Next-Generation Technologies to Determine Plastid Genome Sequences

  • Robert J. Henry
  • Nicole Rice
  • Mark Edwards
  • Catherine J. Nock
Part of the Methods in Molecular Biology book series (MIMB, volume 1132)


Sequencing of chloroplast genomes is a key tool for analysis of chloroplasts and the impact of manipulation of chloroplast genomes by biotechnology. Advances in genome sequencing allow the complete sequencing of the chloroplast genome and assessment of variation in the chloroplast genome sequences within a plant. Isolation of chloroplast DNA has been a traditional starting point in these analyses, but the capacity of current sequencing technologies allows effective analysis of the chloroplast genome sequence by shotgun sequencing of a preparation of total DNA from the plant. Chloroplast insertions in the nuclear genome can be distinguished by their much lower copy number. Short-read sequences are best assembled by alignment with a reference chloroplast genome.

Key words

DNA sequencing Genome assembly Next-generation sequencing NGS Plastid genome 



The authors thank the Australian Plant DNA Bank and Southern Cross Plant Genomics for assistance with samples and sequencing.


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Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Robert J. Henry
    • 1
  • Nicole Rice
    • 2
  • Mark Edwards
    • 2
  • Catherine J. Nock
    • 2
  1. 1.Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbaneAustralia
  2. 2.Southern Cross Plant Science, Centre for Plant Conservation GeneticsSouthern Cross UniversityLismoreAustralia

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