Metatranscriptomics analysis of the fruiting caterpillar fungus collected from the Qinghai-Tibetan plateau

Zhang, Siwei; Cen, Kai; Liu, Yan; Zhuo, Xuan-Wei; Wang, Chengshu

doi:10.1360/n052017-00253

Cited by 5 publications

(7 citation statements)

References 21 publications

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“…There are some shortcomings in these investigations, such as limitations in sampling point, technique level and analysis method, etc. Recently, meta-transcriptomics analysis of Chinese Cordyceps demonstrated that massive transcriptions of the Class I type of retrotransposons and Class II type of DNA transposons were contributing to environmental adaptation of Chinese Cordyceps, active expression of these transposable elements (TEs) could drive the rapid evolution of fungal genomes [15]. Based on the above-mentioned results, it is difficult to assess the diversity of complex bacterial communities in Chinese Cordyceps and its microhabitat soil because of the limitations of the investigation methods and sampling points.…”

Section: Discussionmentioning

confidence: 99%

“…In recent years, a lot of work revolved around the microorganism communities living in Chinese Cordyceps was conducted. The fungal community associated with Chinese Cordyceps had been described by a number of cultures-dependent and independent methods [9–15]. In spite of we reported that there were multiple fungi and bacteria inhibiting Chinese Cordyceps and its microhabitat [10].…”

Section: Introductionmentioning

confidence: 99%

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Composition and predictive functional analysis of bacterial communities inhabiting Chinese Cordyceps insight into conserved core microbiome

et al. 2019

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Background Over the past few decades, most attention to Chinese Cordyceps-associated endogenous microorganism was focused on the fungal community that creates critical bioactive components. Bacterial community associated with Chinese Cordyceps has been previously described; however, most studies were only presenting direct comparisons in the Chinese Cordyceps and its microenvironments. In the current study, our objectives were to reveal the bacterial community structure composition and predict their function. Results We collected samples of Chinese Cordyceps from five sites located in the Qinghai-Tibet Plateau and used a high throughput sequencing method to compare Chinese Cordyceps-associated bacterial community composition and diversity quantitatively across sites. The results indicated that for the Chinese Cordyceps-associated bacterial community there is no single core microbiome, which was dominated by the both Proteobacteria and Actinobacteria. Predictive functional profiling suggested a location specific function pattern for Chinese Cordyceps and bacteria in the external mycelial cortices involved in the biosynthesis of active constituents. Conclusions This study is firstly used high throughput sequencing method to compare the bacterial communities inhabiting Chinese Cordyceps and its microhabitat and to reveal composition functional capabilities of the bacteria, which will accelerate the study of the functions of bacterial communities in the micro-ecological system of Chinese Cordyceps. Electronic supplementary material The online version of this article (10.1186/s12866-019-1472-0) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Composition and predictive functional analysis of bacterial communities inhabiting Chinese Cordyceps insight into conserved core microbiome

et al. 2019

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“…Table 5 shows 6 examples of shotgun reads of SRX2718557 aligned with the 5.8S sequences of O. sinensis genotypes, Paecilomyces hepiali , Tolypocladium sinensis (Group D), and an AB067719-type Group-E fungus (Stensrud et al 2007). The high homology between the shotgun reads and the various 5.8S gene sequences of O. sinensis genotypes may not conclusively identify their fungal sources in natural C. sinensis , which contains >90 species spanning at least 37 fungal genera (Zhang et al 2010, 2018; Xiang et al 2014; Xia et al 2015, 2017).…”

Section: The Resultsmentioning

confidence: 99%

“…2010; Xia et al . 2015; Zhang et al . 2018), with differential co-occurrence of some of 17 Ophiocordyceps sinensis genotypes in different compartments of natural C. sinensis (Engh 1999; Kinjo and Zang 2001; Chen et al .…”

Section: Introductionmentioning

confidence: 99%

Genetic and phylogenetic features of the repetitive ITS copies in theHirsutella sinensisgenome and the genomically independent AT-biasedOphiocordyceps sinensisgenotypes

Wang

Zhu

2022

Preprint

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Li et al. (2013, 2020b) hypothesized that AT-biased genotypes of Ophiocordyceps sinensis are generated through repeat-induced point mutation (RIP) and exist as ITS pseudogenes in a single genome of GC-biased Genotype #1 Hirsutella sinensis. This study revealed multiple GC-biased repetitive ITS copies in the H. sinensis genome, including multiple insertion/deletion and transversion alleles, which might not be generated through RIP mutagenesis that theoretically causes C-to-T and G-to-A transitions. The repetitive ITS copies are genetically and phylogenetically distinct from the AT-biased genotypes of O. sinensis, which possess multiple scattered transition alleles. The sequences of GC- and AT-biased Genotypes #2-17 were absent in the genome assemblies ANOV00000000, JAAVMX000000000, LKHE00000000, LWBQ00000000 and NGJJ00000000 of H. sinensis strains but instead in the genomes of independent O. sinensis fungi. The GC- and AT-biased genotypes of O. sinensis were found to differentially occur in different combinations in different compartments of natural Cordyceps sinensis. Their abundances were dynamically altered in an asynchronous, disproportional manner during C. sinensis maturation. Metatranscriptomic analysis of natural C. sinensis revealed transcriptional silencing of the 5.8S genes of all C. sinensis-colonizing fungi, including H. sinensis. The problematic design of the 5.8S gene transcription assay and data analysis reported by Li et al. (2013) have provided controversial and incomplete evidence to support the notion that the 5.8S genes of AT-biased genotypes of O. sinensis are permanently nonfunctional ITS pseudogenes. These results demonstrate the genomic independence of 17 genotypes belonging to independent O. sinensis fungi. In parallel with GC-biased genotypes, AT-biased O. sinensis genotypes might have been generated during the long history of evolution from a common ancestor through RIP or other mutagenesis mechanisms in response to the extremely harsh environment of the Qinghai-Tibet Plateau.

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“…However, low mummification rates and inconsistent fruiting body development are still major problems that affect artificial cultivation [ 8 ]. Consequently, many researchers have focused on fruiting body formation [ 7 , 9 ] and the influence of environmental factors (such as temperature and light) on fruiting body development [ 10 , 11 ].…”

Section: Introductionmentioning

confidence: 99%

Stable reference gene selection for Ophiocordyceps sinensis gene expression studies under different developmental stages and light-induced conditions

Tong

Wei

Mao³

et al. 2023

PLoS ONE

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The molecular mechanism of Chinese cordyceps formation has received a substantial amount of attention because of its usage as traditional Chinese medicine. The formation process of Chinese cordyceps includes two parts: asexual proliferation (Ophiocordyceps sinensis proliferates in the hemolymph of Thitarodes armoricanus larvae) and sexual development (formation and development of fruiting bodies). Therefore, validation of reference genes under different development stages and experimental conditions is crucial for RT-qPCR analysis. However, there is no report on stable reference genes at the development stage of O. sinensis fruiting body. In this study, 10 candidate reference genes, Actin, Cox5, Tef1, Ubi, 18s, Gpd, Rpb1, Try, Tub1 and Tub2, were selected and calculated their expression stability using four methods: geNorm, NormFinder, BestKeeper, and Comparative △Ct. After comprehensive analysis of the results of these four methods with RefFinder, we determined that the most stable reference genes during asexual reproduction of O. sinensis were Tef1 and Tub1, while the most stable reference genes during fruiting body development were Tyr and Cox5, and the most stable reference genes under light-induced conditions were Tyr and Tef1. Our study provides a guidance for reference genes selections at different proliferation processes with light stress of O. sinensis, and represents a foundation for studying the molecular mechanism of Chinese cordyceps formation.

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Metatranscriptomics analysis of the fruiting caterpillar fungus collected from the Qinghai-Tibetan plateau

Cited by 5 publications

References 21 publications

Composition and predictive functional analysis of bacterial communities inhabiting Chinese Cordyceps insight into conserved core microbiome

Composition and predictive functional analysis of bacterial communities inhabiting Chinese Cordyceps insight into conserved core microbiome

Genetic and phylogenetic features of the repetitive ITS copies in theHirsutella sinensisgenome and the genomically independent AT-biasedOphiocordyceps sinensisgenotypes

Stable reference gene selection for Ophiocordyceps sinensis gene expression studies under different developmental stages and light-induced conditions

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