Design of targeted primers based on 16S rRNA sequences in meta-transcriptomic datasets and identification of a novel taxonomic group in the Asgard archaea

文献类型： 外文期刊

第一作者： Zhang, Ru-Yi

作者： Zhang, Ru-Yi;Zou, Bin;Yan, Yong-Wei;Quan, Zhe-Xue;Yan, Yong-Wei;Jeon, Che Ok;Li, Meng;Cai, Mingwei;Cai, Mingwei

作者机构：

关键词： Meta-transcriptomic datasets; 16S rRNA; Universal primer; Asgard; Taxonomy

期刊名称：BMC MICROBIOLOGY （ 影响因子：3.605； 五年影响因子：4.283 ）

ISSN： 1471-2180

年卷期： 2020 年 20 卷 1 期

页码：

收录情况： SCI

摘要： Background Amplification of small subunit (SSU) rRNA genes with universal primers is a common method used to assess microbial populations in various environmental samples. However, owing to limitations in coverage of these universal primers, some microorganisms remain unidentified. The present study aimed to establish a method for amplifying nearly full-length SSU rRNA gene sequences of previously unidentified prokaryotes, using newly designed targeted primers via primer evaluation in meta-transcriptomic datasets. Methods Primer binding regions of universal primer 8F/Arch21F for bacteria or archaea were used for primer evaluation of SSU rRNA sequences in meta-transcriptomic datasets. Furthermore, targeted forward primers were designed based on SSU rRNA reads from unclassified groups unmatched with the universal primer 8F/Arch21F, and these primers were used to amplify nearly full-length special SSU rRNA gene sequences along with universal reverse primer 1492R. Similarity and phylogenetic analysis were used to confirm their novel status. Results Using this method, we identified unclassified SSU rRNA sequences that were not matched with universal primer 8F and Arch21F. A new group within the Asgard superphylum was amplified by the newly designed specific primer based on these unclassified SSU rRNA sequences by using mudflat samples. Conclusion We showed that using specific primers designed based on universal primer evaluation from meta-transcriptomic datasets, identification of novel taxonomic groups from a specific environment is possible.

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