TY - JOUR
T1 - Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies
AU - Wang, Yong
AU - Qian, Pei-Yuan
N1 - KAUST Repository Item: Exported on 2020-10-01
Acknowledgements: KAUST Global Partnership. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
This publication acknowledges KAUST support, but has no KAUST affiliated authors.
PY - 2009/10/9
Y1 - 2009/10/9
N2 - Bacterial 16S ribosomal DNA (rDNA) amplicons have been widely used in the classification of uncultured bacteria inhabiting environmental niches. Primers targeting conservative regions of the rDNAs are used to generate amplicons of variant regions that are informative in taxonomic assignment. One problem is that the percentage coverage and application scope of the primers used in previous studies are largely unknown. In this study, conservative fragments of available rDNA sequences were first mined and then used to search for candidate primers within the fragments by measuring the coverage rate defined as the percentage of bacterial sequences containing the target. Thirty predicted primers with a high coverage rate (>90%) were identified, which were basically located in the same conservative regions as known primers in previous reports, whereas 30% of the known primers were associated with a coverage rate of
AB - Bacterial 16S ribosomal DNA (rDNA) amplicons have been widely used in the classification of uncultured bacteria inhabiting environmental niches. Primers targeting conservative regions of the rDNAs are used to generate amplicons of variant regions that are informative in taxonomic assignment. One problem is that the percentage coverage and application scope of the primers used in previous studies are largely unknown. In this study, conservative fragments of available rDNA sequences were first mined and then used to search for candidate primers within the fragments by measuring the coverage rate defined as the percentage of bacterial sequences containing the target. Thirty predicted primers with a high coverage rate (>90%) were identified, which were basically located in the same conservative regions as known primers in previous reports, whereas 30% of the known primers were associated with a coverage rate of
UR - http://hdl.handle.net/10754/325281
UR - https://dx.plos.org/10.1371/journal.pone.0007401
UR - http://www.scopus.com/inward/record.url?scp=70350527180&partnerID=8YFLogxK
U2 - 10.1371/journal.pone.0007401
DO - 10.1371/journal.pone.0007401
M3 - Article
C2 - 19816594
SN - 1932-6203
VL - 4
SP - e7401
JO - PLoS ONE
JF - PLoS ONE
IS - 10
ER -