Open Access

Polymorphic microsatellites in the human bloodfluke, Schistosoma japonicum, identified using a genomic resource

  • Ning Xiao1Email author,
  • Justin Remais2,
  • Paul J Brindley3,
  • Dongchuan Qiu1,
  • Robert Spear4,
  • Yang Lei1 and
  • David Blair5
Parasites & Vectors20114:13

DOI: 10.1186/1756-3305-4-13

Received: 8 December 2010

Accepted: 7 February 2011

Published: 7 February 2011

Abstract

Re-emergence of schistosomiasis in regions of China where control programs have ceased requires development of molecular-genetic tools to track gene flow and assess genetic diversity of Schistosoma populations. We identified many microsatellite loci in the draft genome of Schistosoma japonicum using defined search criteria and selected a subset for further analysis. From an initial panel of 50 loci, 20 new microsatellites were selected for eventual optimization and application to a panel of worms from endemic areas. All but one of the selected microsatellites contain simple tri-nucleotide repeats. Moderate to high levels of polymorphism were detected. Numbers of alleles ranged from 6 to 14 and observed heterozygosity was always >0.6. The loci reported here will facilitate high resolution population-genetic studies on schistosomes in re-emergent foci.

Findings

The Asian bloodfluke, Schistosoma japonicum, causes serious human disease in several parts of eastern Asia, and in particular in China where more than 30 million people living in the tropical and subtropical zones are at risk [1]. On the heels of widespread progress in controlling S. japonicum over the past two decades [2], China is facing the challenges posed by re-emergence of schistosomiasis in localities where control activities have nearly ceased and where apparent elimination had been achieved [2, 3]. In comparison to traditional assessment methods, molecular tools will be increasingly important as China targets regions with low prevalence and low infection intensity for elimination [46] on the path to reducing schistosome infection to less than 1% by 2015 [2]. Such tools will be important for high-resolution monitoring of infections in snails and in mammalian hosts, elucidating transmission networks, and improving the targeting of interventions to achieve final elimination of the disease.

This important pathogen has already received attention from population geneticists using microsatellites [7, 8]. Most of the loci used had been found by examination of the GenBank accessions for S. japonicum data existing at that time or through testing of primers that amplified microsatellite loci in another bloodfluke, S. mansoni. A near-complete draft genome of S. japonicum has been released by the Chinese Human Genome Center in Shanghai [9] and the raw data are available at http://lifecenter.sgst.cn/schistosoma/cn/schistosomaCnIndexPage.do. An earlier study [10] reported 17 loci from this resource. In this study we report on additional loci suitable for research into gene flow in S. japonicum in Sichuan Province. Results of this search are presented here. We searched this resource for microsatellite loci using the following criteria:

  • Repeats should be 2, 3 or 4-mer,

  • The number of tandem repeats should be in the range 10-25,

  • Loci should not include compound repeats,

  • Loci should be flanked by single-copy DNA sequences to which PCR primers could be targeted,

  • Loci should be far apart so as to avoid linkage disequilibrium. In practice, since chromosomal assignment of super-contigs is unknown as yet, loci were selected from different super-contigs,

  • Loci should not be in, or close to, known or predicted coding regions.

The search was undertaken using the software SciRoKo [11]. Following the above criteria, we identified 72 new loci for which primers were designed and synthesized. For 30 loci showing a single band of the correct size in a preliminary screening using an agarose gel, new forward primers were synthesized to permit M13 tailing [12, 13]. All 30 loci were then used for genotyping of ten adult worms. Loci failing to provide clear signals in the expected size range, or that lacked polymorphism, were not considered further. Finally 20 new loci, plus two from [10], were optimized for PCR and used in the genotyping of 20 individual adult worms. Primer annealing temperatures were designed to be very similar with eventual multiplexing in mind.

The Sichuan Center for Disease Control and Prevention (SCDC) maintains S. japonicum lifecycles, including S. japonicum from infected snails sourced from Hubei and Anhui Provinces passed through rabbit hosts. For this study, existing samples were obtained from SCDC of adult schistosomes that were derived from a single passage of mixed Hubei and Anhui cercariae through a definitive host. Genomic DNA was extracted from 10 individual male and 10 female worms by incubation in hot sodium hydroxide with pH adjustment using a Tris solution (HotSHOT) [14]. The lysates were used as templates for PCR directly. Each worm was genotyped individually.

All PCRs were carried out in a 10 μl reaction mixture containing 0.5 μl of template DNA (about 17.5 ng), 0.5 μM of each primer but 0.125 μM of any forward primer with an M13 tail, and 5 μl of 2X GoTaq Green Master Mix (Promega Corporation, WI, USA). For PCR amplification, templates were denatured at 94°C for 5 minutes followed by 30 cycles (94°C 30 seconds, 55°C 45 seconds, 72°C 45 seconds), and then by 8 cycles ( 94°C 30 seconds, 53°C 45 seconds, 72°C 45 seconds), and a final extension at 72°C for 10 minutes. PCR products were separated using an ABI 3130 XL automated DNA sequencer with ABI GS500 LIZ internal size standards. Results were read in GeneMapper 4.0 software (Applied Biosystems).

Estimates of heterozygosity were made, tests conducted for Hardy-Weinberg equilibrium and linkage disequilibrium, and alleles counted. The software package GenAlEx [15] was used for most data analysis. Micro-Checker [16] was used to identify loci at which null (non-amplifying) alleles might be present. Use of the Bonferroni-adjusted 95% confidence interval indicates that null alleles may occur only at locus SjP9, one of the loci reported by [10].

Table 1 presents the findings for each locus, including numbers of alleles and observed heterozygosity (H). Observed heterozygosity (Ho) at all loci was high, never below 0.6. A few loci deviated significantly from Hardy Weinberg expectations (Table 1), including SjP9 at which null alleles were suspected. Surprisingly, many pairs of loci were in linkage disequilibrium (data not shown). We consider this to be a consequence of the fact that adult worms were derived from pooled cercariae from infected snails: each snail is likely to yield many sibling/clonal cercariae, resulting in significant linkage disequilibrium (e.g. [10]). The pooling of cercariae from two distinct populations is likely to increase this effect. Previous workers [7] noted a high frequency of linkage disequilibrium in S. japonicum and considered it due to inbreeding and non-random mating.
Table 1

Primer sequences and other characteristics for each of 22 microsatellite loci amplified from 20 specimens of Schistosoma japonicum

Locus name

Primer sequences (tails removed)

Repeat unit

Length of locus in Sj Genome draft (excl tails)

Length range (PCR product - bp excl tail)

No. of alleles

In HWE?

Ho

He

SjP4

F:ACAAGCTCCAATCGTCTCTGA R:GAATACTGCCGCCCTTGTAA

TAA

217

182-244

14

 

0.789

0.831

SjP9

F:GATGAAACAGATACCCAGCAC R:TGCATGTAAAAATGGCTTGC

TAA

283

239-301

14

**

0.600

0.915

SjP18

F:TCCTTTATCTGGGCTGTGGA R:TTTCAGCAGGATAACATGACG

TGA

286

261-298

7

 

0.684

0.703

SjP19

F:GGTATCTTCGCTTTTTAGCATGG

R:TCCTAGGGTGTGGTATCAGAG

ATT

196

161-257

12

**

0.737

0.896

SjP22

F:CAAAGCCTAAACGTCATAGACAG R:CAACCACCGATAAGTAGAGTGGA

TTA

150

105-167

11

*

0.850

0.892

SjP23

F:GTACGATATGAGGGAAAGTTCA R:CTCTCCTTCAGACGAATTGAG

TAA

219

192-253

14

 

1.00

0.933

SjP26

F:CAAGGGAACATTGTACATGAAG R:TGGTAAAGGAGAAAGTGAACG

TAA

307

229-312

7

 

0.700

0.659

SjP28

F:TAACGCCTTTTCCCACATTC R:ATAACCACGATGGGAACCAA

TTA

242

232-269

13

**

0.900

0.926

SjP32

F:TGTCACCGAGTCTTCATTAGC R:ACAGTCAGTAGACCTGGATAAAC

TTA

175

142-192

14

 

0.950

0.929

SjP34

F:GGCGACCATACATAAGGAGAAT R:GACCGATTTCTAATGGAGCA

TAA

409

381-430

13

*

0.778

0.908

SjP37

F:TCCTTGACACGAGGTACATGT R:ATTACGTAACAGAAGGCTGGA

TAT

290

240-314

8

 

0.833

0.714

SjP39

F:GACGACTGTTAAGTCCATCTGA R:ATAACCAATCTCCACGAAAGC

ATT

239

223-251

8

 

0.900

0.871

SjP42

F:GCTGCAGCTTCTGTGTAGTAA R:GTCTTGCTCAGATCAGTTCGT

TAA

216

199-234

9

 

0.950

0.855

SjP43

F:ACAATGGCTATTGGTTGAGTAG R:GGAGCATGCGTATATGGAAAA

TAA

188

184-235

9

 

0.750

0.854

SjP45

F:ATAACACCGAATCTGTTCAGC R:TAATCCGGTCAGGATGTATGT

TAT

156

150-244

13

 

0.850

0.921

SjP48

F:TTGTTGGGTAGTGATGGTAGG R:TAGTTCATTCCACCTCTTGGA

TAA

246

251-273

6

 

0.650

0.795

SjP54

F:TTAGGCTTGTTGGTGCTGATA R:AGGTAAAGCAAATCCCATAGC

GGTA

437

373-446

9

 

1.00

0.712

SjP58

F:TCCCAGTACCAATGTAGATGTG R:CTAATAAAGTCGTCAAGGAGCA

AAT

227

439-499

12

**

0.800

0.921

SjP60

F:CGATTCATTCATAGCCTGACT R:GAATCCCATCACAGATTAACG

TAT

155

134-165

10

 

0.900

0.867

SjP61

F:TCATCTTGTCACCAACTAGGC R:GCTTGGAGGAGGCTAAAATAC

TAT

188

158-238

9

 

0.700

0.679

SjP63

F:ACCGCCACTACCACTAACCTCA R:TTGACCTGAAATCTGTCCCTA

TAA

390

333-389

13

**

0.800

0.904

SjP88

F:GCTTTCCAGGCATAAACTTCAC R:TCTCCTAATGATGGGAACAG

TAA

408

380-417

9

 

0.950

0.887

Sequences of microsatellites reported here have been deposited in GenBank [AB604199 - AB604218].

Note that the first two loci are from [10] and are included for comparative purposes.

The annealing temperature of PCRs for all loci is 55°C

* P < 0.05 ** P < 0.01 as determined in GenAlEx.

The loci presented here are likely to be specific for S. japonicum. Blast searches of the draft genome of S. mansoni (http://www.sanger.ac.uk/Projects/S_mansoni/) failed to find any matches that would indicate conservation of flanking regions in both species (not shown). Searches of the draft genome of S. japonicum yielded only a single "hit" for each locus.

The microsatellite loci reported here are, with one exception (SjP54), perfect trinucleotide repeats, making scoring easier than for dinucleotide and/or compound repeats. The diversity of alleles and genotypes present in the populations we sampled demonstrate the utility of these markers for future studies on epidemiology of S. japonicum in eastern Asia. Finally, the obvious genetic diversity within field populations of S. japonicum in China demonstrated by these polymorphic microsatellite loci confirms the recent report of marked genetic diversity in this parasite detected by analysis of the S. japonicum transcriptome and proteome [4].

Declarations

Acknowledgements

The authors wish to thank Kang Junxing, Director of the Sichuan Center for Disease Control and Prevention (Chengdu, People's Republic of China) for his continued support and collaboration. The authors also wish to acknowledge Zhong Bo, Ye Hong, Cui Lina, Chen Lin, Zhang Yi, Meng Xianhong of the Sichuan Center for Disease Control and Prevention for their contribution to the laboratory work. This work was supported in part by the NIH/NSF Ecology of Infectious Disease Program (grant no. 0622743) and the Emory Global Health Institute. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Authors’ Affiliations

(1)
Institute of Parasitic Diseases, Sichuan Center for Disease Control and Prevention
(2)
Department of Environmental Health, Rollins School of Public Health, Emory University
(3)
Department of Microbiology, Immunology & Tropical Medicine, George Washington University Medical Center
(4)
Department of Environmental Health Sciences, School of Public Health, 50 University Hall, University of California
(5)
School of Marine and Tropical Biology, James Cook University

References

  1. McManus DP, Gray DJ, Li YS, Feng Z, Williams GM, Stewart D, Rey-Ladino J, Ross AG: Schistosomiasis in the People's Republic of China: the era of the Three Gorges Dam. Clin Microbiol Rev. 2010, 23: 442-466. 10.1128/CMR.00044-09.PubMed CentralView ArticlePubMedGoogle Scholar
  2. Zhou XN, Guo JG, Wu XH, Jiang QW, Zheng J, Dang H, Wang XH, Xu J, Zhu HQ, Wu GL, Li YS, Xu XJ, Chen HG, Wang TP, Zhu NQ, Xia G, Wang LY, Zhang SQ, Lin DD, Chen MG, Hao Y: Epidemiology of schistosomiasis in the People's Republic of China, 2004. Emerg Infect Dis. 2007, 13: 1470-1476.PubMed CentralView ArticlePubMedGoogle Scholar
  3. Liang S, Yang CH, Zhong B, Qiu DC: Re-emerging schistosomiasis in hilly and mountainous areas of Sichuan, China. Bull World Health Organ. 2006, 84: 139-144. 10.2471/BLT.05.025031.PubMed CentralView ArticlePubMedGoogle Scholar
  4. Liu F, Lu J, Hu W, Wang SY, Cui SJ, Chi M, Yan Q, Wang XR, Song HD, Xu XN, Wang JJ, Zhang XL, Zhang X, Wang ZQ, Xue CL, Brindley PJ, McManus DP, Feng Z, Chen Z, Han ZG: Comparative transcriptomic and proteomic analyses of the human blood fluke, Schistosoma japonicum. PLoS Pathogens. 2006, 2: e29-10.1371/journal.ppat.0020029.PubMed CentralView ArticlePubMedGoogle Scholar
  5. Xu J, Rong R, Zhang HQ, Shi CJ, Zhu XQ, Xia CM: Sensitive and rapid detection of Schistosoma japonicum DNA by loop-mediated isothermal amplification (LAMP). Int J Parasitol. 2010, 40: 327-331. 10.1016/j.ijpara.2009.08.010.View ArticlePubMedGoogle Scholar
  6. Hung YW, Remais J: Quantitative Detection of Schistosoma japonicum Cercariae in Water by Real-Time PCR. PLoS Negl Trop Dis. 2008, 2: e337-10.1371/journal.pntd.0000337.PubMed CentralView ArticlePubMedGoogle Scholar
  7. Shrivastava J, Qian BZ, McVean G, Webster JP: An insight into the genetic variation of Schistosoma japonicum in mainland China using DNA microsatellite markers. Mol Ecol. 2005, 14: 839-849. 10.1111/j.1365-294X.2005.02443.x.View ArticlePubMedGoogle Scholar
  8. Shrivastava J, Barker GC, Johansen MV, Zhou XN, Aligui GD, McGarvey ST, Webster JP: Isolation and characterization of polymorphic DNA microsatellite markers from Schistosoma japonicum. Mol Ecol Notes. 2003, 3: 406-408. 10.1046/j.1471-8286.2003.00466.x.View ArticleGoogle Scholar
  9. Schistosoma japonicum Genome Sequencing and Functional Analysis Consortium: The Schistosoma japonicum genome reveals features of host-parasite interplay. Nature. 2009, 460: 345-351. 10.1038/nature08140.View ArticleGoogle Scholar
  10. Yin M, Hu W, Mo X, Wang SY, Brindley PJ, McManus DP, Davis GM, Feng Z, Blair D: Multiple near-identical genotypes of Schistosoma japonicum can occur in snails and have implications for population-genetic analyses. Int J Parasitol. 2008, 38: 1681-1691. 10.1016/j.ijpara.2008.05.015.PubMed CentralView ArticlePubMedGoogle Scholar
  11. Kofler R, Schlotterer C, Lelley T: SciRoKo: a new tool for whole genome microsatellite search and investigation. Bioinformatics. 2007, 23: 1683-1685. 10.1093/bioinformatics/btm157.View ArticlePubMedGoogle Scholar
  12. Schuelke M: An economic method for the fluorescent labeling of PCR fragments. Nature Biotech. 2000, 18: 233-234. 10.1038/72708.View ArticleGoogle Scholar
  13. Bandelj D, Jakse J, Javornik B: Amplification of fluorescent-labelled microsatellite markers in olives by a novel, economic method. Acta Agric Slovenica. 2004, 83: 323-329.Google Scholar
  14. Truett E, Mynatt LR, Truett AA, Walker AJ, Warman LM: Preparation of PCR-quality mouse genomic DNA with hot sodium hydroxide and Tris (HotSHOT). BioTechniques. 2000, 29: 52-54.PubMedGoogle Scholar
  15. Peakall R, Smouse PE: GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes. 2006, 6: 288-295. 10.1111/j.1471-8286.2005.01155.x.View ArticleGoogle Scholar
  16. Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P: MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes. 2004, 4: 535-538. 10.1111/j.1471-8286.2004.00684.x.View ArticleGoogle Scholar

Copyright

© Xiao et al; licensee BioMed Central Ltd. 2011

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Advertisement