Metagenetic community analysis of copepods using high throughput sequencing

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  • Hirai Junya
    National Research Institute of Fisheries Science, Fisheries Research Agency
  • Shimode Shinji
    Graduate School of Environment and Information Sciences, Yokohama National University
  • Kuriyama Mikiko
    National Research Institute of Fisheries Science, Fisheries Research Agency
  • Ichikawa Tadafumi
    National Research Institute of Fisheries Science, Fisheries Research Agency
  • Hidaka Kiyotaka
    National Research Institute of Fisheries Science, Fisheries Research Agency
  • Tsuda Atsushi
    Atmosphere and Ocean Research Institute, The University of Tokyo

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Other Title
  • 超並列シーケンサーを用いたメタジェネティクスによるカイアシ類の群集構造解析
  • チョウヘイレツ シーケンサー オ モチイタ メタジェネティクス ニ ヨル カイアシルイ ノ グンシュウ コウゾウ カイセキ

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Abstract

<p>Marine planktonic copepods are an ecologically important group with high species richness and abundance. Here, we propose a metagenetic approach for revealing the community structure of marine planktonic copepods using 454 pyrosequencing of nuclear large subunit ribosomal DNA. We determined an appropriate similarity threshold for clustering pyrosequencing data into molecular operational taxonomic units (MOTUs) using an artificial community containing 33 morphologically identified species. The artificial community was appropriately clustered into MOTUs at 97％ similarity, with little inflation in MOTU numbers and with relatively high species-level resolution. Next, we applied the method to field-collected samples, and the results corresponded reasonably well with morphological analysis of these communities. Numbers of MOTUs were well correlated with species richness at 97％ similarity, and large numbers of sequence reads were generally observed in MOTUs derived from species with large biomass. Further, MOTUs were successfully classified into taxonomic groups at the family level at 97％ similarity; similar patterns of species richness and biomass were revealed within families with metagenetic and morphological analyses. The metagenetic approach reported here can be an effective tool for rapid and comprehensive assessment of copepod community structure. In this paper, we also introduce an example of metagenetic community study of copepods in the tropical and subtropical Pacific.</p>

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