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Updated: May 20, 2026

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons
Published on: August 29, 2014
Pyrosequence read length of 16S rRNA gene affects phylogenetic assignment of plant-associated bacteria
Takashi Okubo1, Seishi Ikeda, Akifumi Yamashita
1Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai 980-8577, Japan.
Abstract:
Pyrosequence targeting of the 16S rRNA gene has been adopted for microbial communities associated with field-grown 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.
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