DNA barcoding of the fungal genus Neonectria and the discovery of two new species

Zhao, Peng; Luo, Jing; Zhuang, Wen-Ying; Liu, Xingzhong; Wu, Ben‐Lai

doi:10.1007/s11427-011-4184-8

Cited by 19 publications

(15 citation statements)

References 56 publications

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“…The current study also supports the treatment of these two taxa as the same species. The species identification performance of EF-1α (84.6%) in this work was comparable with a previous identification rate of 89.5% in the genus Neonectria in Ascomycota (Zhao et al, 2011b); however, it was inferior to a previous 100% identification rate for the seven species of Pleurotus (Li et al, 2017), probably because of the greater sampling range in this study.…”

Section: Discussionsupporting

confidence: 73%

DNA Barcoding Mushroom Spawn Using EF-1α Barcodes: A Case Study in Oyster Mushrooms (Pleurotus)

Zhao

Cheng

et al. 2021

Front. Microbiol.

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Oyster mushrooms (genus Pleurotus) are widespread and comprise the most commonly cultivated edible mushrooms in the world. Species identification of oyster mushroom spawn based on cultural, morphological, and cultivated characteristics is time consuming and can be extraordinarily difficult, which has impeded mushroom breeding and caused economic loss for mushroom growers. To explore a precise and concise approach for species identification, the nuclear ribosomal internal transcribed spacer (ITS), 28S rDNA, and the widely used protein-coding marker translation elongation factor 1α (EF-1α) gene were evaluated as candidate DNA barcode markers to investigate their feasibility in identifying 13 oyster mushroom species. A total of 160 sequences of the candidate loci were analyzed. Intra- and interspecific divergences and the ease of nucleotide sequence acquisition were the criteria used to evaluate the candidate genes. EF-1α showed the best intra- and interspecific variation among the candidate markers and discriminated 84.6% of the species tested, only being unable to distinguish two closely related species Pleurotus citrinopileatus and Pleurotus cornucopiae. Furthermore, EF-1α was more likely to be acquired than ITS or 28S rDNA, with an 84% success rate of PCR amplification and sequencing. For ITS and 28S rDNA, the intraspecific differences of several species were distinctly larger than the interspecific differences, and the species identification efficiency of the two candidate markers was worse (61.5 and 46.2%, respectively). In addition, these markers had some sequencing problems, with 55 and 76% success rates of sequencing, respectively. Hence, we propose EF-1α as a possible DNA barcode marker for oyster mushroom spawn.

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Section: Discussionsupporting

confidence: 73%

DNA Barcoding Mushroom Spawn Using EF-1α Barcodes: A Case Study in Oyster Mushrooms (Pleurotus)

Zhao

Cheng

et al. 2021

Front. Microbiol.

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“…In general, the PCR success rates were lower than those found by other authors (Zhao et al . , ; Schoch et al . ).…”

Section: Discussionmentioning

confidence: 99%

Species delimitation in Cladonia (Ascomycota): a challenge to the DNA barcoding philosophy

Pino-Bodas

Martín

Burgaz

et al. 2013

Molecular Ecology Resources

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The lichen-forming fungal genus Cladonia is species-rich with approximately 500 described species. The accepted barcode for fungi (ITS rDNA) often fails in identifying Cladonia spp. In order to find other markers that, in combination with the ITS rDNA region can be used for species identification in Cladonia, we studied the loci IGS rDNA, ef1α, rpb2 and cox1. A total of 782 sequences from 36 species have been analyzed. PCR amplification success rate, intraspecific and interspecific genetic distance variation, calculated using the K2P model, and the correct identification percentage (PCI) were taken into account to assess possible barcode regions. The marker showing the least intraspecific genetic distance range was cox1, followed by ITS rDNA and ef1α. Of the five studied markers only cox1 showed a barcoding gap. The rpb2 locus showed the highest PCI values, but it was the most difficult to amplify. The highest correct identification rates using blast method were obtained with rpb2.

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“…The two vital conditions for DNA barcode evaluation are sufficient intra-and inter-specific variation, as well as high PCR and sequencing success rates (Zhao et al 2011a(Zhao et al , 2011bZeng 2012;Zhu et al 2014). Taking both these standards into consideration, the use of ITS was considered to be an adequate primary Russula DNA barcode in situations of single gene analysis.…”

Section: Discussionmentioning

confidence: 99%

A preliminary DNA barcode selection for the genus Russula (Russulales, Basidiomycota)

Zhao

Zhang

et al. 2018

Mycology

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Russula is a worldwid genus which has a high species diversity . Aiming accurate and rapid species identification, candidate genes nLSU (28S), ITS, tef-1α, mtSSU, rpb1, and rpb2, were analysed as potential DNA barcodes. This analysis included 433 sequences from 38 well-circumscribed Russula species of eight subgenera. Two vital standards were analysed for success species identification using DNA barcodes, specifically inter-and intra-specific variations together with the success rates of PCR amplification and sequencing. Although the gap between inter-and intra-specific variations was narrow, ITS met the qualification standards for a target DNA barcode. Overlapping inter-and intra-specific pairwise distances were observed in nLSU, tef-1α, mtSSU, and rpb2. The success rates of PCR amplification and sequencing in mtSSU and rpb1 were lower than those of others. Gene combinations were also investigated for resolution of species recognition. ITS-rpb2 was suggested as the likely target DNA barcode for Russula, owing to the two viatal standards above. Since nLSU has the lowest minimum of inter-specific variation, and tef-1α has the highest overlap between intra-and inter-species variations among the candidate genes, they are disqualified from the selection for DNA barcode of Russula. ARTICLE HISTORY

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DNA barcoding of the fungal genus Neonectria and the discovery of two new species

Cited by 19 publications

References 56 publications

DNA Barcoding Mushroom Spawn Using EF-1α Barcodes: A Case Study in Oyster Mushrooms (Pleurotus)

DNA Barcoding Mushroom Spawn Using EF-1α Barcodes: A Case Study in Oyster Mushrooms (Pleurotus)

Species delimitation in Cladonia (Ascomycota): a challenge to the DNA barcoding philosophy

A preliminary DNA barcode selection for the genus Russula (Russulales, Basidiomycota)

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