Development and evaluation of specific PCR primers targeting the ribosomal DNA-internal transcribed spacer (ITS) region of peritrich ciliates in environmental samples -- Journal of Oceanology and Limnology,2018,36(3):818-826

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	SU Lei, ZHANG Qianqian, GONG Jun. Development and evaluation of specific PCR primers targeting the ribosomal DNA-internal transcribed spacer (ITS) region of peritrich ciliates in environmental samples[J]. Journal of Oceanology and Limnology, 2018, 36(3): 818-826

Development and evaluation of specific PCR primers targeting the ribosomal DNA-internal transcribed spacer (ITS) region of peritrich ciliates in environmental samples

SU Lei^1,2, ZHANG Qianqian^1,2, GONG Jun^1,2

1 Laboratory of Microbial Ecology and Matter Cycles, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China;
2 University of Chinese Academy of Sciences, Beijing 100049, China

Abstract:

Peritrich ciliates are highly diverse and can be important bacterial grazers in aquatic ecosystems. Morphological identifications of peritrich species and assemblages in the environment are time-consuming and expertise-demanding. In this study, two peritrich-specific PCR primers were newly designed to amplify a fragment including the internal transcribed spacer (ITS) region of ribosomal rDNA from environmental samples. The primers showed high specificity in silico, and in tests with peritrich isolates and environmental DNA. Application of these primers in clone library construction and sequencing yielded exclusively sequences of peritrichs for water and sediment samples. We also found the ITS1, ITS2, ITS, D1 region of 28S rDNA, and ITS+D1 region co-varied with, and generally more variable than, the V9 region of 18S rDNA in peritrichs. The newly designed specific primers thus provide additional tools to study the molecular diversity, community composition, and phylogeography of these ecologically important protists in different systems.

Received: 2016-12-08 Revised:

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