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Analysis of Variation in Chloroplast DNA Sequences

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Molecular Plant Taxonomy

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1115))

Abstract

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.

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Acknowledgements

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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  1. Department of Genetics, Federal Research Centre for Forests, Vienna, Austria

    Berthold Heinze, Agnieszka Koziel-Monte & Daniela Jahn

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  1. Berthold Heinze
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  2. Agnieszka Koziel-Monte
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  3. Daniela Jahn
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  1. UMR C53 PVBMT Université de la Réunion-Cirad, Université de la Réunion, Ile de la Réunion, France

    Pascale Besse

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Heinze, B., Koziel-Monte, A., Jahn, D. (2014). Analysis of Variation in Chloroplast DNA Sequences. In: Besse, P. (eds) Molecular Plant Taxonomy. Methods in Molecular Biology, vol 1115. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-767-9_5

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  • DOI: https://doi.org/10.1007/978-1-62703-767-9_5

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