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Table 3 Comparison of different DNA extraction and LAMP protocols for Xylella fastidiosa, Ceratocystis platani and Phytophthora ramorum detection

From: Real-time loop-mediated isothermal amplification: an early-warning tool for quarantine plant pathogen detection

Protocol This study Tomlinson et al. (2007) Harper et al. (2010)
DNA extraction
 Target pathogen Xylella fastidiosa, Ceratocystis platani, Phytophthora ramorum Phytophthora ramorum Xylella fastidiosa
 Commercial kit Plant Material Lysis Kit (OptiGene) EZNA Plant DNA Kit (Omega Bio-tek) QuickPick Plant DNA kit (Bio-Nobile) Invimag Plant DNA Mini Kit (Invitek) DNeasy Plant Minikit (Qiagen)
 Use Field Laboratory Field Laboratory Laboratory
 Sample requirement Fresh plant tissue (80–100 mg) Fresh plant tissue (80–100 mg) Fresh plant tissue (15–25 mg) Lyophilized petiole (200 mg) Fresh plant tissue (200 mg)
 Advantages Rapid and simple protocol with few reagents and steps; no laboratory instruments are required Protocol kit with spin columns and buffer supplied Processing up to 24 samples in parallel Simplified sample processing Grounding with beads; kit with spin column and buffer supplied
 Disadvantage Difficult for large number of samples Required laboratories facilities for grinding and DNA extraction Extremely basic equipment is needed Required laboratories facilities for grinding and for DNA extraction Required laboratories facilities for grinding and for DNA extraction
 Time per sample 5 min 1 h 40–50 min > 30 min 1 h
Isothermal DNA amplification
 Instrument Genie II (OptiGene) Smart Cycler (Cepheid) ABI 9700 Thermocycler (Applied Biosystems)
 Use Field Laboratory Laboratory
 Sensitivity (LOD) P. ramorum (0.128 pg) P. ramorum (10 pg)
X. fastidiosa (0.02 pg) X. fastidiosa (1.4 pg)
C. platani (0.02 pg)
 Specificity P. ramorum (high specific; P. lateralis) P. ramorum (high specific; P. lateralis)
X. fastidiosa (very high specific) X. fastidiosa (very high specific)
C. platani (high specific; C. fimbriata)
 Advantages Rapid detection results; amplification and detection reaction is carried out in the same instrument (16 sample per run) High number of samples to be processed High number of samples to be processed
 Disadvantage Strip tubes with amplification mix need to be prepared before in laboratory Additional steps to visualize amplified products (electrophoresis gel, colorimetric detection, fluorescent dye) Electrophoresis gel to visualize amplified products
 Time per sample 30 min > 1 h > 1 h
  1. LOD limit of detection