Genome-wide characterization of microsatellites and marker development in the carcinogenic liver fluke Clonorchis sinensis (original) (raw)

Abstract

Clonorchis sinensis is an important carcinogenic human liver fluke endemic in East and Southeast Asia. There are several conventional molecular markers that have been used for identification and genetic diversity; however, no information about microsatellites of this liver fluke is published so far. We here report microsatellite characterization and marker development for a genetic diversity study in C. sinensis, using a genome-wide bioinformatics approach. Based on our search criteria, a total of 256,990 microsatellites (≥12 base pairs) were identified from a genome database of C. sinensis, with hexanucleotide motif being the most abundant (51 %) followed by pentanucleotide (18.3 %) and trinucleotide (12.7 %). The tetranucleotide, dinucleotide, and mononucleotide motifs accounted for 9.75, 7.63, and 0.14 %, respectively. The total length of all microsatellites accounts for 0. 72 % of 547 Mb of the whole genome size, and the frequency of microsatellites was found to be one microsatellite in every 2.13 kb of DNA. For the di-, tri-, and tetranucleotide, the repeat numbers redundant are six (28 %), four (45 %), and three (76 %), respectively. The ATC repeat is the most abundant microsatellites followed by AT, AAT, and AC, respectively. Within 40 microsatellite loci developed, 24 microsatellite markers showed potential to differentiate between C. sinensis and Opisthorchis viverrini. Seven out of 24 loci showed to be heterozygous with observed heterozygosity that ranged from 0.467 to 1. Four primer sets could amplify both C. sinensis and O. viverrini DNA with different sizes. This study provides basic information of C. sinensis microsatellites, and the genome-wide markers developed may be a useful tool for the genetic study of C. sinensis.

Access this article

Log in via an institution

Subscribe and save

• Starting from 10 chapters or articles per month
• Access and download chapters and articles from more than 300k books and 2,500 journals
• Cancel anytime View plans

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

• Beckmann JS, Weber JL (1992) Survey of human and rat microsatellites. Genomics 12:627–631. doi:10.1016/0888-7543(92)90285-Z
  Article CAS Google Scholar
• Bouvard V et al (2009) A review of human carcinogens—part B: biological agents. Lancet Oncol 10:321–322
  Article PubMed Google Scholar
• Choi DW (1984) Clonorchis sinensis: life cycle, intermediate hosts, transmission to man and geographical distribution in Korea. Arzneimittelforschung 34:1145–1151
  CAS PubMed Google Scholar
• Cui J-Z, Shen X-Y, Yang G-P, Gong Q-L, Gu Q-Q (2005) Characterization of microsatellite DNAs in Takifugu rubripes genome and their utilization in the genetic diversity analysis of T. rubripes and T. pseudommus. Aquaculture 250:129–137. doi:10.1016/j.aquaculture.2005.04.041
  Article CAS Google Scholar
• Dorny P, Praet N, Deckers N, Gabriel S (2009) Emerging food-borne parasites. Vet Parasitol 163:196–206
  Article CAS PubMed Google Scholar
• Ellegren H (2000) Microsatellite mutations in the germline: implications for evolutionary inference. Trends Genet 16:551–558
  Article CAS PubMed Google Scholar
• Gower CM et al (2011) Population genetics of Schistosoma haematobium: development of novel microsatellite markers and their application to schistosomiasis control in Mali. Parasitology 138:978–994. doi:10.1017/S0031182011000722
  Article CAS PubMed Google Scholar
• Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT Nucleic Acid Symposium Series 4:95–98
• Hildebrand CE, Torney DC, Wagner RP (1992) Informativeness of polymorphic DNA markers Los Alamos. Sci 20:100–102
  CAS Google Scholar
• Hong S-T, Fang Y (2012) Clonorchis sinensis and clonorchiasis, an update. Parasitol Int 61:17–24
  Article CAS PubMed Google Scholar
• Hurtrez-Boussès S et al (2004) Isolation and characterization of microsatellite markers in the liver fluke (Fasciola hepatica). Mol Ecol Notes 4:689–690. doi:10.1111/j.1471-8286.2004.00786.x
  Article Google Scholar
• Joshi RK, Kuanar A, Mohanty S, Subudhi E, Nayak S (2010) Mining and characterization of EST derived microsatellites in Curcuma longa L. Bioinformation 5:128–131
  Article PubMed Central PubMed Google Scholar
• Keiser J, Utzinger J (2009) Food-borne trematodiases. Clin Microbiol Rev 22:466–483. doi:10.1128/CMR. 00012-09
  Article PubMed Central PubMed Google Scholar
• Kim J, Choi J-P, Ahmad R, Oh S-K, Kwon S-Y, Hur C-G (2012) RISA: a new web-tool for Rapid Identification of SSRs and Analysis of primers. Genes Genomics 34:583–590. doi:10.1007/s13258-012-0032-x
  Article CAS Google Scholar
• Kofler R, Schlotterer C, Lelley T (2007) SciRoKo: a new tool for whole genome microsatellite search and investigation. Bioinformatics 23:1683–1685. doi:10.1093/bioinformatics/btm157
  Article CAS PubMed Google Scholar
• Laoprom N et al (2010) Microsatellite loci in the carcinogenic liver fluke, Opisthorchis viverrini and their application as population genetic markers. Infect Genet Evol 10:146–153. doi:10.1016/j.meegid.2009.11.005
  Article CAS PubMed Google Scholar
• Lee SU, Huh S (2004) Variation of nuclear and mitochondrial DNAs in Korean and Chinese isolates of Clonorchis sinensis. Korean J Parasitol 42:145–148
  Article PubMed Central PubMed Google Scholar
• Liu GH et al (2012) Genetic variation among Clonorchis sinensis isolates from different geographic regions in China revealed by sequence analyses of four mitochondrial genes. J Helminthol 86:479–484
  Article CAS PubMed Google Scholar
• Park GM (2007) Genetic comparison of liver flukes, Clonorchis sinensis and Opisthorchis viverrini, based on rDNA and mtDNA gene sequences. Parasitol Res 100:351–357. doi:10.1007/s00436-006-0269-x
  Article PubMed Google Scholar
• Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26:841–842. doi:10.1093/bioinformatics/btq033
  Article PubMed Central CAS PubMed Google Scholar
• Saijuntha W et al (2007) Evidence of a species complex within the food-borne trematode Opisthorchis viverrini and possible co-evolution with their first intermediate hosts. Int J Parasitol 37:695–703
  Article PubMed Central PubMed Google Scholar
• Schlotterer C (2000) Evolutionary dynamics of microsatellite DNA. Chromosoma 109:365–371
  Article CAS PubMed Google Scholar
• Sharma PC, Grover A, Kahl G (2007) Mining microsatellites in eukaryotic genomes. Trends Biotechnol 25:490–498. doi:10.1016/j.tibtech.2007.07.013
  Article CAS PubMed Google Scholar
• Shrivastava J, Barker GC, Johansen MV, Xiaonong Z, Aligui GD, McGarvey ST, Webster JP (2003) Isolation and characterization of polymorphic DNA microsatellite markers from Schistosoma japonicum. Mol Ecol Notes 3:406–408. doi:10.1046/j.1471-8286.2003.00466.x
  Article CAS Google Scholar
• Simpson MC, Wilken PM, Coetzee MP, Wingfield MJ, Wingfield BD (2013) Analysis of microsatellite markers in the genome of the plant pathogen Ceratocystis fimbriata. Fungal Biol 117:545–555. doi:10.1016/j.funbio.2013.06.004
  Article CAS PubMed Google Scholar
• Sun J et al (2013) Low divergence of in China based on multilocus analysis. PLoS ONE 18:e67006
  Article Google Scholar
• Tang S, Popongviwat A, Klinbunga S, Tassanakajon A, Jarayabhand P, Menasveta P (2005) Genetic heterogeneity of the tropical abalone (Haliotis asinina) revealed by RAPD and microsatellite analyses. J Biochem Mol Biol 38:182–190
  Article CAS PubMed Google Scholar
• Tatonova YV, Chelomina GN, Besprosvannykh VV (2012) Genetic diversity of nuclear ITS1–5.8S–ITS2 rDNA sequence in Clonorchis sinensis Cobbold, 1875 (Trematoda: Opisthorchidae) from the Russian Far East. Parasitol Int 61:664–674. doi:10.1016/j.parint.2012.07.005
  Article CAS PubMed Google Scholar
• Tatonova YV, Chelomina GN, Besprozvannykh VV (2013) Genetic diversity of Clonorchis sinensis (Trematoda: Opisthorchiidae) in the Russian southern Far East based on mtDNA cox1 sequence variation. Folia Parasitol 60:155–162
  Article CAS PubMed Google Scholar
• Toth G, Gaspari Z, Jurka J (2000) Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res 10:967–981
  Article PubMed Central CAS PubMed Google Scholar
• Wang X et al (2011) The draft genome of the carcinogenic human liver fluke Clonorchis sinensis. Genome Biol 12:R107. doi:10.1186/gb-2011-12-10-r107
  Article PubMed Central CAS PubMed Google Scholar
• Wu TD, Nacu S (2010) Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26:873–881. doi:10.1093/bioinformatics/btq057
  Article PubMed Central CAS PubMed Google Scholar
• Xiao JY et al (2013) Genetic variation among Clonorchis sinensis isolates from different hosts and geographical locations revealed by sequence analysis of mitochondrial and ribosomal DNA regions. Mitochondrial DNA 24:559–564
  Article CAS PubMed Google Scholar
• Xiao N, Remais J, Brindley PJ, Qiu D, Spear R, Lei Y, Blair D (2011) Polymorphic microsatellites in the human bloodfluke, Schistosoma japonicum, identified using a genomic resource. Parasitol Vectors 4:13. doi:10.1186/1756-3305-4-13
  Article CAS Google Scholar
• You F et al (2008) BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinformatics 9:253
  Article PubMed Central PubMed Google Scholar

Download references

Acknowledgments

This work was supported by the Higher Education Research Promotion and National Research University Project of Thailand, Office of the Higher Education Commission, through the Health Cluster (SHeP-GMS), Khon Kaen University, Thailand; the Thailand Research Fund (TRF); the National Institute of Allergy and Infectious Diseases (NIAID), award number P50AI098639; and the United States Army Medical Research and Materiel Command (USAMRMC), contract number W81XWH-12-C-0267. NBT is supported by the Faculty of Medicine, Khon Kaen University scholarship. BS is a Senior TRF Scholar. The content is solely the responsibility of the authors and does not necessarily represent the official views of the USAMRMC, NIAID, or the NIH or the funders.

Author information

Authors and Affiliations

1. WHO Collaborating Centre for Research and Control of Opisthorchiasis (Southeast Asian Liver Fluke Disease), Tropical Disease Research Laboratory, Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
   Thao T. B. Nguyen, Yuji Arimatsu & Banchob Sripa
2. Center for Public Health & Ecosystem Research, Hanoi School of Public Health, 138 GiangVo St., BaDinh, Hanoi, Vietnam
   Thao T. B. Nguyen
3. Department of Medical Environmental Biology, Chung-Ang University College of Medicine, Dongjak-gu, Seoul, 156-756, Republic of Korea
   Sung-Jong Hong
4. Department of Microbiology, Immunology & Tropical Medicine, George Washington University Medical Center, 2300 Eye Street, NW, Washington, DC, 20037, USA
   Paul J. Brindley
5. School of Marine and Tropical Biology, James Cook University, Townsville, Queensland, 4811, Australia
   David Blair
6. Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
   Thewarach Laha

Authors

1. Thao T. B. Nguyen
2. Yuji Arimatsu
3. Sung-Jong Hong
4. Paul J. Brindley
5. David Blair
6. Thewarach Laha
7. Banchob Sripa

Corresponding author

Correspondence toBanchob Sripa.

Rights and permissions

About this article

Cite this article

Nguyen, T.T.B., Arimatsu, Y., Hong, SJ. et al. Genome-wide characterization of microsatellites and marker development in the carcinogenic liver fluke Clonorchis sinensis .Parasitol Res 114, 2263–2272 (2015). https://doi.org/10.1007/s00436-015-4419-x

Download citation

• Received: 20 January 2015
• Accepted: 04 March 2015
• Published: 19 March 2015
• Issue date: June 2015
• DOI: https://doi.org/10.1007/s00436-015-4419-x

Keywords