您好，欢迎访问中国水产科学研究院 机构知识库！
中国水产科学研究院机构知识库

全部

  • 全部
  • 标题
  • 学者
  • 机构
  • 关键词

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

作者： Zhang, Ru-Yi 1 ; Zou, Bin 1 ; Yan, Yong-Wei 1 ; Jeon, Che Ok 3 ; Li, Meng 4 ; Cai, Mingwei 4 ; Quan, Zhe-Xue 1 ;

作者机构： 1.Fudan Univ, Key Lab Biodivers Sci & Ecol Engn, Minist Educ, Inst Biodivers Sci,Sch Life Sci, Shanghai, Peoples R China

2.Chinese Acad Fishery Sci, Lab Marine Fisheries Sci & Food Prod Proc, Qingdao Natl Lab Marine Sci & Technol,Yellow Sea, Key Lab Maricultural Organism Dis Control,Minist, Qingdao, Peoples R China

3.Chung Ang Univ, Sch Life Sci, Seoul, South Korea

4.Shenzhen Univ, Inst Adv Study, Shenzhen Key Lab Marine Microbiome Engn, Shenzhen, Peoples R China

5.Shenzhen Univ, Key Lab Optoelect Devices & Syst, Minist Educ & Guangdong Prov, Coll Optoelect Engn, Shenzhen, Peoples R China

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.

  • 相关文献
作者其他论文 更多>>
置顶
购物车
反馈

© 京ICP备09089781号-29 主办单位：中国水产科学研究院

学术资源： 中国农业科学院 农业专业知识服务系统 农科联盟资源共建共享平台 中国农业科技文献与信息服务平台 中国农业期刊集成服务平台