Towards standardizing taxonomic ranks using divergence times – a case study for reconstruction of the Agaricus taxonomic system

Zhao, Rui-Lin; Zhou, Junliang; Chen, Jie; Margaritescu, Simona; Sánchez‐Ramírez, Santiago; Hyde, Kevin D.; Callac, Philippe; Parra, Luis A.; Li, Guojie; Moncalvo, Jean‐Marc

doi:10.1007/s13225-016-0357-x

Cited by 77 publications

(116 citation statements)

References 57 publications

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“…Notes -The morphological characters of A. catenariocystidiasus match the circumscription of section Subrutilescentes well (Zhao et al 2016), and the phylogenetic analysis also supports its placement in this section. Compared with the known species of section Subrutilescentes and section Spissicaules, Agaricus catenariocystidiasus is different from A. Linzhiensis and A. brunneopileatus by having wider or thinner basidiospores than A. catenariocystidiasus in Zhao et al (2016), A. Linzhiensis spores that are broadly ellipsoid, Qm = 1.3; A. brunneopileatus spores elongate ellipsoid Qm =1.7).…”

Section: Resultsmentioning

confidence: 53%

“…Notes -The morphological characters of the specimens from this study generally match those of A. inthanoensis (Zhao et al 2016), with the exception of the 10% NaOH reaction, which is absent from the original description, but is yellow in the specimens from this study. However, in the phylogenetic tree, they are separated.…”

Section: Resultsmentioning

confidence: 59%

“…Compared with the known species of section Subrutilescentes and section Spissicaules, Agaricus catenariocystidiasus is different from A. Linzhiensis and A. brunneopileatus by having wider or thinner basidiospores than A. catenariocystidiasus in Zhao et al (2016), A. Linzhiensis spores that are broadly ellipsoid, Qm = 1.3; A. brunneopileatus spores elongate ellipsoid Qm =1.7). Agaricus impudicus develops strong red or reddish brown discoloration on its gills when bruised, while A. catenariocystidiosus lacks such a discoloration.…”

Section: Resultsmentioning

confidence: 79%

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Characterization of four species including one new species of Agaricus subgenus Spissicaules from Eastern China

Dai¹

2016

Mycosphere

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Four species of Agaricus subgenus Spissicaules, including a new species A. catenariocystidiosus, are identified from Eastern China based on morphological and molecular data. All of the species are introduced with full descriptions. Phylogenetic relationships were inferred based on the nuclear ribosomal internal transcribed spacer (ITS) region. The known species A. inthanoensis, A. parasubrutilescens and A. planipileus are compared with their original descriptions, and several supplementary morphological characters are provided.

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Section: Resultsmentioning

confidence: 53%

Section: Resultsmentioning

confidence: 59%

Section: Resultsmentioning

confidence: 79%

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Characterization of four species including one new species of Agaricus subgenus Spissicaules from Eastern China

Dai¹

2016

Mycosphere

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“…Another gene often used in fungal phylogenetic analyses is tef-1α (Jaklitsch et al 2006;Stenglein et al 2010;Zhao et al 2016He et al 2017), which had the second highest PCR and sequencing success rates (Table 3). This gene has previously been regarded as the target DNA barcode in certain groups (Geiser et al 2004;Druzhinina et al 2005;Li et al 2013); however, our analyses showed that tef-1α the occurrence of overlap between intra-and inter-species variation among the candidate genes (Figs.…”

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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“…Molecular phylogenetic methods have been widely applied in basidiomycete studies, and have elucidated several taxonomic issues (Drehmel et al 1999, Zhang et al 2004, Dentinger et al 2010, Zhao et al 2011Thongklang et al 2014;Gui et al 2015;Chen et al 2016;Zhao et al 2016). However, only a few studies (Li et al 2014, Adamčík et al 2015 have incorporated phylogenetic analyses in their taxonomic descriptions of the genus Phallus.…”

Section: Introductionmentioning

confidence: 99%

Phallus haitangensis, a new species of stinkhorn from Yunnan Province, China

Mortimer

et al. 2016

Phytotaxa

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Four specimens of Phallus were collected during surveys in a Pinus armandii forest in Baoshan, Yunnan Province, China. Macro-and micro-characteristics, together with Internal Transcribed Spacer (ITS) sequence data, showed that the four specimens belong to a new species, here named Phallus haitangensis. The ITS phylogenetic analyses, morphological descriptions, color photographs, and line drawings are provided, and compared with closely related species in the genus.

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Towards standardizing taxonomic ranks using divergence times – a case study for reconstruction of the Agaricus taxonomic system

Cited by 77 publications

References 57 publications

Characterization of four species including one new species of Agaricus subgenus Spissicaules from Eastern China

Characterization of four species including one new species of Agaricus subgenus Spissicaules from Eastern China

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

Phallus haitangensis, a new species of stinkhorn from Yunnan Province, China

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