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.

A chloroplast genealogy of hordeum (poaceae): Long-term persisting haplotypes, incomplete lineage sorting, regional extinction, and the consequences for phylogenetic inference.

To analyze reasons for inconclusive results of earlier chloroplast phylogenies in the grass genus Hordeum, we established a genealogy of chloroplast haplotypes by sequencing the trnL-trnF region in 875 individuals, covering all 31 species of the genus. Although the outcomes of phenetic and parsimony analyses of 88 haplotypes were ambiguous, a network approach showed that in Hordeum ancient chloroplast types co-occur with their descendants. Moreover, we found up to 18 different chloroplast haplotypes within a single species and up to 6 species sharing single haplotypes.