Science China Life Sciences

, Volume 55, Issue 1, pp 80–88 | Cite as

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

  • ZhaoQing Zeng
  • Peng Zhao
  • Jing Luo
  • WenYing Zhuang
  • ZhiHe Yu
Open Access
Research Paper

Abstract

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. Intra- and 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 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.

Keywords

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

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© The Author(s) 2012

This article is published under license to BioMed Central Ltd. Open Access This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution and reproduction in any medium, provided the original author(s) and source are credited.

Authors and Affiliations

  • ZhaoQing Zeng
    • 1
    • 2
  • Peng Zhao
    • 1
  • Jing Luo
    • 1
  • WenYing Zhuang
    • 1
  • ZhiHe Yu
    • 3
  1. 1.State Key Laboratory of Mycology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
  2. 2.Graduate University of Chinese Academy of SciencesBeijingChina
  3. 3.College of Life SciencesYangtze UniversityJingzhouChina

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