Analysis of Variation in Chloroplast DNA Sequences

  • Berthold Heinze
  • Agnieszka Koziel-Monte
  • Daniela Jahn
Part of the Methods in Molecular Biology book series (MIMB, volume 1115)


This chapter introduces and reviews methods for analyzing variation in chloroplast DNA, mainly by polymerase chain reaction (PCR) and subsequent revelation of polymorphisms. Sources for chloroplast primers are discussed, as well as methods such as Sanger sequencing, PCR followed by restriction fragment length polymorphism (RFLP), gel electrophoresis, fragment analysis on automated DNA sequencers, denaturing high-performance liquid chromatography (dHPLC), and next-generation sequencing (NGS). A special section deals with peculiarities of chloroplast DNA variation, such as tandem repeats and mini- and microsatellites.

Key words

Chloroplast DNA PCR PCR-RFLP Sanger sequencing dHPLC Next-generation sequencing Gel electrophoresis Tandem repeats 



We thank Irena Nanista, Bianca Widmar, Ingrid Gerstl, and Renate Slunsky for technical assistance in the laboratory over the years. Funding for projects was by the European Commission—research project RAP—Realising Ash’ Potential, QLK5-2001-00631; Jubiläumsfond der Stadt Wien (Migrationsforschung); and the Austrian Science Funds (P 22716-B16 Gentianella).


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Copyright information

© Springer New York 2014

Authors and Affiliations

  • Berthold Heinze
    • 1
  • Agnieszka Koziel-Monte
    • 1
  • Daniela Jahn
    • 1
  1. 1.Department of GeneticsFederal Research Centre for ForestsViennaAustria

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