論文

査読有り 筆頭著者 責任著者
2017年7月1日

Evaluation of metagenetic community analysis of planktonic copepods using Illumina MiSeq: Comparisons with morphological classification and metagenetic analysis using Roche 454

PLoS ONE
  • Junya Hirai
  • ,
  • Satoshi Nagai
  • ,
  • Kiyotaka Hidaka

12
7
記述言語
英語
掲載種別
研究論文(学術雑誌)
DOI
10.1371/journal.pone.0181452
出版者・発行元
Public Library of Science

Metagenetics is a rapid and taxonomically comprehensive method for revealing community structures within environmental samples, based on large amounts of sequence data produced by high-throughput sequencers. Because community structures of planktonic copepods are important in the ocean owing to their high diversity and abundance, a metagenetic analysis of the 28S D2 region using Roche 454 was previously developed. However, the Illumina MiSeq platform with a high sequence output is being used more frequently in metagenetics, and non-calanoid copepods have not previously been fully evaluated. Here, we evaluated an Illumina MiSeq-based metagenetic analysis using a mock community and field-collected samples that were examined in a previous study using Roche 454, and the community structure, including non-calanoid copepods, was compared among morphological and metagenetic analyses. We removed a singleton read and applied an appropriate abundance threshold to remove erroneous Molecular Operational Taxonomic Units (MOTUs) with low-abundance sequences in the MiSeq-based analysis. Results showed that the copepod community was successfully characterized using Illumina MiSeq. Higher-quality sequences were obtained using MiSeq than by Roche 454, which reduced the overestimation of diversity, especially at a strict 99% similarity threshold for MOTU clustering. Taxonomic compositions in terms of both biomass and presence/absence of species, including non-calanoids, were more appropriately represented in the MiSeq- than in Roche 454-based analysis. Our data showed that metagenetic analysis using Illumina MiSeq is more useful for revealing copepod communities than Roche 454, owing to the lower cost and higher quality.

Web of Science ® 被引用回数 : 10

リンク情報
DOI
https://doi.org/10.1371/journal.pone.0181452
PubMed
https://www.ncbi.nlm.nih.gov/pubmed/28715458
Web of Science
https://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=JSTA_CEL&SrcApp=J_Gate_JST&DestLinkType=FullRecord&KeyUT=WOS:000443975500057&DestApp=WOS_CPL
ID情報
  • DOI : 10.1371/journal.pone.0181452
  • ISSN : 1932-6203
  • PubMed ID : 28715458
  • SCOPUS ID : 85024893449
  • Web of Science ID : WOS:000443975500057

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