Optimal Eukaryotic 18S and Universal 16S/18S Ribosomal RNA Primers and Their Application in a Study of Symbiosis
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ArticleDate
2014Permanent link to this record
http://hdl.handle.net/10754/671365
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Eukaryotic 18S ribosomal RNA (rRNA) gene primers that feature a wide coverage are critical in detecting the composition of eukaryotic microscopic organisms in ecosystems. Here, we predicted 18S rRNA primers based on consecutive conserved sites and evaluated their coverage efficiency and scope of application to different eukaryotic groups. After evaluation, eight of them were considered as qualified 18S primers based on coverage rate. Next, we examined common conserved regions in prokaryotic 16S and eukaryotic 18S rRNA sequences to design 16S/18S universal primers. Three 16S/18S candidate primers, U515, U1390 and U1492, were then considered to be suitable for simultaneous amplification of the rRNA sequences in three domains. Eukaryotic 18S and prokaryotic 16S rRNA genes in a sponge were amplified simultaneously using universal primers U515 and U1390, and the subsequent sorting of pyrosequenced reads revealed some distinctive communities in different parts of the sample. The real difference in biodiversity between prokaryotic and eukaryotic symbionts could be discerned as the dissimilarity between OTUs was increased from 0.005 to 0.1. A network of the communities in external and internal parts of the sponge illustrated the co-variation of some unique microbes in certain parts of the sponge, suggesting that the universal primers are useful in simultaneous detection of prokaryotic and eukaryotic microbial communities. © 2014 Wang et al.Citation
Wang, Y., Tian, R. M., Gao, Z. M., Bougouffa, S., & Qian, P.-Y. (2014). Optimal Eukaryotic 18S and Universal 16S/18S Ribosomal RNA Primers and Their Application in a Study of Symbiosis. PLoS ONE, 9(3), e90053. doi:10.1371/journal.pone.0090053Sponsors
This study was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences(CAS) (No. DB06010100 and DB06010200), National Basic Research Program of China (973 Program, No. 2012CB417304), the Nature Science Foundation of China (U1301232) and awards from the Sany a Institute of Deep Sea Science and Engineering, CAS (SIDSSE-201206, SIDSSE-201305) and SIDSSE-BR-201303) and from King Abdullah University of Science and Technology (SA-C0040/UK-C0016). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Publisher
Public Library of Science (PLoS)Journal
PLOS ONEAdditional Links
https://dx.plos.org/10.1371/journal.pone.0090053ae974a485f413a2113503eed53cd6c53
10.1371/journal.pone.0090053