The application of a species name is determined by the nomenclatural type, which is usually a single specimen to which the name is permanently attached. Therefore, information from the study on the type is important for the correct understanding of a species concept. DNA sequences from the type of a species can, for the most part, provide unambiguous information for the delimitation and identification of fungal species. However, obtaining high-quality DNA from historical types is often a challenging task due to DNA degradation in specimens. With the continuous development of next-generation sequencing technology, it has become possible to extract sufficiently long DNA sequences from historical specimens. In this study, genome skimming was successfully employed on an Illumina sequencing system to generate sequences from the type specimens of thirteen macrofungal species, namely Acetabula purpurea M. Zang, Cordyceps liangshanensis M. Zang et al., C. szemaoensis M. Zang, Gyromitra sichuanensis Korf & W.Y. Zhuang, Agrocybe salicaceicola Zhu L. Yang et al., Coprinus giganteosporus M. Zang & Y. Fei, Cyathus discoideus M. Zang, Dictyophora echinovolvata M. Zang et al., D. rubrovolvata M. Zang et al., Endophallus yunnanensis M. Zang & R.H. Petersen, Phallus megacephalus M. Zang, P. tenuissimus T.H. Li et al., and P. fragrans M. Zang. Sequences of the internal transcribed spacers (ITS), the nuclear ribosomal large subunit (nrLSU), the translation elongation factor 1-α (TEF1), the RNA polymerase II first largest subunit (RPB1), and RNA polymerase II second largest subunit (RPB2) were successfully generated and 48 sequences in total were newly obtained. Phylogenetic analyses indicated that A. purpurea, P. rubrovolvatus, A. salicaceicola, and C. discoideus are distinct species within the genera Otidea, Phallus, Cyclocybe, and Cyathus, respectively. In contrast, C. szemaoensis should be transferred to the genus Perennicordyceps. The study also indicated that the genus Endophallus should be merged into Phallus. Endophallus yunnanensis and the present commercially widely used name P. dongsun are later synonyms of P. fragrans. Three names of Phallus published in this century are synonyms of P. megacephalus described in the last century. One new combination and eight new synonyms are suggested. This study is of importance for enhancing the scientific value and security of type specimens, as well as for the accurate recognition of the species.

Linking historical types with the current taxonomy: DNA sequence generation and molecular phylogenetic inferences for thirteen macrofungal species

期刊论文
发表日期：

2025年6月13日

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Jin-Yan Tang,
Jian-Wei Liu,
Hong Yu,
Zhu L. Yang

摘要

The application of a species name is determined by the nomenclatural type, which is usually a single specimen to which the name is permanently attached. Therefore, information from the study on the type is important for the correct understanding of a species concept. DNA sequences from the type of a species can, for the most part, provide unambiguous information for the delimitation and identification of fungal species. However, obtaining high-quality DNA from historical types is often a challenging task due to DNA degradation in specimens. With the continuous development of next-generation sequencing technology, it has become possible to extract sufficiently long DNA sequences from historical specimens. In this study, genome skimming was successfully employed on an Illumina sequencing system to generate sequences from the type specimens of thirteen macrofungal species, namely Acetabula purpurea M. Zang, Cordyceps liangshanensis M. Zang et al., C. szemaoensis M. Zang, Gyromitra sichuanensis Korf & W.Y. Zhuang, Agrocybe salicaceicola Zhu L. Yang et al., Coprinus giganteosporus M. Zang & Y. Fei, Cyathus discoideus M. Zang, Dictyophora echinovolvata M. Zang et al., D. rubrovolvata M. Zang et al., Endophallus yunnanensis M. Zang & R.H. Petersen, Phallus megacephalus M. Zang, P. tenuissimus T.H. Li et al., and P. fragrans M. Zang. Sequences of the internal transcribed spacers (ITS), the nuclear ribosomal large subunit (nrLSU), the translation elongation factor 1-α (TEF1), the RNA polymerase II first largest subunit (RPB1), and RNA polymerase II second largest subunit (RPB2) were successfully generated and 48 sequences in total were newly obtained. Phylogenetic analyses indicated that A. purpurea, P. rubrovolvatus, A. salicaceicola, and C. discoideus are distinct species within the genera Otidea, Phallus, Cyclocybe, and Cyathus, respectively. In contrast, C. szemaoensis should be transferred to the genus Perennicordyceps. The study also indicated that the genus Endophallus should be merged into Phallus. Endophallus yunnanensis and the present commercially widely used name P. dongsun are later synonyms of P. fragrans. Three names of Phallus published in this century are synonyms of P. megacephalus described in the last century. One new combination and eight new synonyms are suggested. This study is of importance for enhancing the scientific value and security of type specimens, as well as for the accurate recognition of the species.