.2012.02.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 01/08/2012] [Accepted: 02/08/2012] [Indexed: 11/26/2022]
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Genetic diversity within Schistosoma haematobium: DNA barcoding reveals two distinct groups. PLoS Negl Trop Dis 2012; 6:e1882. [PMID: 23145200 PMCID: PMC3493392 DOI: 10.1371/journal.pntd.0001882] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 09/12/2012] [Indexed: 12/03/2022] Open
Abstract
Background Schistosomiasis in one of the most prevalent parasitic diseases, affecting millions of people and animals in developing countries. Amongst the human-infective species S. haematobium is one of the most widespread causing urogenital schistosomiasis, a major human health problem across Africa, however in terms of research this human pathogen has been severely neglected. Methodology/Principal Findings To elucidate the genetic diversity of Schistosoma haematobium, a DNA ‘barcoding’ study was performed on parasite material collected from 41 localities representing 18 countries across Africa and the Indian Ocean Islands. Surprisingly low sequence variation was found within the mitochondrial cytochrome oxidase subunit I (cox1) and the NADH-dehydrogenase subunit 1 snad1). The 61 haplotypes found within 1978 individual samples split into two distinct groups; one (Group 1) that is predominately made up of parasites from the African mainland and the other (Group 2) that is made up of samples exclusively from the Indian Ocean Islands and the neighbouring African coastal regions. Within Group 1 there was a dominance of one particular haplotype (H1) representing 1574 (80%) of the samples analyzed. Population genetic diversity increased in samples collected from the East African coastal regions and the data suggest that there has been movement of parasites between these areas and the Indian Ocean Islands. Conclusions/Significance The high occurrence of the haplotype (H1) suggests that at some point in the recent evolutionary history of S. haematobium in Africa the population may have passed through a genetic ‘bottleneck’ followed by a population expansion. This study provides novel and extremely interesting insights into the population genetics of S. haematobium on a large geographic scale, which may have consequence for control and monitoring of urogenital schistosomiasis. Schistosomiasis is a disease caused by parasitic blood flukes of the genus Schistosoma. Species that infect humans are prevalent in developing countries, having a major impact on public health and well-being as well as an impediment to socioeconomic development. More people are infected with Schistosoma haematobium than with all the other schistosome species combined, however mainly due to the inability to maintain S. haematobium in the laboratory system empirical studies on this parasite are minimal. The genetic variation of this Schistosoma species on a wide geographical scale has never been investigated. In this study, we have used a DNA ?barcoding? approach to document the genetic variation and population structure of S. haematobium sampled from 18 countries across Africa and the Indian ocean Islands. The study revealed a distinct genetic separation of S. haematobium from the Indian Ocean Islands and the closely neighbouring coastal regions from S. haematobium found throughout the African mainland, the latter of which exhibited extremely low levels of mitochondrial diversity within and between populations of parasites sampled. The data from this study provides a novel insight into the population genetics of S. haematobium and will have an impact on future research strategies.
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