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Applied and Environmental Microbiology, December 2007, p. 7947-7958, Vol. 73, No. 24
0099-2240/07/$08.00+0     doi:10.1128/AEM.00842-07
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

Autoscreening of Restriction Endonucleases for PCR-Restriction Fragment Length Polymorphism Identification of Fungal Species, with Pleurotus spp. as an Example{triangledown} ,{dagger}

Zhi-Hui Yang,1,2,3 Ji-Xiang Huang,1 and Yi-Jian Yao1,4*

Key Laboratory of Systematic Mycology and Lichenology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101,1 College of Plant Protection, Agricultural University of Hebei, Baoding 071001,2 Graduate School of Chinese Academy of Sciences, Beijing 100049, China,3 Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, United Kingdom4

Received 13 April 2007/ Accepted 14 October 2007

A molecular method based on PCR-restriction fragment length polymorphism (RFLP) analysis of internal transcribed spacer (ITS) ribosomal DNA sequences was designed to rapidly identify fungal species, with members of the genus Pleurotus as an example. Based on the results of phylogenetic analysis of ITS sequences from Pleurotus, a PCR-RFLP endonuclease autoscreening (PRE Auto) program was developed to screen restriction endonucleases for discriminating multiple sequences from different species. The PRE Auto program analyzes the endonuclease recognition sites and calculates the sizes of the fragments in the sequences that are imported into the program in groups according to species recognition. Every restriction endonuclease is scored through the calculation of the average coefficient for the sequence groups and the average coefficient for the sequences within a group, and then virtual electrophoresis maps for the selected restriction enzymes, based on the results of the scoring system, are displayed for the rapid determination of the candidate endonucleases. A total of 85 haplotypes representing 151 ITS sequences were used for the analysis, and 2,992 restriction endonucleases were screened to find the candidates for the identification of species. This method was verified by an experiment with 28 samples representing 12 species of Pleurotus. The results of the digestion by the restriction enzymes showed the same patterns of DNA fragments anticipated by the PRE Auto program, apart from those for four misidentified samples. ITS sequences from 14 samples (of which nine sequences were obtained in this study), including four originally misidentified samples, confirmed the species identities revealed by the PCR-RFLP analysis. The method developed here can be used for the identification of species of other living microorganisms.

* Corresponding author. Mailing address: Key Laboratory of Systematic Mycology and Lichenology, Institute of Microbiology, Chinese Academy of Sciences, P.O. Box 2714, Beijing 100101, People's Republic of China. Phone: 86 10 64807496. Fax: 86 10 64807518. E-mail: yaoyj{at}sun.im.ac.cn

{triangledown} Published ahead of print on 26 October 2007.

{dagger} Supplemental material for this article may be found at http://aem.asm.org/.

Applied and Environmental Microbiology, December 2007, p. 7947-7958, Vol. 73, No. 24
0099-2240/07/$08.00+0     doi:10.1128/AEM.00842-07
Copyright © 2007, American Society for Microbiology. All Rights Reserved.





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