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Comparative study of the validity of three regions of the 18S‐ rRNA gene for massively parallel sequencing‐based monitoring of the planktonic eukaryote community
Author(s) -
Tanabe Akifumi S.,
Nagai Satoshi,
Hida Kohsuke,
Yasuike Motoshige,
Fujiwara Atushi,
Nakamura Yoji,
Takano Yoshihito,
Katakura Seiji
Publication year - 2016
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.12459
Subject(s) - biology , amplicon , massive parallel sequencing , 18s ribosomal rna , in silico , genetics , primer (cosmetics) , ribosomal rna , computational biology , polymerase chain reaction , eukaryote , gene , evolutionary biology , dna sequencing , genome , chemistry , organic chemistry
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 ( INSD s), 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 INSD s. We also examined the primer universality and the taxonomic identification power, using MPS ‐based environmental surveys in the Sea of Okhotsk, 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 INSD s 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 the most suitable for future MPS ‐based monitoring of natural eukaryote communities, as the number of sequences deposited in INSD s increases.