The use of a non-coding region of chloroplast DNA in phylogenetic studies of the subtribe Sonchinae (Asteraceae : Lactuceae)

The systematic utility of sequences from a non-coding region of chloroplast DNA (cpDNA) between psbA and trnH((GUG)) was examined by assessing phyloge netic relationships in subtribe Sonchinae (Asteraceae: Lactuceae). Primers constructed against highly conserved regions of tRNA genes were used for PC R amplification and sequencing. The psbA-trnH intergenic spacer contains se veral insertions and deletions (indels) in Sonchinae with the length varyin g from 385 to 450 bp. Sequence divergence ranges from 0.00% to 7.54% within Sonchinae, with an average of 2.4%. Average sequence divergence in Sonchus subg. Sonchus is 2.0%, while the mean for subg. Dendrosonchus and its clos e relatives in Macaronesia (the woody Sonchus alliance) is 1.0%. Our result s suggest that this region does not evolve rapidly enough to resolve relati onships among closely related genera or insular endemics in the Asteraceae. The phylogenetic utility of psbA-trnH sequences of the non-coding cpDNA wa s compared to sequences from the ITS region of nuclear ribosomal DNA. The r esults suggest that ITS sequences evolve nearly four times faster than psbA -trnH intergenic spacer sequences. Furthermore, the ITS sequences provide m ore variable and phylogenetically informative sites and generate more highl y resolved trees with more strongly supported clades, and thus are more sui table for phylogenetic comparisons at lower taxonomic levels than the psbA- trnH intergenic chloroplast sequences.