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Practice towards DNA barcoding of the nectriaceous fungi

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Abstract

Fungi of Nectriaceae are economically important and of high species diversity. For the purpose of accurate and rapid species identification, ITS, 28S rDNA, β-tubulin gene and EF-1α gene were selected as the candidate DNA barcode markers to investigate their feasibility in identification of 28 well-circumscribed species belonging to 9 genera of the nectriaceous fungi. A total of 216 sequences of the candidate genes were analyzed. Intra- and inter-specific variations and success rate of PCR amplification and sequencing were considered as important criteria to estimate the candidate genes. The partial β-tubulin gene met the requirements for an ideal DNA barcode and functions well for correct species delimitation. No overlapping between the intra- and inter-specific pairwise distances was found. The smallest inter-specific distance of β-tubulin gene was 3.45%, while the largest intra-specific distance was 2.77%; which appeared to possess the appropriate intra- and inter-specific variations. Twenty-eight clusters were recognized in accordance with the 28 morphological species tested. In addition, it had a high PCR and sequencing success rate. As to the other candidates, EF-1α gene showed fairly good sequence variations among species, but the PCR and sequencing success rate reached only 75.3%. ITS had a high PCR and sequencing success rate (93.5%) and recognizes 92.9% of the total number of species, nevertheless, overlapping occurred between the intra- and inter-specific distances, which may lead to incorrect species identification. 28S rDNA is most conservative compared with any other candidate markers and able to recognize merely 60.7% of the total species. We propose β-tubulin gene as the possible barcode for the nectriaceous fungi.

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Acknowledgements

The authors express their deep thanks to Prof. R. P. Korf for corrections of the language, and Dr. R. Meier for providing a useful reference. This project was supported by the State 863 Project (no. 2008AA02Z312) and Special Project for Fundamental Research (no. 2006FY120100) from the Ministry of Science and Technology of China, and the National Natural Science Foundation of China (no. 31070015) to WYZ.

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Authors and Affiliations

  1. Key Laboratory of Systematic Mycology and Lichenology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China

    Peng Zhao, Jing Luo & Wen-Ying Zhuang

  2. Graduate University of Chinese Academy of Sciences, Beijing, 100049, China

    Peng Zhao

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  1. Peng Zhao
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  2. Jing Luo
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  3. Wen-Ying Zhuang
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Correspondence to Wen-Ying Zhuang.

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Peng Zhao and Jing Luo contributed equally to this work.

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Suppl. Fig. 1

Neighbor-joining tree based on ITS sequences from 28 species of Nectriaceae with Bionectria wenpingii as outgroup. TreeBase S10405 (GIF 163 kb)

High resolution image (TIFF 544 kb)

Suppl. Fig. 2

Neighbor-joining tree based on 28 S rDNA sequences from 28 species of Nectriaceae with Bionectria wenpingii as outgroup. TreeBase S10406 (GIF 190 kb)

High resolution image (TIFF 545 kb)

Suppl. Fig. 3

Neighbor-joining tree based on β-tubulin gene sequences from 28 species of Nectriaceae with Bionectria wenpingii as outgroup. TreeBase S10407 (GIF 173 kb)

High resolution image (TIFF 615 kb)

Suppl. Fig. 4

Neighbor-joining tree based on EF-1α gene sequences from 28 species of Nectriaceae with Bionectria wenpingii as outgroup. TreeBase S10408 (GIF 184 kb)

High resolution image (TIFF 545 kb)

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Zhao, P., Luo, J. & Zhuang, WY. Practice towards DNA barcoding of the nectriaceous fungi. Fungal Diversity 46, 183–191 (2011). https://doi.org/10.1007/s13225-010-0064-y

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