Data from: Comparative study of the validity of three regions of 18S-rRNA gene for massively parallel sequencing-based monitoring of the planktonic eukaryote community

The nuclear 18S-rRNA gene has been used as a metabarcoding marker in massively parallel sequencing (MPS)-based environmental surveys for plankton biodiversity research. However, different hypervariable regions have been used in different studies, and their utility has been debated among researchers. In this study, detailed investigations into 18S-rRNA were carried out; we investigated the effective number of sequences deposited in international nucleotide sequence databases (INSDs), the amplification bias, and the amplicon sequence variability among the three variable regions, V1–3, V4–5, and V7–9, using in silico polymerase chain reaction (PCR) amplification based on INSDs. We also examined the primer universality and the taxonomic identification power, using MPS-based environmental surveys, to determine which region is more useful for MPS-based monitoring. The primer universality was not significantly different among the three regions, but the number of sequences deposited in INSDs was markedly larger for the V4–5 region than for the other two regions. The sequence variability was significantly different, with the highest variability in the V1–3 region, followed by the V7–9 region, and the lowest variability in the V4–5 region. The results of the MPS-based environmental surveys showed significantly higher identification power in the V1–3 and V7–9 regions than in the V4–5 region, but no significant difference was detected between the V1–3 and V7–9 regions. We therefore conclude that the V1–3 region will be most suitable for future MPS-based monitoring of natural eukaryote communities, as the number of sequences deposited in INSDs increases.

核基因组18S核糖体RNA（18S-rRNA）基因已被用作大规模并行测序（MPS）环境调查中的元条形码标记位点，用于浮游生物多样性研究。然而不同研究中所选用的高变区各不相同，其应用价值也在研究者间存在争议。本研究针对18S-rRNA基因开展了细致分析：基于国际核苷酸序列数据库（INSDs）的计算机模拟聚合酶链式反应（PCR）扩增，我们评估了V1–3、V4–5及V7–9三个高变区的INSDs收录有效序列数、扩增偏倚及扩增子序列变异度；同时结合基于MPS的环境调查，我们检测了引物通用性与物种分类鉴定能力，以筛选更适用于MPS监测的高变区。结果显示，三个高变区的引物通用性无显著差异，但V4–5区在INSDs中的收录序列数显著多于另外两个区域；序列变异度则存在显著差异，V1–3区变异度最高，其次为V7–9区，V4–5区变异度最低。基于MPS的环境调查结果表明，V1–3与V7–9区的分类鉴定能力显著高于V4–5区，但V1–3与V7–9区间未检测到显著差异。综上，随着INSDs收录序列数的不断增加，V1–3区将最适用于未来基于MPS的自然真核生物群落监测。