PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample.
The contribution of PCR artifacts to 16S rRNA gene sequence diversity from a complex bacterioplankton sample was estimated. Taq DNA polymerase errors were found to be the dominant sequence artifact but could be constrained by clustering the sequences into 99% sequence similarity groups. Other artifacts (chimeras and heteroduplex molecules) were significantly reduced by employing modified amplification protocols. Surprisingly, no skew in sequence types was detected in the two libraries constructed from PCR products amplified for different numbers of cycles. Recommendations for modification of amplification protocols and for reporting diversity estimates at 99% sequence similarity as a standard are given.
Acinas
Silvia G
SG
Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
Sarma-Rupavtarm
Ramahi
R
Klepac-Ceraj
Vanja
V
Polz
Martin F
MF
D000818:Animals; D016477:Artifacts; D019143:Evolution, Molecular; D015723:Gene Library; D010933:Plankton / Q000235:genetics*; D016133:Polymerase Chain Reaction / Q000379:methods* / Q000592:standards*; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D015203:Reproducibility of Results; D019914:Taq Polymerase
D012336:RNA, Ribosomal, 16S; D019914:Taq Polymerase