Mycological Progress

, Volume 16, Issue 3, pp 191–203 | Cite as

Species clarification of oyster mushrooms in China and their DNA barcoding

Original Article

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.

Keywords

Phylogenetic analyses Species recognition Strain identification DNA sequence markers 

Supplementary material

11557_2016_1266_Fig5_ESM.gif (362 kb)
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)

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High Resolution (TIF 3012 kb)
11557_2016_1266_Fig6_ESM.gif (1.2 mb)
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)

11557_2016_1266_MOESM2_ESM.tif (31.1 mb)
High Resolution (TIF 31805 kb)
11557_2016_1266_Fig7_ESM.gif (445 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)

11557_2016_1266_MOESM3_ESM.tif (250.3 mb)
High Resolution (TIF 256266 kb)
11557_2016_1266_Fig8_ESM.gif (130 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)

11557_2016_1266_Fig9_ESM.gif (126 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)

11557_2016_1266_MOESM4_ESM.tif (63.4 mb)
High Resolution (TIF 64912 kb)
11557_2016_1266_MOESM5_ESM.tif (116.3 mb)
High Resolution (TIF 119085 kb)
11557_2016_1266_Fig10_ESM.jpg (1 mb)
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)

11557_2016_1266_MOESM6_ESM.doc (566 kb)
Suppl. Table 1Collections of Pleurotus species used in this study and their GenBank accession numbers (DOC 565 kb)

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Copyright information

© German Mycological Society and Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  1. 1.Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of BotanyChinese Academy of SciencesKunmingChina
  2. 2.University of Chinese Academy of SciencesBeijingChina
  3. 3.State Key Laboratory of Conservation and Utilization for Bioresources in YunnanYunnan UniversityKunmingChina

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