Optimal Eukaryotic 18S and Universal 16S/18S Ribosomal RNA Primers and Their Application in a Study of Symbiosis
Wang, Yong1,2; Tian, Ren Mao1; Gao, Zhao Ming1; Bougouffa, Salim1; Qian, Pei-Yuan1
2014-03-03
Source PublicationPLOS ONE
Volume9Issue:3
AbstractEukaryotic 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.
SubtypeArticle
WOS HeadingsScience & Technology
DOI10.1371/journal.pone.0090053
Indexed BySCI
Language英语
WOS KeywordDEEP-SEA ; BACTERIAL COMMUNITIES ; COPY NUMBER ; GENOME SIZE ; DIVERSITY ; SUBUNIT ; GENES ; LIFE ; PCR ; ENVIRONMENT
WOS SubjectMultidisciplinary Sciences
WOS IDWOS:000332468900059
Citation statistics
Cited Times:17[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Version出版稿
Identifierhttp://ir.idsse.ac.cn/handle/183446/773
Collection深海科学研究部_深海生物学研究室_海洋微生物宏基因组与分子进化研究组
Affiliation1.Hong Kong Univ Sci & Technol, Div Life Sci, Hong Kong, Hong Kong, Peoples R China
2.Chinese Acad Sci, Sanya Inst Deep Sea Sci & Engn, San Ya, Hai Nan, Peoples R China
First Author AffilicationInstitute of Deep-sea Science and Engineering,CAS
Recommended Citation
GB/T 7714
Wang, Yong,Tian, Ren Mao,Gao, Zhao Ming,et al. Optimal Eukaryotic 18S and Universal 16S/18S Ribosomal RNA Primers and Their Application in a Study of Symbiosis[J]. PLOS ONE,2014,9(3).
APA Wang, Yong,Tian, Ren Mao,Gao, Zhao Ming,Bougouffa, Salim,&Qian, Pei-Yuan.(2014).Optimal Eukaryotic 18S and Universal 16S/18S Ribosomal RNA Primers and Their Application in a Study of Symbiosis.PLOS ONE,9(3).
MLA Wang, Yong,et al."Optimal Eukaryotic 18S and Universal 16S/18S Ribosomal RNA Primers and Their Application in a Study of Symbiosis".PLOS ONE 9.3(2014).
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