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3. Analysis of variation in chloroplast DNA sequences.

Author

Heinze B, Koziel-Monte A, and Jahn D

Subjects
Base Sequence, Chromatography, High Pressure Liquid, DNA Primers genetics, DNA, Chloroplast chemistry, DNA, Chloroplast isolation & purification, Databases, Genetic, Electrophoresis, Agar Gel, Electrophoresis, Polyacrylamide Gel, High-Throughput Nucleotide Sequencing, Nucleic Acid Denaturation, Polymerase Chain Reaction, Polymorphism, Genetic, Polymorphism, Restriction Fragment Length, Sequence Analysis, DNA, Tandem Repeat Sequences genetics, DNA, Chloroplast genetics, Genetic Techniques, Genetic Variation
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.

Published
2014
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