Assessing intraspecific diversity in a lichen-forming fungus and its green algal symbiont: Evaluation of eight molecular markers

To facilitate marker selection in sequence-based studies on genetic diversity and symbiont selectivity in lichens we conducted a comparison of eight molecular markers in the lichen-forming fungus Lasallia pustulata and its trebouxioid photobiont. We compared mtSSU rDNA, mtLSU rDNA, MCM7, TSR1 (mycobiont) and nrITS rDNA, COX2, psbJ-L intergenic spacer, rbcL (photobiont) of 45 individuals from European populations of L. pustulata. Mycobiont and photobiont loci had congruent phylogenetic signals. Based on the results of this study we recommend the use of MCM7 and TSR1 (mycobiont), and nrITS rDNA and COX2 (photobiont). In this specific study system we found no sequence variability in the mycobiont loci EF1, nrITS rDNA, RPB1, and RPB2, which we sequenced for a subset of individuals. We had limited success amplifying GPD (mycobiont), actin and chloroplast LSU rDNA (photobiont), however, we do not rule out that these loci could be valuable markers in other species.