The Experts below are selected from a list of 6729 Experts worldwide ranked by ideXlab platform
Yongjie Zhang - One of the best experts on this subject based on the ideXlab platform.
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determining novel molecular markers in the chinese caterpillar fungus ophiocordyceps sinensis by screening a shotgun genomic library
Applied Microbiology and Biotechnology, 2012Co-Authors: Yongjie Zhang, Shu Zhang, Feirong Bai, Xingzhong LiuAbstract:The Chinese caterpillar fungus Ophiocordyceps sinensis, endemic to alpine regions on the Tibetan Plateau, is one of the most valuable Medicinal Fungi in the world. Genetic differentiation within this fungus was observed; however, due to lack of highly efficient molecular markers, the overall genetic structure of this fungus has not been clarified. In this study, a shotgun genomic library of O. sinensis was constructed, and >181,848 nt were analyzed from >250 random clones. Primers from 33 sequenced fragments were then designed to amplify O. sinensis samples collected from widely separated regions on the Tibetan Plateau. Ten of the 33 fragments had no amplification or poor sequencing quality from all or certain samples. Sequence variations of the remaining 23 fragments among different samples were investigated in detail. Three fragments (OSRC14, OSRC19, and OSRC32) were the most variable with 7–43 single-nucleotide polymorphism (SNP) sites, representing the SNP frequency of 1.2–6.7 % per nucleotide site. These three fragments have the potential to be useful molecular markers for studying the population genetics of O. sinensis. These results also showed that constructing and screening a shotgun genomic library was an efficient approach to identify novel molecular markers from non-model organisms.
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high diversity of the fungal community structure in naturally occurring ophiocordyceps sinensis
PLOS ONE, 2010Co-Authors: Yongjie Zhang, Shu Zhang, Mu Wang, Fengyan Bai, Xingzhong LiuAbstract:Background Ophiocordyceps sinensis (syn. Cordyceps sinensis), which is a parasite of caterpillars and is endemic to alpine regions on the Tibetan Plateau, is one of the most valuable Medicinal Fungi in the world. “Natural O. sinensis specimens” harbor various other Fungi. Several of these other Fungi that have been isolated from natural O. sinensis specimens have similar chemical components and/or pharmaceutical effects as O. sinensis. Nevertheless, the mycobiota of natural O. sinensis specimens has not been investigated in detail. Methodology/Principal Findings Based on the technique of PCR-single-strand conformation polymorphism (PCR-SSCP), the mycobiota of three different sections (stromata, sclerotia, and mycelial cortices) from natural O. sinensis specimens were investigated using both culture-dependent and -independent methods. For the culture-dependent method, 572 fungal strains were isolated, and 92 putative operational taxonomic units (OTUs) were identified from 226 sequenced strains with the threshold of 97%. For the culture-independent method, 490 fungal clones were identified from about 3000 clones of ITS fragments from the whole-community DNA; based on PCR-SSCP analyses, 266 of these clones were selected to be sequenced, and 118 putative OTUs were detected. The overwhelming majority of isolates/clones and OTUs were detected from mycelial cortices; only a few were detected from stromata and sclerotia. The most common OTUs detected with both methods belonged to Ascomycota; however, only 13 OTUs were detected simultaneously by both methods. Potential novel lineages were detected by each of the two methods. Conclusions/Significance A great number of fungal species present in the mycobiota of naturally-occurring O. sinensis specimens were detected, and many of them may represent undescribed lineages. That only a few of the same OTUs were detected by both methods indicated that different methods should be used. This study increased our understanding about the fungal community structure of this valuable Medicinal herb.
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genetic diversity of ophiocordyceps sinensis a Medicinal fungus endemic to the tibetan plateau implications for its evolution and conservation
BMC Evolutionary Biology, 2009Co-Authors: Yongjie Zhang, Xingzhong Liu, Shu Zhang, Mu Wang, Yinglan GuoAbstract:Background Ophiocordyceps sinensis (syn. Cordyceps sinensis), endemic to alpine regions on the Tibetan plateau, is one of the most valuable Medicinal Fungi in the world. Huge commercial demand has led to excessive harvest and a dramatic decline in its numbers. The diversity of terrains and climates on the Tibetan Plateau and the broad insect host range (more than 50 species in the family Hepialidae) may have resulted in substantial intraspecific genetic diversity for this fungus. The objective of this study was to evaluate the population distribution of O. sinensis from geographically diverse regions of the Tibetan Plateau based on nrDNA ITS and MAT1-2-1 gene sequences. Understanding of the genetic diversity and genesis of O. sinensis will provide important information for the evolution and conservation of this fungus.
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genetic diversity of ophiocordyceps sinensis a Medicinal fungus endemic to the tibetan plateau implications for its evolution and conservation
BMC Evolutionary Biology, 2009Co-Authors: Yongjie Zhang, Xingzhong Liu, Shu Zhang, Mu Wang, Yinglan GuoAbstract:Ophiocordyceps sinensis (syn. Cordyceps sinensis), endemic to alpine regions on the Tibetan plateau, is one of the most valuable Medicinal Fungi in the world. Huge commercial demand has led to excessive harvest and a dramatic decline in its numbers. The diversity of terrains and climates on the Tibetan Plateau and the broad insect host range (more than 50 species in the family Hepialidae) may have resulted in substantial intraspecific genetic diversity for this fungus. The objective of this study was to evaluate the population distribution of O. sinensis from geographically diverse regions of the Tibetan Plateau based on nrDNA ITS and MAT1-2-1 gene sequences. Understanding of the genetic diversity and genesis of O. sinensis will provide important information for the evolution and conservation of this fungus. Significant sequence variations in the ITS and MAT1-2-1 genes (27 and 23 informative sites, eight and seven haplotypes, respectively) were observed. Phylogenetic analysis based on ITS sequences, MAT1-2-1 sequences, or their combined data set, clustered isolates from northern regions in one clade (clade I), whereas isolates from southern regions were dispersed in all four clades (clade I-IV). Single-strand conformation polymorphism (SSCP) analyses of 2639 ITS clones from seven samples revealed 91 different SSCP patterns that were subsequently sequenced. ITS heterogeneity was found in XZ-LZ07-H1 (Nyingchi population), and 17 informative sites and five haplotypes were detected from 15 clones. The five haplotypes clustered into three clades (clade I, II, and IV). Significant genetic divergence in O. sinensis was observed and the genetic diversification was greater among southern isolates than that among northern isolates. The polymorphism of nrDNA ITS sequences suggested that O. sinensis spread from a center of origin (the Nyingchi District) to southern regions and subsequently to northern areas. These results suggest that southern populations are important reservoirs of genetic diversity and should be taken into account in conservation programs.
Yijian Yao - One of the best experts on this subject based on the ideXlab platform.
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comparison of different sequencing and assembly strategies for a repeat rich fungal genome ophiocordyceps sinensis
Journal of Microbiological Methods, 2016Co-Authors: Tom Hsiang, Wenjing Wang, Xiaoliang Wang, Lei Jiao, Rui-heng Yang, Ke Wang, Yijian YaoAbstract:Ophiocordyceps sinensis is one of the most expensive Medicinal Fungi world-wide, and has been used as a traditional Chinese medicine for centuries. In a recent report, the genome of this fungus was found to be expanded by extensive repetitive elements after assembly of Roche 454 (223Mb) and Illumina HiSeq (10.6Gb) sequencing data, producing a genome of 87.7Mb with an N50 scaffold length of 12kb and 6972 predicted genes. To test whether the assembly could be improved by deeper sequencing and to assess the amount of data needed for optimal assembly, genomic sequencing was run several times on genomic DNA extractions of a single ascospore isolate (strain 1229) on an Illumina HiSeq platform (25Gb total data). Assemblies were produced using different data types (raw vs. trimmed) and data amounts, and using three freely available assembly programs (ABySS, SOAP and Velvet). In nearly all cases, trimming the data for low quality base calls did not provide assemblies with higher N50 values compared to the non-trimmed data, and increasing the amount of input data (i.e. sequence reads) did not always lead to higher N50 values. Depending on the assembly program and data type, the maximal N50 was reached with between 50% to 90% of the total read data, equivalent to 100× to 200× coverage. The draft genome assembly was improved over the previously published version resulting in a 114Mb assembly, scaffold N50 of 70kb and 9610 predicted genes. Among the predicted genes, 9213 were validated by RNA-Seq analysis in this study, of which 8896 were found to be singletons. Evidence from genome and transcriptome analyses indicated that species assemblies could be improved with defined input material (e.g. haploid mono-ascospore isolate) without the requirement of multiple sequencing technologies, multiple library sizes or data trimming for low quality base calls, and with genome coverages between 100× and 200×.
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bacterial diversity in native habitats of the Medicinal fungus ophiocordyceps sinensis on tibetan plateau as determined using illumina sequencing data
Fems Microbiology Letters, 2015Co-Authors: Rui-heng Yang, Xiaoliang Wang, Siping Jiang, Yijian YaoAbstract:Ophiocordyceps sinensis is one of the most well-known traditional Chinese Medicinal Fungi. In this study, bacterial diversity in the soils of native habitats of O. sinensis was investigated using Illumina sequencing data. A total of 525 000 sequences of V6-16S rRNA were analyzed. The number of OTUs from each sample ranged from 13 858 to 15 978 at 97% sequence similarity cut-off. The results demonstrated that the deep sequencing approach provides improved access to rare genotypes. Richness indices and Shannon's diversity index did not differ significantly between samples collected from locations where O. sinensis was present (Os1-3) and not present (NOs1-3). Classified bacterial sequences were grouped into 23 phyla including Proteobacteria, Actinobacteria, Acidobacteria, Verrucomicrobia , etc. The Venn diagram revealed that 7183 OTUs belonging to 14 phyla were shared by Os, NOs and MP (mycelial pellicle wrapping the sclerotium of O. sinensis ) samples, possibly representing a core microbiome existing in native habitats of O. sinensis , and that 863 belonging to 12 phyla were shared by Os and MP samples, possibly related to the occurrence of O. sinensis. Overall, the results revealed a high bacterial diversity in the soil samples and the relationships between the bacterial diversity and O. sinensis merit further investigation.
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evaluation of nutritional and physical stress conditions during vegetative growth on conidial production and germination in ophiocordyceps sinensis
Fems Microbiology Letters, 2013Co-Authors: Shuyu Ren, Yijian YaoAbstract:The influence of nutritional and physical stress on sporulation, conidial germination and vegetative biomass of Ophiocordyceps sinensis, one of the most important Medicinal Fungi in China and now globally, was evaluated using a two-stage culture method. All the treatments, except nutrient deprivation, enhanced conidial production and vegetative biomass to some extent. However, conidia produced under stress showed decreased germination in comparison with those continuously cultured on the enriched potato dextrose agar (PDA; as the control). Among 10 treatments tested, the physical stress of frozen-shock produced the largest number of conidia, 7.5 times higher than that of the control, followed by heat-shock treatment. These results demonstrate that the fungus has strong physiological adaptations to environmental stress that may have evolved because it is endemic to the Tibetan Plateau. This report will be relevant to the study of the pathogenicity and artificial cultivation of this endangered fungus.
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non concerted its evolution in Fungi as revealed from the important Medicinal fungus ophiocordyceps sinensis
Molecular Phylogenetics and Evolution, 2013Co-Authors: Lei Jiao, Yijian YaoAbstract: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.
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development of conventional and nested pcr assays for the detection of ophiocordyceps sinensis
Journal of Basic Microbiology, 2013Co-Authors: Guosheng Jin, Wenjing Wang, Xiaoliang Wang, Rui-heng Yang, Shuyu Ren, Yijian YaoAbstract:Ophiocordyceps sinensis, endemic to the Tibetan Plateau, is one of the most important Medicinal Fungi with a huge economic value. In the present study, specific primer pairs were designed based on a comprehensive ITS sequence dataset of O. sinensis and its related Fungi, and tested for specificity and sensitivity through PCR experiments using 27 individuals of O. sinensis from different geographical origins and 40 other related fungal species in terms of phylogeny or ecology. A primer pair highly specific to O. sinensis was obtained, yielding a 275 bp PCR product from all the individuals of O. sinensis but no product from the other Fungi tested. The detection limit of the primers was demonstrated to be 10 ng of pure O. sinensis DNA for conventional PCR and 10 pg for nested PCR in a 25 µl reaction system. Soil samples collected from the habitat of O. sinensis were also tested using this PCR assay. The results showed that the primer pair and PCR-based assays developed in this study can be applied to the rapid detection of O. sinensis in its natural habitat.
Xingzhong Liu - One of the best experts on this subject based on the ideXlab platform.
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Genome Studies on Nematophagous and Entomogenous Fungi in China
MDPI AG, 2016Co-Authors: Weiwei Zhang, Xingzhong Liu, Xiaoli Cheng, Meichun XiangAbstract:The nematophagous and entomogenous Fungi are natural enemies of nematodes and insects and have been utilized by humans to control agricultural and forestry pests. Some of these Fungi have been or are being developed as biological control agents in China and worldwide. Several important nematophagous and entomogenous Fungi, including nematode-trapping Fungi (Arthrobotrys oligospora and Drechslerella stenobrocha), nematode endoparasite (Hirsutella minnesotensis), insect pathogens (Beauveria bassiana and Metarhizium spp.) and Chinese Medicinal Fungi (Ophiocordyceps sinensis and Cordyceps militaris), have been genome sequenced and extensively analyzed in China. The biology, evolution, and pharmaceutical application of these Fungi and their interacting with host nematodes and insects revealed by genomes, comparing genomes coupled with transcriptomes are summarized and reviewed in this paper
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determining novel molecular markers in the chinese caterpillar fungus ophiocordyceps sinensis by screening a shotgun genomic library
Applied Microbiology and Biotechnology, 2012Co-Authors: Yongjie Zhang, Shu Zhang, Feirong Bai, Xingzhong LiuAbstract:The Chinese caterpillar fungus Ophiocordyceps sinensis, endemic to alpine regions on the Tibetan Plateau, is one of the most valuable Medicinal Fungi in the world. Genetic differentiation within this fungus was observed; however, due to lack of highly efficient molecular markers, the overall genetic structure of this fungus has not been clarified. In this study, a shotgun genomic library of O. sinensis was constructed, and >181,848 nt were analyzed from >250 random clones. Primers from 33 sequenced fragments were then designed to amplify O. sinensis samples collected from widely separated regions on the Tibetan Plateau. Ten of the 33 fragments had no amplification or poor sequencing quality from all or certain samples. Sequence variations of the remaining 23 fragments among different samples were investigated in detail. Three fragments (OSRC14, OSRC19, and OSRC32) were the most variable with 7–43 single-nucleotide polymorphism (SNP) sites, representing the SNP frequency of 1.2–6.7 % per nucleotide site. These three fragments have the potential to be useful molecular markers for studying the population genetics of O. sinensis. These results also showed that constructing and screening a shotgun genomic library was an efficient approach to identify novel molecular markers from non-model organisms.
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high diversity of the fungal community structure in naturally occurring ophiocordyceps sinensis
PLOS ONE, 2010Co-Authors: Yongjie Zhang, Shu Zhang, Mu Wang, Fengyan Bai, Xingzhong LiuAbstract:Background Ophiocordyceps sinensis (syn. Cordyceps sinensis), which is a parasite of caterpillars and is endemic to alpine regions on the Tibetan Plateau, is one of the most valuable Medicinal Fungi in the world. “Natural O. sinensis specimens” harbor various other Fungi. Several of these other Fungi that have been isolated from natural O. sinensis specimens have similar chemical components and/or pharmaceutical effects as O. sinensis. Nevertheless, the mycobiota of natural O. sinensis specimens has not been investigated in detail. Methodology/Principal Findings Based on the technique of PCR-single-strand conformation polymorphism (PCR-SSCP), the mycobiota of three different sections (stromata, sclerotia, and mycelial cortices) from natural O. sinensis specimens were investigated using both culture-dependent and -independent methods. For the culture-dependent method, 572 fungal strains were isolated, and 92 putative operational taxonomic units (OTUs) were identified from 226 sequenced strains with the threshold of 97%. For the culture-independent method, 490 fungal clones were identified from about 3000 clones of ITS fragments from the whole-community DNA; based on PCR-SSCP analyses, 266 of these clones were selected to be sequenced, and 118 putative OTUs were detected. The overwhelming majority of isolates/clones and OTUs were detected from mycelial cortices; only a few were detected from stromata and sclerotia. The most common OTUs detected with both methods belonged to Ascomycota; however, only 13 OTUs were detected simultaneously by both methods. Potential novel lineages were detected by each of the two methods. Conclusions/Significance A great number of fungal species present in the mycobiota of naturally-occurring O. sinensis specimens were detected, and many of them may represent undescribed lineages. That only a few of the same OTUs were detected by both methods indicated that different methods should be used. This study increased our understanding about the fungal community structure of this valuable Medicinal herb.
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genetic diversity of ophiocordyceps sinensis a Medicinal fungus endemic to the tibetan plateau implications for its evolution and conservation
BMC Evolutionary Biology, 2009Co-Authors: Yongjie Zhang, Xingzhong Liu, Shu Zhang, Mu Wang, Yinglan GuoAbstract:Background Ophiocordyceps sinensis (syn. Cordyceps sinensis), endemic to alpine regions on the Tibetan plateau, is one of the most valuable Medicinal Fungi in the world. Huge commercial demand has led to excessive harvest and a dramatic decline in its numbers. The diversity of terrains and climates on the Tibetan Plateau and the broad insect host range (more than 50 species in the family Hepialidae) may have resulted in substantial intraspecific genetic diversity for this fungus. The objective of this study was to evaluate the population distribution of O. sinensis from geographically diverse regions of the Tibetan Plateau based on nrDNA ITS and MAT1-2-1 gene sequences. Understanding of the genetic diversity and genesis of O. sinensis will provide important information for the evolution and conservation of this fungus.
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genetic diversity of ophiocordyceps sinensis a Medicinal fungus endemic to the tibetan plateau implications for its evolution and conservation
BMC Evolutionary Biology, 2009Co-Authors: Yongjie Zhang, Xingzhong Liu, Shu Zhang, Mu Wang, Yinglan GuoAbstract:Ophiocordyceps sinensis (syn. Cordyceps sinensis), endemic to alpine regions on the Tibetan plateau, is one of the most valuable Medicinal Fungi in the world. Huge commercial demand has led to excessive harvest and a dramatic decline in its numbers. The diversity of terrains and climates on the Tibetan Plateau and the broad insect host range (more than 50 species in the family Hepialidae) may have resulted in substantial intraspecific genetic diversity for this fungus. The objective of this study was to evaluate the population distribution of O. sinensis from geographically diverse regions of the Tibetan Plateau based on nrDNA ITS and MAT1-2-1 gene sequences. Understanding of the genetic diversity and genesis of O. sinensis will provide important information for the evolution and conservation of this fungus. Significant sequence variations in the ITS and MAT1-2-1 genes (27 and 23 informative sites, eight and seven haplotypes, respectively) were observed. Phylogenetic analysis based on ITS sequences, MAT1-2-1 sequences, or their combined data set, clustered isolates from northern regions in one clade (clade I), whereas isolates from southern regions were dispersed in all four clades (clade I-IV). Single-strand conformation polymorphism (SSCP) analyses of 2639 ITS clones from seven samples revealed 91 different SSCP patterns that were subsequently sequenced. ITS heterogeneity was found in XZ-LZ07-H1 (Nyingchi population), and 17 informative sites and five haplotypes were detected from 15 clones. The five haplotypes clustered into three clades (clade I, II, and IV). Significant genetic divergence in O. sinensis was observed and the genetic diversification was greater among southern isolates than that among northern isolates. The polymorphism of nrDNA ITS sequences suggested that O. sinensis spread from a center of origin (the Nyingchi District) to southern regions and subsequently to northern areas. These results suggest that southern populations are important reservoirs of genetic diversity and should be taken into account in conservation programs.
Mu Wang - One of the best experts on this subject based on the ideXlab platform.
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genetic diversity and distribution patterns of host insects of caterpillar fungus ophiocordyceps sinensis in the qinghai tibet plateau
PLOS ONE, 2014Co-Authors: Qingmei Quan, Mu Wang, Xiaoling Yang, Yunguo Zhu, Ling-ling Chen, Xi Wang, Zhou ChengAbstract:The caterpillar fungus Ophiocordyceps sinensis is one of the most valuable Medicinal Fungi in the world, and it requires host insects in family Hepialidae (Lepidoptera) to complete its life cycle. However, the genetic diversity and phylogeographic structures of the host insects remain to be explored. We analyzed the genetic diversity and temporal and spatial distribution patterns of genetic variation of the host insects throughout the O. sinensis distribution. Abundant haplotype and nucleotide diversity mainly existed in the areas of Nyingchi, ShangriLa, and around the edge of the Qinghai-Tibet Plateau, where are considered as the diversity center or micro-refuges of the host insects of O. sinensis. However, there was little genetic variation among host insects from 72.1% of all populations, indicating that the host species composition might be relatively simple in large-scale O. sinensis populations. All host insects are monophyletic except for those from four O. sinensis populations around Qinghai Lake. Significant phylogeographic structure (NST>GST, P<0.05) was revealed for the monophyletic host insects, and the three major phylogenetic groups corresponded with specific geographical areas. The divergence of most host insects was estimated to have occurred at ca. 3.7 Ma, shortly before the rapid uplift of the QTP. The geographical distribution and star-like network of the haplotypes implied that most host insects were derived from the relicts of a once-widespread host that subsequently became fragmented. Neutrality tests, mismatch distribution analysis, and expansion time estimation confirmed that most host insects presented recent demographic expansions that began ca. 0.118 Ma in the late Pleistocene. Therefore, the genetic diversity and distribution of the present-day insects should be attributed to effects of the Qinghai-Tibet Plateau uplift and glacial advance/retreat cycles during the Quaternary ice age. These results provide valuable information to guide the protection and sustainable use of these host insects as well as O. sinensis.
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Genetic Diversity and Distribution Patterns of Host Insects of Caterpillar Fungus Ophiocordyceps sinensis in the Qinghai-Tibet Plateau
2014Co-Authors: Qingmei Quan, Mu Wang, Xiaoling Yang, Yunguo Zhu, Ling-ling Chen, Xi Wang, Zhou ChengAbstract:The caterpillar fungus Ophiocordyceps sinensis is one of the most valuable Medicinal Fungi in the world, and it requires host insects in family Hepialidae (Lepidoptera) to complete its life cycle. However, the genetic diversity and phylogeographic structures of the host insects remain to be explored. We analyzed the genetic diversity and temporal and spatial distribution patterns of genetic variation of the host insects throughout the O. sinensis distribution. Abundant haplotype and nucleotide diversity mainly existed in the areas of Nyingchi, ShangriLa, and around the edge of the Qinghai-Tibet Plateau, where are considered as the diversity center or micro-refuges of the host insects of O. sinensis. However, there was little genetic variation among host insects from 72.1% of all populations, indicating that the host species composition might be relatively simple in large-scale O. sinensis populations. All host insects are monophyletic except for those from four O. sinensis populations around Qinghai Lake. Significant phylogeographic structure (NST>GST, P
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high diversity of the fungal community structure in naturally occurring ophiocordyceps sinensis
PLOS ONE, 2010Co-Authors: Yongjie Zhang, Shu Zhang, Mu Wang, Fengyan Bai, Xingzhong LiuAbstract:Background Ophiocordyceps sinensis (syn. Cordyceps sinensis), which is a parasite of caterpillars and is endemic to alpine regions on the Tibetan Plateau, is one of the most valuable Medicinal Fungi in the world. “Natural O. sinensis specimens” harbor various other Fungi. Several of these other Fungi that have been isolated from natural O. sinensis specimens have similar chemical components and/or pharmaceutical effects as O. sinensis. Nevertheless, the mycobiota of natural O. sinensis specimens has not been investigated in detail. Methodology/Principal Findings Based on the technique of PCR-single-strand conformation polymorphism (PCR-SSCP), the mycobiota of three different sections (stromata, sclerotia, and mycelial cortices) from natural O. sinensis specimens were investigated using both culture-dependent and -independent methods. For the culture-dependent method, 572 fungal strains were isolated, and 92 putative operational taxonomic units (OTUs) were identified from 226 sequenced strains with the threshold of 97%. For the culture-independent method, 490 fungal clones were identified from about 3000 clones of ITS fragments from the whole-community DNA; based on PCR-SSCP analyses, 266 of these clones were selected to be sequenced, and 118 putative OTUs were detected. The overwhelming majority of isolates/clones and OTUs were detected from mycelial cortices; only a few were detected from stromata and sclerotia. The most common OTUs detected with both methods belonged to Ascomycota; however, only 13 OTUs were detected simultaneously by both methods. Potential novel lineages were detected by each of the two methods. Conclusions/Significance A great number of fungal species present in the mycobiota of naturally-occurring O. sinensis specimens were detected, and many of them may represent undescribed lineages. That only a few of the same OTUs were detected by both methods indicated that different methods should be used. This study increased our understanding about the fungal community structure of this valuable Medicinal herb.
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genetic diversity of ophiocordyceps sinensis a Medicinal fungus endemic to the tibetan plateau implications for its evolution and conservation
BMC Evolutionary Biology, 2009Co-Authors: Yongjie Zhang, Xingzhong Liu, Shu Zhang, Mu Wang, Yinglan GuoAbstract:Background Ophiocordyceps sinensis (syn. Cordyceps sinensis), endemic to alpine regions on the Tibetan plateau, is one of the most valuable Medicinal Fungi in the world. Huge commercial demand has led to excessive harvest and a dramatic decline in its numbers. The diversity of terrains and climates on the Tibetan Plateau and the broad insect host range (more than 50 species in the family Hepialidae) may have resulted in substantial intraspecific genetic diversity for this fungus. The objective of this study was to evaluate the population distribution of O. sinensis from geographically diverse regions of the Tibetan Plateau based on nrDNA ITS and MAT1-2-1 gene sequences. Understanding of the genetic diversity and genesis of O. sinensis will provide important information for the evolution and conservation of this fungus.
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genetic diversity of ophiocordyceps sinensis a Medicinal fungus endemic to the tibetan plateau implications for its evolution and conservation
BMC Evolutionary Biology, 2009Co-Authors: Yongjie Zhang, Xingzhong Liu, Shu Zhang, Mu Wang, Yinglan GuoAbstract:Ophiocordyceps sinensis (syn. Cordyceps sinensis), endemic to alpine regions on the Tibetan plateau, is one of the most valuable Medicinal Fungi in the world. Huge commercial demand has led to excessive harvest and a dramatic decline in its numbers. The diversity of terrains and climates on the Tibetan Plateau and the broad insect host range (more than 50 species in the family Hepialidae) may have resulted in substantial intraspecific genetic diversity for this fungus. The objective of this study was to evaluate the population distribution of O. sinensis from geographically diverse regions of the Tibetan Plateau based on nrDNA ITS and MAT1-2-1 gene sequences. Understanding of the genetic diversity and genesis of O. sinensis will provide important information for the evolution and conservation of this fungus. Significant sequence variations in the ITS and MAT1-2-1 genes (27 and 23 informative sites, eight and seven haplotypes, respectively) were observed. Phylogenetic analysis based on ITS sequences, MAT1-2-1 sequences, or their combined data set, clustered isolates from northern regions in one clade (clade I), whereas isolates from southern regions were dispersed in all four clades (clade I-IV). Single-strand conformation polymorphism (SSCP) analyses of 2639 ITS clones from seven samples revealed 91 different SSCP patterns that were subsequently sequenced. ITS heterogeneity was found in XZ-LZ07-H1 (Nyingchi population), and 17 informative sites and five haplotypes were detected from 15 clones. The five haplotypes clustered into three clades (clade I, II, and IV). Significant genetic divergence in O. sinensis was observed and the genetic diversification was greater among southern isolates than that among northern isolates. The polymorphism of nrDNA ITS sequences suggested that O. sinensis spread from a center of origin (the Nyingchi District) to southern regions and subsequently to northern areas. These results suggest that southern populations are important reservoirs of genetic diversity and should be taken into account in conservation programs.
Yinglan Guo - One of the best experts on this subject based on the ideXlab platform.
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genetic diversity of ophiocordyceps sinensis a Medicinal fungus endemic to the tibetan plateau implications for its evolution and conservation
BMC Evolutionary Biology, 2009Co-Authors: Yongjie Zhang, Xingzhong Liu, Shu Zhang, Mu Wang, Yinglan GuoAbstract:Background Ophiocordyceps sinensis (syn. Cordyceps sinensis), endemic to alpine regions on the Tibetan plateau, is one of the most valuable Medicinal Fungi in the world. Huge commercial demand has led to excessive harvest and a dramatic decline in its numbers. The diversity of terrains and climates on the Tibetan Plateau and the broad insect host range (more than 50 species in the family Hepialidae) may have resulted in substantial intraspecific genetic diversity for this fungus. The objective of this study was to evaluate the population distribution of O. sinensis from geographically diverse regions of the Tibetan Plateau based on nrDNA ITS and MAT1-2-1 gene sequences. Understanding of the genetic diversity and genesis of O. sinensis will provide important information for the evolution and conservation of this fungus.
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genetic diversity of ophiocordyceps sinensis a Medicinal fungus endemic to the tibetan plateau implications for its evolution and conservation
BMC Evolutionary Biology, 2009Co-Authors: Yongjie Zhang, Xingzhong Liu, Shu Zhang, Mu Wang, Yinglan GuoAbstract:Ophiocordyceps sinensis (syn. Cordyceps sinensis), endemic to alpine regions on the Tibetan plateau, is one of the most valuable Medicinal Fungi in the world. Huge commercial demand has led to excessive harvest and a dramatic decline in its numbers. The diversity of terrains and climates on the Tibetan Plateau and the broad insect host range (more than 50 species in the family Hepialidae) may have resulted in substantial intraspecific genetic diversity for this fungus. The objective of this study was to evaluate the population distribution of O. sinensis from geographically diverse regions of the Tibetan Plateau based on nrDNA ITS and MAT1-2-1 gene sequences. Understanding of the genetic diversity and genesis of O. sinensis will provide important information for the evolution and conservation of this fungus. Significant sequence variations in the ITS and MAT1-2-1 genes (27 and 23 informative sites, eight and seven haplotypes, respectively) were observed. Phylogenetic analysis based on ITS sequences, MAT1-2-1 sequences, or their combined data set, clustered isolates from northern regions in one clade (clade I), whereas isolates from southern regions were dispersed in all four clades (clade I-IV). Single-strand conformation polymorphism (SSCP) analyses of 2639 ITS clones from seven samples revealed 91 different SSCP patterns that were subsequently sequenced. ITS heterogeneity was found in XZ-LZ07-H1 (Nyingchi population), and 17 informative sites and five haplotypes were detected from 15 clones. The five haplotypes clustered into three clades (clade I, II, and IV). Significant genetic divergence in O. sinensis was observed and the genetic diversification was greater among southern isolates than that among northern isolates. The polymorphism of nrDNA ITS sequences suggested that O. sinensis spread from a center of origin (the Nyingchi District) to southern regions and subsequently to northern areas. These results suggest that southern populations are important reservoirs of genetic diversity and should be taken into account in conservation programs.