Species clarification of oyster mushrooms in China and their DNA barcoding

Li, Jing; He, Xing; Liu, Xiaobin; Yang, Zhu L.; Zhao, Zhi-Wei

doi:10.1007/s11557-016-1266-9

Cited by 21 publications

(21 citation statements)

References 89 publications

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“…Specific information on voucher specimens and strains, including GenBank accession numbers, geographical locations, and substrates is in Table 1. Species belonging to Pleurotus have been reported from the temperate areas of East and West Asia, North and South America, Europe, Africa and the tropical areas of Southeast Asia (Albertó et al 2002;Petersen and Hughes 1997;Petersen and Krisai-Greilhuber 1999;Vilgalys et al 1993;Vilgalys and Sun 1994b;Zervakis and Balis 1996;Zervakis et al 2004Zervakis et al , 2014, whereas those belonging to Hohenbuehelia has been reported as the allied group of Pleurotus (Gao et al 2008b;Li and Yao 2004;Li et al 2017;Menolli Jr. et al 2014;Singer 1986;Thorn et al 2000). Most mushrooms analyzed here were chosen to cover as much of the known distribution range of the P. ostreatus species complex in the world as possible.…”

Section: Screening Of Taxa Used In the Phylogenetic Analysis For A Lamentioning

confidence: 99%

“…(Phanerochaetaceae/ Polyporales/Agaricomycetes) were downloaded from the FUNYBASE database of fungal nuclear single-copy orthologous gene sequences, and the PCR primers that amplify single-copy genes of Agaricomycetes were designed by Sato et al (2017). To screen for PCR amplification rate, 96 markers from their study with the expected product size ranging from 280 to 450 bp were initially tested and screened against ten diverse specimens taken from different species within the P. ostreatus species complex recognized by previous studies based on morphological characteristics and molecular analyses (Bao et al 2004;Hilber 1982;Li et al 2017;Liu et al 2015Liu et al , 2016Singer 1986;Zervakis et al 2014;Zhao et al 2016aZhao et al , 2016b. The amplification reactions were performed in an ABI 2720 Thermal Cycler or a SimpliAmp Thermal Cycler (Applied Biosystems, Foster City, CA, USA) with the following protocol: one cycle at 94°C for 3 min; followed by 35 cycles at 94°C for 30 s, an annealing step at 50, 52 or 54°C for 30 s, 72°C for 1 min; and a final extension step of 72°C for 7 min.…”

Section: Selection Of Nuclear Single-copy Orthologous Genesmentioning

confidence: 99%

“…An interesting study on the biogeography of the whole genus Pleurotus has suggested an ancient origin for some intersterile groups with worldwide distributions, while other intersterile groups in the Northern Hemisphere underwent more recent radiation and allopatric speciation (Vilgalys and Sun 1994b). Although a series of taxonomic and phylogenetic studies based on limited molecular markers have been published recently (Avin et al 2014;Gao et al 2008a;He et al 2016;Kawai et al 2008;Li et al 2017;Thorn et al 2000;Vilgalys et al 1993;Zhao et al 2016b;Zheng et al 2006), a deep understanding of the diversity within this group is still lacking.…”

Section: Introductionmentioning

confidence: 99%

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The saprotrophic Pleurotus ostreatus species complex: late Eocene origin in East Asia, multiple dispersal, and complex speciation

Han

Liu

et al. 2020

IMA Fungus

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The Pleurotus ostreatus species complex is saprotrophic and of significant economic and ecological importance. However, species delimitation has long been problematic because of phenotypic plasticity and morphological stasis. In addition, the evolutionary history is poorly understood due to limited sampling and insufficient gene fragments employed for phylogenetic analyses. Comprehensive sampling from Asia, Europe, North and South America and Africa was used to run phylogenetic analyses of the P. ostreatus species complex based on 40 nuclear single-copy orthologous genes using maximum likelihood and Bayesian inference analyses. Here, we present a robust phylogeny of the P. ostreatus species complex, fully resolved from the deepest nodes to species level. The P. ostreatus species complex was strongly supported as monophyletic, and 20 phylogenetic species were recognized, with seven putatively new species. Data from our molecular clock analyses suggested that divergence of the genus Pleurotus probably occurred in the late Jurassic, while the most recent common ancestor of the P. ostreatus species complex diversified about 39 Ma in East Asia. Species of the P. ostreatus complex might migrate from the East Asia into North America across the North Atlantic Land Bridge or the Bering Land Bridge at different times during the late Oligocene, late Miocene and late Pliocene, and then diversified in the Old and New Worlds simultaneously through multiple dispersal and vicariance events. The dispersal from East Asia to South America in the middle Oligocene was probably achieved by a long-distance dispersal event. Intensification of aridity and climate cooling events in the late Miocene and Quaternary glacial cycling probably had a significant influence on diversification patterns of the complex. The disjunctions among East Asia, Europe, North America and Africa within Clade IIc are hypothesized to be a result of allopatric speciation. Substrate transitions to Apiaceae probably occurred no earlier than 6 Ma. Biogeographic analyses suggested that the global cooling of the late Eocene, intensification of aridity caused by rapid uplift of the QTP and retreat of the Tethys Sea in the late Miocene, climate cooling events in Quaternary glacial cycling, and substrate transitions have contributed jointly to diversification of the species complex.

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Section: Screening Of Taxa Used In the Phylogenetic Analysis For A Lamentioning

confidence: 99%

Section: Selection Of Nuclear Single-copy Orthologous Genesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The saprotrophic Pleurotus ostreatus species complex: late Eocene origin in East Asia, multiple dispersal, and complex speciation

Han

Liu

et al. 2020

IMA Fungus

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“…According to the phylogenetic analysis based on the ITS region, the eight Lepista species received high support (≥98%), which demonstrates that ITS could be used for the identification of Manuscript to be reviewed Amillariella (Guo et al, 2016) and Pleurotus (Li et al, 2017). In future research, the morphological characteristics of Lepista sp 1 and L. sp 2 should be described, and the utility of ITS as a barcode for identification of additional Lepista species should be evaluated.…”

Section: Discussionmentioning

confidence: 95%

“…The internal transcribed spacer (ITS) region of the nuclear ribosomal RNA gene has been used as a general barcode marker for some groups in the Basidiomycota (Dentinger et al, 2011;Cai et al, 2012;Buyck et al, 2014;Badotti et al, 2017). Other candidate segments that have been used as barcoding markers for mushrooms previously, including the mitochondrial cytochrome oxidase I gene (cox1) (Vialle et al, 2009), the second subunit of RNA polymerase II (RPB2) (Li et al, 2017), and the β-tubulin and elongation factor 1-α (tef1) (Guo et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Peer Review #3 of "Evaluation of five regions as DNA barcodes for identification of Lepista species (Tricholomataceae, Basidiomycota) from China (v0.1)"

2019

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Background. Distinguishing among species in the genus Lepista is difficult because of their similar morphologies. Methods. To identify a suitable DNA barcode for identification of Lepista species, we assessed the following five regions: ITS, IGS, nLSU, mtSSU, and tef1. A total of 134 sequences from 34 samples belong to eight Lepista species were analyzed. The utility of each region as a DNA barcode was assessed based on the success rates of its PCR amplification and sequencing, and on its intra-and inter-specific variations. Results. The results indicated that the ITS region could distinguish all species tested. We therefore propose that the ITS region can be used as a DNA barcode for the genus Lepista. In addition, a phylogenetic tree based on the ITS region showed that the tested eight Lepista species, including two unrecognized species, formed eight separate and well-supported clades.

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Using a DNA mini-barcode within the ITS region to identify toxic Amanita in mushroom poisoning cases

Xing,

Bai,

et al. 2024

Appl Microbiol Biotechnol

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Mushroom poisoning contributes significantly to global foodborne diseases and related fatalities. Amanita mushrooms frequently cause such poisonings; however, identifying these toxic species is challenging due to the unavailability of fresh and intact samples. It is often necessary to analyze residues, vomitus, or stomach extracts to obtain DNA sequences for the identification of species responsible for causing food poisoning. This usually proves challenging to obtain usable DNA sequences that can be analyzed using conventional molecular biology techniques. Therefore, this study aimed to develop a DNA mini-barcoding method for the identification of Amanita species. Following the evaluation and optimization of universal primers for DNA mini-barcoding in Amanita mushrooms, we found that the internal transcribed spacer (ITS) gene sequence primer ITS-a was the most suitable DNA barcode primer for identifying Amanita species. Forty-three Amanita samples were subsequently amplified and sequenced. The sequences obtained were analyzed for intra- and inter-species genetic distances, and a phylogenetic tree was constructed. The findings indicated that the designed primers had strong universality among the Amanita samples and could accurately identify the target gene fragment with a length of 290 bp. Notably, the DNA mini-barcode accurately identified the 43 Amanita samples, demonstrating high consistency with the conventional DNA barcode. Furthermore, it effectively identified DNA from digested samples. In summary, this DNA mini-barcode is a promising tool for detecting accidental ingestion of toxic Amanita mushrooms. It may be used as an optimal barcode for species identification and traceability in events of Amanita-induced mushroom poisoning. Key points • Development of a DNA mini-barcoding method for Amanita species identification without fresh samples. • The ITS-a primer set was optimized for robust universality in Amanita samples. • The mini-barcode is suitable for screening toxic mushroom species in mushroom poisoning cases. Graphical Abstract

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Species clarification of oyster mushrooms in China and their DNA barcoding

Cited by 21 publications

References 89 publications

The saprotrophic Pleurotus ostreatus species complex: late Eocene origin in East Asia, multiple dispersal, and complex speciation

The saprotrophic Pleurotus ostreatus species complex: late Eocene origin in East Asia, multiple dispersal, and complex speciation

Peer Review #3 of "Evaluation of five regions as DNA barcodes for identification of Lepista species (Tricholomataceae, Basidiomycota) from China (v0.1)"

Using a DNA mini-barcode within the ITS region to identify toxic Amanita in mushroom poisoning cases

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