Optimal eukaryotic 18S and universal 16S/18S ribosomal RNA primers and their application in a study of symbiosis.
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 app...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2014-01-01
|
| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3940700?pdf=render |
| _version_ | 1811230532744249344 |
|---|---|
| author | Yong Wang Ren Mao Tian Zhao Ming Gao Salim Bougouffa Pei-Yuan Qian |
| author_facet | Yong Wang Ren Mao Tian Zhao Ming Gao Salim Bougouffa Pei-Yuan Qian |
| author_sort | Yong Wang |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-12T10:30:03Z |
| format | Article |
| id | doaj.art-1c247c2aa85d4f9e8c5b18ac14284b55 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-12T10:30:03Z |
| publishDate | 2014-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-1c247c2aa85d4f9e8c5b18ac14284b552022-12-22T03:36:52ZengPublic Library of Science (PLoS)PLoS ONE1932-62032014-01-0193e9005310.1371/journal.pone.0090053Optimal eukaryotic 18S and universal 16S/18S ribosomal RNA primers and their application in a study of symbiosis.Yong WangRen Mao TianZhao Ming GaoSalim BougouffaPei-Yuan QianEukaryotic 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.http://europepmc.org/articles/PMC3940700?pdf=render |
| spellingShingle | Yong Wang Ren Mao Tian Zhao Ming Gao Salim Bougouffa Pei-Yuan Qian Optimal eukaryotic 18S and universal 16S/18S ribosomal RNA primers and their application in a study of symbiosis. PLoS ONE |
| title | Optimal eukaryotic 18S and universal 16S/18S ribosomal RNA primers and their application in a study of symbiosis. |
| title_full | Optimal eukaryotic 18S and universal 16S/18S ribosomal RNA primers and their application in a study of symbiosis. |
| title_fullStr | Optimal eukaryotic 18S and universal 16S/18S ribosomal RNA primers and their application in a study of symbiosis. |
| title_full_unstemmed | Optimal eukaryotic 18S and universal 16S/18S ribosomal RNA primers and their application in a study of symbiosis. |
| title_short | Optimal eukaryotic 18S and universal 16S/18S ribosomal RNA primers and their application in a study of symbiosis. |
| title_sort | optimal eukaryotic 18s and universal 16s 18s ribosomal rna primers and their application in a study of symbiosis |
| url | http://europepmc.org/articles/PMC3940700?pdf=render |
| work_keys_str_mv | AT yongwang optimaleukaryotic18sanduniversal16s18sribosomalrnaprimersandtheirapplicationinastudyofsymbiosis AT renmaotian optimaleukaryotic18sanduniversal16s18sribosomalrnaprimersandtheirapplicationinastudyofsymbiosis AT zhaominggao optimaleukaryotic18sanduniversal16s18sribosomalrnaprimersandtheirapplicationinastudyofsymbiosis AT salimbougouffa optimaleukaryotic18sanduniversal16s18sribosomalrnaprimersandtheirapplicationinastudyofsymbiosis AT peiyuanqian optimaleukaryotic18sanduniversal16s18sribosomalrnaprimersandtheirapplicationinastudyofsymbiosis |