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Species clarification of oyster mushrooms in China and their DNA barcoding

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Abstract

Species of the Pleurotus ostreatus complex (oyster mushrooms) are one of the main groups of cultivated edible mushrooms in China, with abundant strains and a complex genetic background. Although the cultivation of oyster mushrooms is a very important industry in China, the inconsistent nomenclature of the complex is controversial and has led to much confusion and economic loss in the mushroom industry. In this study, we performed molecular identification of the species complex based on sequences of the internal transcribed spacer region (ITS), translation elongation factor 1-α (TEF1), and two genes that encode subunits of RNA polymerase II (RPB1 and RPB2). A total of 284 samples with different commercial names gathered from different mushroom spawn preservation centers, companies, and field isolations were investigated via phylogenetic analyses inferred from a single locus or multi-loci. Our analyses indicated that 56% of the strains were labeled with improper scientific names and that all of the strains could be divided into seven lineages, representing one morphological species each, namely P. abieticola, P. eryngii, P. cf. floridanus, P. ostreatus, P. placentodes, P. pulmonarius, and P. tuoliensis. Reference sequences for accurate identification of the taxa were developed or suggested. Meanwhile, we evaluated the suitability of the four candidate segments as DNA barcodes. Our analyses indicated that RPB2 was the most promising candidate segment of DNA barcode for the P. ostreatus species complex, taking into consideration the polymorphisms and other aspects of the four markers.

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Acknowledgments

The authors are very grateful to Prof. Dr. Y.C. Zhao (Yunnan Academy of Agricultural Sciences), Mr. F. Nie (Anhui Academy of Agricultural Sciences), Ms. J. Yang (Fujian Academy of Agricultural Sciences), Dr. P. Zhang (Hunan Normal University), Prof. J.W. Shen (Henan Agricultural University), and Dr. X.D. Yu (Shenyang Agricultural University) for providing strains and specimens for this study. The anonymous reviewers are acknowledged for their constructive comments and suggestions. This study is supported by the National Basic Research Program of China (973 Program, No. 2014CB138305) and the Large-scale Scientific Facilities of the Chinese Academy of Sciences (2009-LSFGBOWS-01).

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  1. Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China

    Jing Li, Xing He, Xiao-Bin Liu & Zhu L. Yang

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

    Jing Li, Xing He & Xiao-Bin Liu

  3. State Key Laboratory of Conservation and Utilization for Bioresources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China

    Jing Li & Zhi-Wei Zhao

Authors
  1. Jing Li
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  2. Xing He
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  3. Xiao-Bin Liu
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  4. Zhu L. Yang
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  5. Zhi-Wei Zhao
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Corresponding authors

Correspondence to Zhu L. Yang or Zhi-Wei Zhao.

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Section Editor: Marc Stadler

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Suppl. Fig. 1

Phylogenetic tree inferred from ML analysis with branch support obtained by ML and BI analyses based on a four-locus (ITS, TEF1, RPB1, and RPB2) dataset. Branch support values are indicated by numbers above branches (ML-BP/BI-PP). Taxon labels indicate strain number listed in Suppl. Table 1. Location of P. ostreatus (P382, P383, CCMSSC 00323) and P. cf. floridanus (P289, P290) are highlighted in blue and red, respectively (GIF 361 kb)

High Resolution (TIF 3012 kb)

Suppl. Fig. 2

Phylogenetic tree inferred from ML analysis with branch support obtained by ML and BI analyses based on ITS, TEF1, RPB1, and RPB2. Branch support values are indicated by numbers above branches (ML-BP/BI-PP). Taxon labels indicate strain number listed in Suppl. Table 1. Strains of P. ostreatus and P. cf. floridanus in single gene phylogeny (ITS, TEF1, and RPB1) are highlighted in purple and red, respectively (GIF 1184 kb)

High Resolution (TIF 31805 kb)

Suppl. Fig. 3

Phylogenetic tree inferred from ML analysis with branch support obtained by ML and BI analyses based on RPB2. Branch support values are indicated by numbers above branches (ML-BP/BI-PP). The strain names labeled on our collections correspond to Suppl. Fig. 2 (GIF 445 kb)

High Resolution (TIF 256266 kb)

Suppl. Fig. 4

Phylogenetic tree inferred from ML analysis with branch support obtained by ML and BI analyses based on TEF1(a) and, RPB1(b). Branch support values are indicated by numbers above branches (ML-BP/BI-PP). The samples of P. ostreatus and P. cf. floridanus were highlighted in different colors (GIF 130 kb)

(GIF 126 kb)

High Resolution (TIF 64912 kb)

High Resolution (TIF 119085 kb)

Suppl. Fig. 5

Phylogenetic relationships among reference collections and other samples of Pleurotus inferred from ITS sequences using ML analysis. Branch support values are indicated by numbers above branches (ML-BP ≥ 70%). Accession numbers for sequences retrieved from GenBank database are listed in Suppl. Table 1. Specimens in P. ostreatus species complex from China are highlighted in blue. Reference collections in single-locus and multi-locus phylogenetic analyses are labeled with a black rectangle (JPEG 1.03 MB)

Suppl. Table 1

Collections of Pleurotus species used in this study and their GenBank accession numbers (DOC 565 kb)

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Li, J., He, X., Liu, XB. et al. Species clarification of oyster mushrooms in China and their DNA barcoding. Mycol Progress 16, 191–203 (2017). https://doi.org/10.1007/s11557-016-1266-9

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  • DOI: https://doi.org/10.1007/s11557-016-1266-9

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