Plant-Microbe DNA Extraction Protocol

The total DNAs of the plants and associated microbes were extracted from 10 twigs (0.5–1 cm in length) per tree using a DNA extraction kit (Omega Bio-tek, Norcross, GA, USA), and the resultant DNA extracts were evaluated via 1% agarose gel electrophoresis. The DNA concentrations were quantified using a NanoDrop2000 spectrophotometer (Thermo Scientific, Waltham, MA, USA) and normalized for use as the templates for generating PCR amplicons. Total DNA was extracted from fungal mycelia and cultured on PDA with cellophane using the phenol-based method as described previously [33 (link)].

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Tian M., Wei S., Bian R., Luo J., Khan H.A., Tai H., Kondo H., Hadidi A., Andika I.B, & Sun L. (2022). Natural Cross-Kingdom Spread of Apple Scar Skin Viroid from Apple Trees to Fungi. Cells, 11(22), 3686.

Publication 2022

DNA extraction kit NanoDrop2000 spectrophotometer

A dna Agarose gel electrophoresis Cellophane Fungal mycelia Phenol Plants dnas Tree

Corresponding Organization : Okayama University

Other organizations : United States Department of Agriculture, Agricultural Research Service, Qingdao Agricultural University

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Variable analysis

independent variables

DNA extraction method

dependent variables

DNA concentration
DNA quality (evaluated via agarose gel electrophoresis)

control variables

Number of twigs per tree (10 twigs per tree)
Twig length (0.5–1 cm in length)
Use of DNA extraction kit (Omega Bio-tek, Norcross, GA, USA)
Use of NanoDrop2000 spectrophotometer (Thermo Scientific, Waltham, MA, USA) for DNA quantification
Use of phenol-based method for fungal DNA extraction as described previously [33]

controls

Positive control: Not specified
Negative control: Not specified

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