Single nucleotide sequence analysis: a cost- and time-effective protocol for the analysis of microsatellite- and indel-rich chloroplast DNA regions

We present a simple method to screen for DNA sequence variation in microsatellite- and indel-rich regions of the chloroplast genome. The single nucleotide sequence (SNS) analysis provides a trade-off between the time- and cost-effective, but less informative and homoplasy-sensitive electrophoretic detection of microsatellite and indel size variation on the one hand, and more costly, but also more accurate methods like DNA sequencing on the other. The principle of the SNS method is to sequence one instead of all four nucleotides of a target region amplified by polymerase chain reaction. By careful selection of the respective nucleotide, almost the same amount of information can be retrieved from these partial sequences as could be from complete sequences; however, only a third to a fourth of the money and time resources are needed.