Table 1 Comparison of various DNA methods (adapted from [135, 237, 245, 247])
From: DNA methods for identification of Chinese medicinal materials
| Â | SCAR | ARMS | SSR | PCR-RFLP | RP-PCR | ISSR | AFLP | Sequencing | Hybridization |
|---|---|---|---|---|---|---|---|---|---|
Development cost | medium | medium | high | medium a | low | low | low | medium | medium |
Running cost | low | low | medium | medium a | low | low | medium | medium | medium |
Polymorphism | low b | low c | high d | low e | medium f | medium f | medium f | medium-low g | only for detection h |
Detection of contamination by DNA of the same target species (mixture) | no | no | yes | yes/noi | no | no | no | yes/nok | yes/nok |
Detection of contamination by non-target species DNA (mixture) | no | no | no | yes j | no | no | no | yes/nok | yes/nok |
Detection of contamination by DNA of the same target species (mixture) | no | no | yes | yes/no i | no | no | no | yes/nok | yes/nok |
Detection of contamination by non-target species DNA (mixture) | no | No | no | yesj | No | no | no | yes/nok | yes/nok |
Multi-locus/single locus | single locus | single locus | single locus | single locus | multi-loci | multi-loci | multi-loci | single locus | single locus |
Level of identification (taxonomic level) | species | species to strain | strain | species to strain | species to strain | species to strain | species to strain | family to strain | genus to subspecies |
Quality of DNA required (integrity) | medium | medium | low | medium | high | high | high | medium | medium |
Quality of DNA required (purity) | high l | high l | medium | high | high | high | high | high l | high |
Prior sequence knowledge requirement (including universal primer sequence) | yes | yes | yes | no | no | no | no | yes | yes |
Throughput | low | low | high | low | high | high | high | low | high |
Level of skills required | low | low | low-medium | low | low | low | medium | medium | medium |
Automation | yes | yes | yes | difficult | yes | yes | yes | yes | difficult |
Reliability | high | high | high | high | low | medium | high | high | medium |