title: Analysis of variation in chloroplast DNA sequences.
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.
authors.affiliation: Department of Genetics, Federal Research Centre for Forests, Vienna, Austria.
authors.forename: Berthold
authors.initials: B
authors.lastname: Heinze
authors.forename: Agnieszka
authors.initials: A
authors.lastname: Koziel-Monte
authors.forename: Daniela
authors.initials: D
authors.lastname: Jahn
mesh_terms: D001483:Base Sequence; D002851:Chromatography, High Pressure Liquid; D017931:DNA Primers / Q000235:genetics; D018742:DNA, Chloroplast / Q000737:chemistry / Q000235:genetics* / Q000302:isolation & purification; D030541:Databases, Genetic; D004587:Electrophoresis, Agar Gel; D004591:Electrophoresis, Polyacrylamide Gel; D005821:Genetic Techniques; D014644:Genetic Variation; D059014:High-Throughput Nucleotide Sequencing; D009691:Nucleic Acid Denaturation; D016133:Polymerase Chain Reaction; D011110:Polymorphism, Genetic; D012150:Polymorphism, Restriction Fragment Length; D017422:Sequence Analysis, DNA; D020080:Tandem Repeat Sequences / Q000235:genetics
chemical_list: D017931:DNA Primers; D018742:DNA, Chloroplast