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

• Published in: Science China. Life sciences Vol. 55; no. 1; pp. 80 - 88
• Main Authors: Zeng, ZhaoQing, Zhao, Peng, Luo, Jing, Zhuang, WenYing, Yu, ZhiHe
• Format: Journal Article
• Language: English
• Published: Beijing Science China Press 2012; Springer Nature B.V
• Subjects: Automatic Data Processing; Biomedical and Life Sciences; DNA - genetics; Fungi; Genetic Markers; Genetic Variation; Genome, Fungal; Genomes; HSP90; Hsp90 protein; Hypocreales - classification; Hypocreales - genetics; Life Sciences; Neurospora crassa; Nucleotide sequence; PCR扩增; Polymerase chain reaction; Primers; Research Paper; Sequence Analysis, DNA; Species diversity; 丝状真菌; 基因组DNA; 最小距离; 条码; 物种多样性; 粗糙脉孢菌; expect value; fungal genomes; homologous sequence; sequence variation; barcoding gap; PCR and sequencing success rate
• ISSN: 1674-7305; 1869-1889
• DOI: 10.1007/s11427-012-4266-2

A DNA barcode is a short segment of sequence that is able to distinguish species. A barcode must ideally contain enough vari- ation 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. Intra- and inter-specific variations and the success rate of PCR amplification and sequencing were considered as important criteria for es- timation 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 intra- and inter-specific variations, which could lead to misidentification. Therefore, we propose the EF3 gene as a possible DNA barcode for the nectriaceous fungi.