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Patterns of PCR Amplification Artifacts of the Fungal Barcode Marker in a Hybrid Mushroom

文献类型： 外文期刊

作者： Zhou, Jun-Liang 1 ; Xu, Jianping 3 ; Jiao, An-Guo 1 ; Yang, Li 1 ; Chen, Jie 6 ; Callac, Philippe 7 ; Liu, Yu 1 ; Wang, S 1 ;

作者机构： 1.Beijing Acad Agr & Forestry Sci, Beijing Engn Res Ctr Edible Mushroom, Inst Plant & Environm Protect, Beijing, Peoples R China

2.Kunming Univ, Int Exchange & Cooperat Dept, Kunming, Yunnan, Peoples R China

3.McMaster Univ, Dept Biol, Hamilton, ON, Canada

4.Yunnan Univ, Lab Conservat & Utilizat Bioresources, Minist Educ, Kunming, Yunnan, Peoples R China

5.Yunnan Univ, Key Lab Microbial Resources, Minist Educ, Kunming, Yunnan, Peoples R China

6.Inst Ecol, Xalapa, Veracruz, Mexico

7.INRA, MycSA, Villenave Dornon, France

关键词： polymerase chain reaction; ITS; mutation spectrum; chimera sequence; recombination

期刊名称：FRONTIERS IN MICROBIOLOGY （ 影响因子：5.64； 五年影响因子：6.32 ）

ISSN： 1664-302X

年卷期： 2019 年 10 卷

页码：

收录情况： SCI

摘要： The polymerase chain reaction (PCR) is widely used in modern biology and medicine. However, PCR artifacts can complicate the interpretation of PCR-based results. The internal transcribed spacer (ITS) region of the ribosomal RNA gene cluster is the consensus fungal barcode marker and suspected PCR artifacts have been reported in many studies, especially for the analyses of environmental fungal samples. At present, the patterns of PCR artifacts in the whole fungal ITS region (ITS1+5.8S+ITS2) are not known. In this study, we analyzed the error rates of PCR at three template complexity levels using the divergent copies of ITS from the mushroom Agaricus subrufescens. Our results showed that PCR using the Phusion High-Fidelity DNA Polymerase has a per nucleotide error rate of about 4 x 10(-6) per replication. Among the detected mutations, transitions were much more frequent than transversions, insertions, and deletions. When divergent alleles were mixed as templates in the same reaction, a significant proportion (similar to 30%) of recombinant molecules were detected. The in vitro mixed-template results were comparable to those obtained from using the genomic DNA of the original mushroom specimen as template. Our results indicate that caution should be in place when interpreting ITS sequences from individual fungal specimens, especially those containing divergent ITS copies. Similar results could also happen to PCR-based analyses of other multicopy DNA fragments as well as single-copy DNA sequences with divergent alleles in diploid organisms.

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