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Back to basics: an evaluation of NaOH and alternative rapid DNA extraction protocols for DNA barcoding, genotyping, and disease diagnostics from fungal and oomycete samples

Authors

  • Todd W. Osmundson,

    Corresponding author
    1. Forest Pathology and Mycology Laboratory, Department of Environmental Science, Policy & Management, University of California, Berkeley, CA, USA
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  • Catherine A. Eyre,

    1. Forest Pathology and Mycology Laboratory, Department of Environmental Science, Policy & Management, University of California, Berkeley, CA, USA
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  • Katherine M. Hayden,

    1. Forest Pathology and Mycology Laboratory, Department of Environmental Science, Policy & Management, University of California, Berkeley, CA, USA
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  • Jaskirn Dhillon,

    1. Forest Pathology and Mycology Laboratory, Department of Environmental Science, Policy & Management, University of California, Berkeley, CA, USA
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  • Matteo M. Garbelotto

    1. Forest Pathology and Mycology Laboratory, Department of Environmental Science, Policy & Management, University of California, Berkeley, CA, USA
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Abstract

The ubiquity, high diversity and often-cryptic manifestations of fungi and oomycetes frequently necessitate molecular tools for detecting and identifying them in the environment. In applications including DNA barcoding, pathogen detection from plant samples, and genotyping for population genetics and epidemiology, rapid and dependable DNA extraction methods scalable from one to hundreds of samples are desirable. We evaluated several rapid extraction methods (NaOH, Rapid one-step extraction (ROSE), Chelex 100, proteinase K) for their ability to obtain DNA of quantity and quality suitable for the following applications: PCR amplification of the multicopy barcoding locus ITS1/5.8S/ITS2 from various fungal cultures and sporocarps; single-copy microsatellite amplification from cultures of the phytopathogenic oomycete Phytophthora ramorum; probe-based P. ramorum detection from leaves. Several methods were effective for most of the applications, with NaOH extraction favored in terms of success rate, cost, speed and simplicity. Frozen dilutions of ROSE and NaOH extracts maintained PCR viability for over 32 months. DNA from rapid extractions performed poorly compared to CTAB/phenol-chloroform extracts for TaqMan diagnostics from tanoak leaves, suggesting that incomplete removal of PCR inhibitors is an issue for sensitive diagnostic procedures, especially from plants with recalcitrant leaf chemistry. NaOH extracts exhibited lower yield and size than CTAB/phenol-chloroform extracts; however, NaOH extraction facilitated obtaining clean sequence data from sporocarps contaminated by other fungi, perhaps due to dilution resulting from low DNA yield. We conclude that conventional extractions are often unnecessary for routine DNA sequencing or genotyping of fungi and oomycetes, and recommend simpler strategies where source materials and intended applications warrant such use.

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