Abstract
The genus Monoraphidium is a green microalgae distributed globally in freshwater ecosystems, and it is difficult to classify morphologically. Molecular genetic markers have been used for their taxonomy, although they have not been thoroughly evaluated. Here, we investigated three nuclear rRNA molecules (18S, internal transcribed spacer [ITS] + 5.8S, and 28S) and four chloroplast genes (psbB, psbC, rbcL, and tufA) using 16 Monoraphidium strains consisting of 9 species. Upon comparisons of genetic diversity and marker performance evaluation, we found that ITS was the best marker for Monoraphidium to discriminate each species, followed by tufA. The taxonomic discrimination power of the ITS was supported by the neighbor-joining tree. In addition, a secondary structure of ITS2 combined with compensatory base changes showed the distinct differences among individual species of Monoraphidium. These suggest that ITS may be the best marker for species differentiation of the coccoid green algae Monoraphidium.