Skip to main content
SpringerLink
Log in

Isolation and characterisation of new microsatellite markers for the stonefly Brachyptera braueri comparing a traditional approach with high throughput 454 sequencing

  • Technical Note
  • Published:
Conservation Genetics Resources Aims and scope Submit manuscript

Abstract

We developed thirteen microsatellite markers for the stonefly Brachytpera braueri, a rare aquatic insect. We compared a “traditional” approach yielding an enriched library by cloning of positive host cells, hybridising and Sanger sequencing of target fragments with a 454 next generation sequencing approach. From a total of 881 fragments containing a repeat motif thirteen polymorphic loci were developed and tested for two populations. Number of alleles ranged from 4 to 20 and values of heterozygosity varied from 0.17 to 0.91 (HO) and 0.26 to 0.91 (HE). The markers are essential to investigate the colonisation potential of freshwater insects.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

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

Instant access to the full article PDF.

Institutional subscriptions

References

  • Brettfeld R, Bellstedt R (2000) Wiederfund der steinfliege brachyptera braueri (Klapálek, 1900) nach fast hundert Jahren in Thüringen (Insecta: Plecoptera). Abhandlungen und Berichte des Museums der Nat Gotha 21:111–112

    Google Scholar 

  • Holleley CE, Geerts PG (2009) Multiplex manager 1.0: a cross-platform computer program that plans and optimizes multiplex PCR. Biotechniques 46(7):511–517. doi:10.2144/000113156

    Article  PubMed  CAS  Google Scholar 

  • Küttner R, Hohlmann M, Plesky B, Voigt H (2008) Zur verbreitung und ökologie von Brachyptera braueri (Klapálek, 1900) (Insecta: Plecoptera) in mitteldeutschland unter berücksichtigung weiterer plecoptera-arten des zeitigen frühjahres. Lauterbornia 63:31–50

    Google Scholar 

  • Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and clustal X version 2.0. Bioinformatics 23(21):2947–2948. doi:10.1093/bioinformatics/btm404

    Article  PubMed  CAS  Google Scholar 

  • Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen ZT, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer MLI, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu PG, Begley RF, Rothberg JM (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437(7057):376–380. doi:10.1038/nature03959

    PubMed  CAS  Google Scholar 

  • Meglecz E, Costedoat C, Dubut V, Gilles A, Malausa T, Pech N, Martin J-F (2010) QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects. Bioinformatics 26(3):403–404. doi:10.1093/bioinformatics/btp670

    Article  PubMed  CAS  Google Scholar 

  • Ronaghi M (2001) Pyrosequencing sheds light on DNA sequencing. Genome Res 11(1):3–11. doi:10.1101/gr.11.1.3

    Article  PubMed  CAS  Google Scholar 

  • Rousset F (2008) GENEPOP’007: a complete re-implementation of the GENEPOP software for windows and linux. Mol Ecol Resour 8(1):103–106. doi:10.1111/j.1471-8286.2007.01931.x

    Article  PubMed  Google Scholar 

  • Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol (Clifton, NJ) 132:365–386

    CAS  Google Scholar 

  • Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4(3):535–538. doi:10.1111/j.1471-8286.2004.00684.x

    Article  Google Scholar 

  • Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31(13):3406–3415. doi:10.1093/nar/gkg595

    Article  PubMed  CAS  Google Scholar 

  • Zwick P (1992) Stream habitat fragmentation—a threat to biodiversity. Biodivers Conserv 1(2):80–97. doi:10.1007/bf00731036

    Article  Google Scholar 

Download references

Acknowledgments

We thank Ralph Küttner and Bodo Plesky for providing the samples. Funding comes from the Deutsche Forschungsgemeinschaft (HA3431/4-1). Additional funding is provided by the research funding program Landes-Offensive zur Entwicklung Wissenschaftlich-ökonomischer Exzellenz (LOEWE) of Hesse’s Ministry of Higher Education, Research, and the Arts.

Author information

Authors and Affiliations

  1. Department of River Ecology and Conservation, Conservation Genetics Group, Senckenberg Research Institutes and Natural History Museums, Clamecystrasse 12, Gelnhausen, Germany

    Jutta Geismar & Carsten Nowak

  2. Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany

    Carsten Nowak

Authors
  1. Jutta Geismar
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Carsten Nowak
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jutta Geismar.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Geismar, J., Nowak, C. Isolation and characterisation of new microsatellite markers for the stonefly Brachyptera braueri comparing a traditional approach with high throughput 454 sequencing. Conservation Genet Resour 5, 413–416 (2013). https://doi.org/10.1007/s12686-012-9816-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12686-012-9816-1

Keywords

Search

Navigation