Pyrosequence Read Length of 16S rRNA Gene Affects Phylogenetic Assignment of Plant-associated Bacteria
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- Okubo Takashi
- Graduate School of Life Sciences, Tohoku University
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- Ikeda Seishi
- Graduate School of Life Sciences, Tohoku University Memuro Research Station, National Agricultural Research Center for Hokkaido Region
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- Yamashita Akifumi
- Graduate School of Life Sciences, Tohoku University
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- Terasawa Kimihiro
- Graduate School of Life Sciences, Tohoku University
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- Minamisawa Kiwamu
- Graduate School of Life Sciences, Tohoku University
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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.<br>
収録刊行物
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- Microbes and environments
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Microbes and environments 27 (2), 204-208, 2012
日本微生物生態学会 / 日本土壌微生物学会 / Taiwan Society of Microbial Ecology / 植物微生物研究会 / 極限環境微生物学会
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詳細情報
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- CRID
- 1390282679323174656
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- NII論文ID
- 10030432208
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- NII書誌ID
- AA11551577
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- COI
- 1:STN:280:DC%2BC38jps1Kntg%3D%3D
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- ISSN
- 13474405
- 13426311
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- NDL書誌ID
- 023727962
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- PubMed
- 22791055
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- 本文言語コード
- en
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- データソース種別
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- JaLC
- NDL
- Crossref
- PubMed
- CiNii Articles
- KAKEN
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- 抄録ライセンスフラグ
- 使用不可