Comparative study in validity of three regions of 18S-rRNA for eukaryote amplicon sequence analyses

In the present study, we performed a detailed investigation of the 18S-rDNA, namely, numbers of registered sequences, frequencies of amplification success, the amplicon sequence variability among three regions containing V1-V3, V4-V5 and V7-V9 regions using in silico PCRs based on public databases, and the identification power by NGS-based environmental surveys of planktonic eukaryote community. Although the number of registered sequences in V4-V5 regions was remarkably higher than other regions, the identification power in NGS-based environmental surveys was lowest in V4-V5 regions due to the lowest sequence variability. The number of registered sequences in V1-V3 region was ca. two times smaller than V7-V9 region, and the sequence variability in V1-V3 region was significantly higher than that in V7-V9 region. Then, the identification power was not significant between these two regions, implying identification power is affected by combination of numbers of registered sequences and the sequence variability. We therefore believe V1-V3 region will be the best one for applying to NGS-based monitoring of planktonic eukaryote community in the near future as the number of sequences deposited increases in public databases.