Pyrosequence read length of 16S rRNA gene affects phylogenetic assignment of plant-associated bacteria

Takashi Okubo, Seishi Ikeda, Akifumi Yamashita, Kimihiro Terasawa, Kiwamu Minamisawa

Research output: Contribution to journalArticlepeer-review

19 Citations (Scopus)

Abstract

Pyrosequence targeting of the 16S rRNA gene has been adopted for microbial communities associated with fieldgrown plants. To examine phylogenetic drifts according to read length and bioinformatic tools, original and chopped sequences (250-570 bp) covering the V1-V4 regions of 16S rRNA genes were compared using pyrosequence and Sanger reads of rice root microbiomes. The phylogenetic assignment at genus level depended on read length, especially in the genus Bradyrhizobium, which is one of the ecologically important bacterial genera associated with plants. We discuss the methodology of phylogenetic assignments of plant-associated bacteria by 16S rRNA pyrosequence.

Original languageEnglish
Pages (from-to)204-208
Number of pages5
JournalMicrobes and Environments
Volume27
Issue number2
DOIs
Publication statusPublished - 2012

Keywords

  • 16S rRNA gene
  • Bacterial community
  • Phylogenetic analysis
  • Plant-associated bacteria

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