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Selection of a DNA barcode for Nectriaceae from fungal whole-genomes

Science China(Life Sciences) 2012年第1期55卷 80-88页

作者： ZENG ZhaoQing ZHAO Peng LUO Jing ZHUANG WenYing YU ZhiHe State Key Laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China Graduate University of Chinese Academy of Sciences Beijing 100049China College of Life Sciences Yangtze UniversityJingzhou 434025China

A DNA barcode is a short segment of sequence that is able to distinguish species. A barcode must ideally contain enough variation to distinguish every individual species and be easily obtained. Fungi of Nectriaceae are economically important and show high species diversity. To establish a standard DNA barcode for this group of fungi, the genomes of Neurospora crassa and 30 other filamentous fungi were compared. The expect value was treated as a criterion to recognize homologous sequences. Four candidate markers, Hsp90, AAC, CDC48, and EF3, were tested for their feasibility as barcodes in the identification of 34 well-established species belonging to 13 genera of Nectriaceae. Two hundred and fifteen sequences were analyzed. Intraand inter-specific variations and the success rate of PCR amplification and sequencing were considered as important criteria for estimation of the candidate markers. Ultimately, the partial EF3 gene met the requirements for a good DNA barcode: No overlap was found between the intra-and inter-specific pairwise distances. The smallest inter-specific distance of EF3 gene was 3.19%, while the largest intra-specific distance was 1.79%. In addition, there was a high success rate in PCR and sequencing for this gene (96.3%). CDC48 showed sufficiently high sequence variation among species, but the PCR and sequencing success rate was 84% using a single pair of primers. Although the Hsp90 and AAC genes had higher PCR and sequencing success rates (96.3% and 97.5%, respectively), overlapping occurred between the intraand inter-specific variations, which could lead to misidentification. Therefore, we propose the EF3 gene as a possible DNA barcode for the nectriaceous fungi.

关键词： barcoding gap expect value fungal genomes homologous sequence PCR and sequencing success rate sequence variation

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