Genomic DNA Extraction and Barcoding of Endophytic Fungi

  • Patricia L. Diaz
  • James R. Hennell
  • Nikolaus J. SucherEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 862)


Endophytes live inter- and/or intracellularly inside healthy aboveground tissues of plants without causing disease. Endophytic fungi are found in virtually every vascular plant species examined. The origins of this symbiotic relationship between endophytes go back to the emergence of vascular plants. Endophytic fungi receive nutrition and protection from their hosts while the plants benefit from the production of fungal secondary metabolites, which enhance the host plants’ resistance to herbivores, pathogens, and various abiotic stresses. Endophytic fungi have attracted increased interest as potential sources of secondary metabolites with agricultural, industrial, and medicinal use. This chapter provides detailed protocols for isolation of genomic DNA from fungal endophytes and its use in polymerase chain reaction-based amplification of the internal transcribed spacer region between the conserved flanking regions of the small and large subunit of ribosomal RNA for barcoding purposes.

Key words

Fungal endophytes Internal transcribed spacer Fusarium oxysporum Polymerase chain reaction PCR Molecular identification techniques 



We thank Dr Jeremy Burdon and Dr Bo Wang from the CSIRO Plant Industry in Canberra for providing us with their extensive collection of endophytes isolated from wild cotton species in Australia (21). Many thanks to Dr Kendall Martin and Dr Paul Rygiewicz for granting use of Fig. 1.


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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Patricia L. Diaz
    • 1
  • James R. Hennell
    • 1
  • Nikolaus J. Sucher
    • 2
    Email author
  1. 1.Centre for Complementary Medicine Research, School of Science and HealthUniversity of Western SydneyPenrithAustralia
  2. 2.Department of Science, Technology, Engineering & Math (S.T.E.M.)Roxbury Community CollegeBostonUSA

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