Phylogenetic analyses of Nitella subgenus Tieffallenia (Charales, Charophyceae) using nuclear ribosomal DNA internal transcribed spacer sequences

Nucleotide sequences from the nuclear ribosomal DNA internal transcribed spacers (ITS1 and ITS2) and 5.8S ribosomal RNA (rRNA) gene were obtained for 13 Nitella species belonging to the subgenus Tieffallenia in order to test the chloroplast gene phylogeny previously used for taxonomic studies. The phylogenetic relationships of the 13 Nitella species based on nuclear DNA markers were congruent with those in the chloroplast gene phylogeny using the combined sequence data set for the genes encoding the beta subunit of ATP synthase (atpB) and the large subunit of Rubisco (rbcL). Therefore, the chloroplast gene phylogeny at the species level within the subgenus Tieffallenia seems to be unaffected by the maternal inheritance of chloroplast genes and can be used to obtain a natural taxonomy at the species level. This may result from the monoecious sexual reproduction that occurs in all the Nitella species examined. Phylogenetic analyses based on the concatenated chloroplast atp/B and rbcL and nuclear 5.8S rRNA and ITS sequences generally gave higher resolution at or above species level within the subgenus Tieffallenia than the ITS-5.8S rRNA phylogeny or the rbcL-atpB analyses.