Phylogenetic utility of the trnH–psbA IGR and stem-loop diversity of the 3′ UTR in Cactaceae (Caryophyllales)

The ultrastructure of the psbA–trnH intergenic region (hereafter IGR) of the Cactaceae was characterised based on 642 sequences identifying a conserved region and a mutational hot spot with different evolutionary rates. The first section of the IGR includes a highly conserved 3′ UTR of the psbA containing a TATA-box and a stem-loop. The second section of the IGR is a highly variable intergenic spacer (hereafter IGS) with a mutational hot spot. The phylogenetic utility of this IGR was tested by applying four different partitioned schemes to the same data set and searching for trees under different evolutionary models. The IGR showed 90 different stem-loop conformations with the highest diversity found in the Cactoideae with 78 architectures, the Opuntioideae with nine and the Pereskioideae with seven different architectures. The shortest stem-loop was recovered for Rhipsalis paradoxa with 47 nt, while the longest stem-loop was found in five species of Echinocereus. The organisation of the IGR in the Cactaceae follows the overall general organisation analysed for other angiosperms, and it seems that within the family, there is a general tendency to the reduction in length of the IGR in Maihuenia + Opuntioideae + Cacteae compared with Pereskia. The over-partition of the data set reduces resolution and support, while the un-partitioned analysis, disregarding primary homology assessment, shows good support and resolution but builds a phylogeny on ambiguous grounds. The best proposal scheme for this IGR is a partitioned analysis including three different regions that shows high support and resolution and considers primary homology assessment as a fundamental step in phylogeny reconstruction.