Yi-jian Yao - Academia.edu (original) (raw)

Papers by Yi-jian Yao

Journal of Integrative Plant Biology, 2006

Molecular Phylogenetics and Evolution, 2013

The internal transcribed spacer (ITS) of nuclear ribosomal DNA (nrDNA) has been widely used as a ... more The internal transcribed spacer (ITS) of nuclear ribosomal DNA (nrDNA) has been widely used as a molecular marker in phylogenetic studies and has been selected as a DNA barcode for fungi. It is generally believed that nrDNA conforms to concerted evolution in most eukaryotes; however, intraindividual-intraspecific polymorphisms of this region were reported in various organisms, suggesting a non-concerted evolutionary process. In Ophiocordyceps sinensis, one of the most valuable medicinal fungi, a remarkable variation of the ITS region has been revealed. Some highly divergent sequences were thought to represent cryptic species, different species or genotypes in previous studies. To clarify the unusual ITS polymorphisms observed in O. sinensis, specific primers were designed to amplify ITS paralogs from pure cultures of both single-ascospore and tissue isolates in this study. All of the available ITS sequences, including those generated by this group and those in GenBank, were analyzed. Several AT-biased ITS paralogs were classified as pseudogenes based on their nucleotide compositions, secondary structures and minimum free energies of their 5.8S rRNAs, substitution rates, phylogenetic positions and gene expression analyses. Furthermore, ITS pseudogenes were amplified with specific primers from 10 of the 28 strains tested, including eight single-ascospore and two tissue isolates. Divergent ITS paralogs were proved to coexist in individual genomes, suggesting a non-concerted mechanism of evolution in the ITS region of O. sinensis. The hypotheses that divergent ITS paralogs represent cryptic or other species or different genotypes were thus rejected.

PloS one, 2014

Ganoderma has been considered a very difficult genus among the polypores to classify and is curre... more Ganoderma has been considered a very difficult genus among the polypores to classify and is currently in a state of taxonomic chaos. In a study of Ganoderma collections including numerous type specimens, we found that six species namely G. cupreum, G. densizonatum, G. limushanense, G. mastoporum, G. orbiforme, G. subtornatum, and records of G. fornicatum from Mainland China and Taiwan are very similar to one another in basidiocarp texture, pilear cuticle structure, context color, pore color and basidiospore characteristics. Further, we sequenced the nrDNA ITS region (ITS1 and ITS2) and partial mtDNA SSU region of the studied materials, and performed phylogenetic analyses based on these sequence data. The nrDNA ITS sequence analysis results show that the eight nrDNA ITS sequences derived from this study have single-nucleotide polymorphisms in ITS1 and/or ITS2 at inter- and intra-individual levels. In the nrDNA ITS phylogenetic trees, all the sequences from this study are grouped toge...

Taxon, 2015

ABSTRACT Paecilomyces hepiali is an important fungus for medicinal and healthcare products genera... more ABSTRACT Paecilomyces hepiali is an important fungus for medicinal and healthcare products generating an economic value of one billion CNY annually. It has been the subject of much research attention, especially due to its isolation from field collections of Ophiocordyceps sinensis (the caterpillar fungus or Dōng chóng xià căo) prized for its reputed medicinal properties. However, research on this important fungus is currently hampered by the fact that the holotype and ex-type strain are unavailable for study on loan and in person due to institutional policies of confidentiality. Thus the holotype is effectively “lost” for the purposes of the Code. To facilitate further research and to enable the unambiguous application of the name, a neotype is designated for P. hepiali, based on a recent collection from the type locality.

PLoS ONE, 2012

Ling-zhi, a widely cultivated fungus in China, has a long history in traditional Chinese medicine... more Ling-zhi, a widely cultivated fungus in China, has a long history in traditional Chinese medicine. Although the name 'Ganoderma lucidum', a species originally described from England, has been applied to the fungus, their identities are not the same. This study aims to clarify the identity of this medicinally and economically important fungus. Specimens of Ling-zhi from China (field collections and cultivated basidiomata of the Chinese 'G. lucidum'), G. lucidum from UK and other related Ganoderma species, were examined both morphologically and molecularly. High variability of basidioma morphology was found in the cultivated specimens of the Chinese 'G. lucidum', while some microscopic characters were more or less consistent, i.e. short clavate cutis elements, Bovista-type ligative hyphae and strongly echinulate basidiospores. These characters were also found in the holotype of G. sichuanense, a species originally described from Sichuan, China, and in recent collections made in the type locality of the species, which matched the diagnostic characters in the prologue. For comparison, specimens of closely related species, G. lucidum, G. multipileum, G. resinaceum, G. tropicum and G. weberianum, were also examined. DNA sequences were obtained from field collections, cultivated basidiomata and living strains of the Chinese 'G. lucidum', specimens from the type locality of G. sichuanense, and specimens of the closely related species studied. Three-gene combined analyses (ITS+IGS+rpb2) were performed and the results indicated that the Chinese 'G. lucidum' shared almost identical sequences with G. sichuanense. Based on both morphological and molecular data, the identity of the Chinese 'G. lucidum' (Ling-zhi) is considered conspecific with G. sichuanense. Detailed morphological descriptions and illustrations are provided in addition to discussion of nomenclature implications.

Mycological Research, 1996

Mycological Research, 1995

Journal of Applied Microbiology, 2005

Mycological Research, 2001

IMA fungus, 2014

Ophiocordycipitaceae is a diverse family comprising ecologically, economically, medicinally, and ... more Ophiocordycipitaceae is a diverse family comprising ecologically, economically, medicinally, and culturally important fungi. The family was recognized due to the polyphyly of the genus Cordyceps and the broad diversity of the mostly arthropod-pathogenic lineages of Hypocreales. The other two cordyceps-like families, Cordycipitaceae and Clavicipitaceae, will be revised taxonomically elsewhere. Historically, many species were placed in Cordyceps, but other genera have been described in this family as well, including several based on anamorphic features. Currently there are 24 generic names in use across both asexual and sexual life stages for species of Ophiocordycipitaceae. To reflect changes in Art. 59 in the International Code of Nomenclature for algae, fungi, and plants (ICN), we propose to protect and to suppress names within Ophiocordycipitaceae, and to present taxonomic revisions in the genus Tolypocladium, based on rigorous and extensively sampled molecular phylogenetic analys...

Journal of Invertebrate Pathology, 2001

Yao, Y.-J. and Spooner, B.M. (2006). Species of Sowerbyella in the British Isles, with validation... more Yao, Y.-J. and Spooner, B.M. (2006). Species of Sowerbyella in the British Isles, with validation of Pseudombrophila sect. Nannfeldtiella (Pezizales). Fungal Diversity 22: 267-279. Notes on the nomenclature and taxonomy of British taxa of Sowerbyella are presented, together with the description of a new variety, S. radiculata var. kewensis, and a new combination, S. radiculata var. petaloidea. Three varieties of S. radiculata are recognised from the British Isles. In addition, current status of the known taxa of Sowerbyella is summarised and a key for their identification provided. A new section in the genus Pseudombrophila, P. sect. Nannfeldtiella, is also validated and a lectotype for Geopyxis cookei designated.

The Journal of Microbiology, 2011

Journal of Integrative Plant Biology, 2006

Molecular Phylogenetics and Evolution, 2013

The internal transcribed spacer (ITS) of nuclear ribosomal DNA (nrDNA) has been widely used as a ... more The internal transcribed spacer (ITS) of nuclear ribosomal DNA (nrDNA) has been widely used as a molecular marker in phylogenetic studies and has been selected as a DNA barcode for fungi. It is generally believed that nrDNA conforms to concerted evolution in most eukaryotes; however, intraindividual-intraspecific polymorphisms of this region were reported in various organisms, suggesting a non-concerted evolutionary process. In Ophiocordyceps sinensis, one of the most valuable medicinal fungi, a remarkable variation of the ITS region has been revealed. Some highly divergent sequences were thought to represent cryptic species, different species or genotypes in previous studies. To clarify the unusual ITS polymorphisms observed in O. sinensis, specific primers were designed to amplify ITS paralogs from pure cultures of both single-ascospore and tissue isolates in this study. All of the available ITS sequences, including those generated by this group and those in GenBank, were analyzed. Several AT-biased ITS paralogs were classified as pseudogenes based on their nucleotide compositions, secondary structures and minimum free energies of their 5.8S rRNAs, substitution rates, phylogenetic positions and gene expression analyses. Furthermore, ITS pseudogenes were amplified with specific primers from 10 of the 28 strains tested, including eight single-ascospore and two tissue isolates. Divergent ITS paralogs were proved to coexist in individual genomes, suggesting a non-concerted mechanism of evolution in the ITS region of O. sinensis. The hypotheses that divergent ITS paralogs represent cryptic or other species or different genotypes were thus rejected.

PloS one, 2014

Ganoderma has been considered a very difficult genus among the polypores to classify and is curre... more Ganoderma has been considered a very difficult genus among the polypores to classify and is currently in a state of taxonomic chaos. In a study of Ganoderma collections including numerous type specimens, we found that six species namely G. cupreum, G. densizonatum, G. limushanense, G. mastoporum, G. orbiforme, G. subtornatum, and records of G. fornicatum from Mainland China and Taiwan are very similar to one another in basidiocarp texture, pilear cuticle structure, context color, pore color and basidiospore characteristics. Further, we sequenced the nrDNA ITS region (ITS1 and ITS2) and partial mtDNA SSU region of the studied materials, and performed phylogenetic analyses based on these sequence data. The nrDNA ITS sequence analysis results show that the eight nrDNA ITS sequences derived from this study have single-nucleotide polymorphisms in ITS1 and/or ITS2 at inter- and intra-individual levels. In the nrDNA ITS phylogenetic trees, all the sequences from this study are grouped toge...

Taxon, 2015

ABSTRACT Paecilomyces hepiali is an important fungus for medicinal and healthcare products genera... more ABSTRACT Paecilomyces hepiali is an important fungus for medicinal and healthcare products generating an economic value of one billion CNY annually. It has been the subject of much research attention, especially due to its isolation from field collections of Ophiocordyceps sinensis (the caterpillar fungus or Dōng chóng xià căo) prized for its reputed medicinal properties. However, research on this important fungus is currently hampered by the fact that the holotype and ex-type strain are unavailable for study on loan and in person due to institutional policies of confidentiality. Thus the holotype is effectively “lost” for the purposes of the Code. To facilitate further research and to enable the unambiguous application of the name, a neotype is designated for P. hepiali, based on a recent collection from the type locality.

PLoS ONE, 2012

Ling-zhi, a widely cultivated fungus in China, has a long history in traditional Chinese medicine... more Ling-zhi, a widely cultivated fungus in China, has a long history in traditional Chinese medicine. Although the name 'Ganoderma lucidum', a species originally described from England, has been applied to the fungus, their identities are not the same. This study aims to clarify the identity of this medicinally and economically important fungus. Specimens of Ling-zhi from China (field collections and cultivated basidiomata of the Chinese 'G. lucidum'), G. lucidum from UK and other related Ganoderma species, were examined both morphologically and molecularly. High variability of basidioma morphology was found in the cultivated specimens of the Chinese 'G. lucidum', while some microscopic characters were more or less consistent, i.e. short clavate cutis elements, Bovista-type ligative hyphae and strongly echinulate basidiospores. These characters were also found in the holotype of G. sichuanense, a species originally described from Sichuan, China, and in recent collections made in the type locality of the species, which matched the diagnostic characters in the prologue. For comparison, specimens of closely related species, G. lucidum, G. multipileum, G. resinaceum, G. tropicum and G. weberianum, were also examined. DNA sequences were obtained from field collections, cultivated basidiomata and living strains of the Chinese 'G. lucidum', specimens from the type locality of G. sichuanense, and specimens of the closely related species studied. Three-gene combined analyses (ITS+IGS+rpb2) were performed and the results indicated that the Chinese 'G. lucidum' shared almost identical sequences with G. sichuanense. Based on both morphological and molecular data, the identity of the Chinese 'G. lucidum' (Ling-zhi) is considered conspecific with G. sichuanense. Detailed morphological descriptions and illustrations are provided in addition to discussion of nomenclature implications.

Mycological Research, 1996

Mycological Research, 1995

Journal of Applied Microbiology, 2005

Mycological Research, 2001

IMA fungus, 2014

Ophiocordycipitaceae is a diverse family comprising ecologically, economically, medicinally, and ... more Ophiocordycipitaceae is a diverse family comprising ecologically, economically, medicinally, and culturally important fungi. The family was recognized due to the polyphyly of the genus Cordyceps and the broad diversity of the mostly arthropod-pathogenic lineages of Hypocreales. The other two cordyceps-like families, Cordycipitaceae and Clavicipitaceae, will be revised taxonomically elsewhere. Historically, many species were placed in Cordyceps, but other genera have been described in this family as well, including several based on anamorphic features. Currently there are 24 generic names in use across both asexual and sexual life stages for species of Ophiocordycipitaceae. To reflect changes in Art. 59 in the International Code of Nomenclature for algae, fungi, and plants (ICN), we propose to protect and to suppress names within Ophiocordycipitaceae, and to present taxonomic revisions in the genus Tolypocladium, based on rigorous and extensively sampled molecular phylogenetic analys...

Journal of Invertebrate Pathology, 2001

Yao, Y.-J. and Spooner, B.M. (2006). Species of Sowerbyella in the British Isles, with validation... more Yao, Y.-J. and Spooner, B.M. (2006). Species of Sowerbyella in the British Isles, with validation of Pseudombrophila sect. Nannfeldtiella (Pezizales). Fungal Diversity 22: 267-279. Notes on the nomenclature and taxonomy of British taxa of Sowerbyella are presented, together with the description of a new variety, S. radiculata var. kewensis, and a new combination, S. radiculata var. petaloidea. Three varieties of S. radiculata are recognised from the British Isles. In addition, current status of the known taxa of Sowerbyella is summarised and a key for their identification provided. A new section in the genus Pseudombrophila, P. sect. Nannfeldtiella, is also validated and a lectotype for Geopyxis cookei designated.

The Journal of Microbiology, 2011