Chloroplast Biotechnology pp 39-46

Part of the Methods in Molecular Biology book series (MIMB, volume 1132) | Cite as

Next-Generation Technologies to Determine Plastid Genome Sequences

  • Robert J. Henry
  • Nicole Rice
  • Mark Edwards
  • Catherine J. Nock
Protocol

Abstract

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 

References

  1. 1.
    Atherton RA, McComish BJ, Shepherd LD, Berry LA, Albert NW, Lockhart PJ (2010) Whole genome sequencing of enriched chloroplast DNA using the Illumina GAII platform. Plant Methods 6:22PubMedCentralPubMedCrossRefGoogle Scholar
  2. 2.
    Nock CJ, Waters DLE, Edwards MA, Bowen S, Rice N, Cordeiro GM, Henry RJ (2010) Chloroplast genome sequence from total DNA for plant identification. Plant Biotechnol J 9:328–333PubMedCrossRefGoogle Scholar
  3. 3.
    Li X, Gao H, Song JY, Wang JY, Henry R, Wu HZ, Hu ZG, Yao H, Luo HM, Luo K, Pan HL, Chen AL (2012) Complete chloroplast genome sequence of Magnolia grandiflora and comparative analysis with related species. Sci China Ser C 56:189–198CrossRefGoogle Scholar
  4. 4.
    McPherson H, van der Merwe M, Delaney SK, Edwards MA, Henry RJ, McIntosh E, Rymer PD, Milner ML, Siow J, Rossetto M (2013) Capturing chloroplast variation for molecular ecology studies: a simple next generation sequencing approach applied to a rainforest tree. BMC Ecol 13:8PubMedCentralPubMedCrossRefGoogle Scholar
  5. 5.
    Yang M, Zhang X, Liu G, Chen K, Yun Q, Zhao D, Al-Mssallem IS, Yu J (2010) The complete chloroplast genome sequence of the date palm (Phoenix dactylifera L.). PLoS One 5:e12762PubMedCentralPubMedCrossRefGoogle Scholar
  6. 6.
    Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM (2009) The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res 38:1767–1771PubMedCentralPubMedCrossRefGoogle Scholar
  7. 7.
    Wyman SK, Jansen RK, Boore JL (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252–3255PubMedCrossRefGoogle Scholar
  8. 8.
    Miller JR, Koren S, Sutton G (2010) Assembly algorithms for next-generation sequencing data. Genomics 95:315–327PubMedCentralPubMedCrossRefGoogle Scholar

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

Personalised recommendations