Dataset Information

A New High-Quality Draft Genome Assembly of the Chinese Cordyceps Ophiocordyceps sinensis.

ABSTRACT: Ophiocordyceps sinensis (Berk.) is an entomopathogenic fungus endemic to the Qinghai-Tibet Plateau. It parasitizes and mummifies the underground ghost moth larvae, then produces a fruiting body. The fungus-insect complex, called Chinese cordyceps or "DongChongXiaCao," is not only a valuable traditional Chinese medicine, but also a major source of income for numerous Himalayan residents. Here, taking advantage of rapid advances in single-molecule sequencing, we assembled a highly contiguous genome assembly of O. sinensis. The assembly of 23 contigs was ∼110.8 Mb with a N50 length of 18.2 Mb. We used RNA-seq and homologous protein sequences to identify 8,916 protein-coding genes in the IOZ07 assembly. Moreover, 63 secondary metabolite gene clusters were identified in the improved assembly. The improved assembly and genome features described in this study will further inform the evolutionary study and resource utilization of Chinese cordyceps.

SUBMITTER: Shu R

PROVIDER: S-EPMC7486949 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

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A New High-Quality Draft Genome Assembly of the Chinese Cordyceps Ophiocordyceps sinensis.

Shu Ruihao R Zhang Jihong J Meng Qian Q Zhang Huan H Zhou Guiling G Li Miaomiao M Wu Peipei P Zhao Yanni Y Chen Chao C Qin Qilian Q

Genome biology and evolution 20200701 7

Ophiocordyceps sinensis (Berk.) is an entomopathogenic fungus endemic to the Qinghai-Tibet Plateau. It parasitizes and mummifies the underground ghost moth larvae, then produces a fruiting body. The fungus-insect complex, called Chinese cordyceps or "DongChongXiaCao," is not only a valuable traditional Chinese medicine, but also a major source of income for numerous Himalayan residents. Here, taking advantage of rapid advances in single-molecule sequencing, we assembled a highly contiguous genom ...[more]

PMID: 32579174

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Project description:ObjectiveTo examine the differential occurrence of Ophiocordyceps sinensis genotypes in the stroma, stromal fertile portion (SFP) densely covered with numerous ascocarps, and ascospores of natural Cordyceps sinensis.MethodsImmature and mature C. sinensis specimens were harvested. Mature C. sinensis specimens were continuously cultivated in our laboratory (altitude 2,200 m). The SFPs (with ascocarps) and ascospores of C. sinensis were collected for microscopic and molecular analyses using species-/genotype-specific primers. Sequences of mutant genotypes of O. sinensis were aligned with that of Genotype #1 Hirsutella sinensis and compared phylogenetically using a Bayesian majority-rule method.ResultsFully and semiejected ascospores were collected from the same specimens. The semiejected ascospores tightly adhered to the surface of the asci as observed by the naked eye and under optical and confocal microscopies. The multicellular heterokaryotic ascospores showed uneven staining of nuclei. The immature and mature stromata, SFPs (with ascocarps) and ascospores were found to differentially contain several GC- and AT-biased genotypes of O. sinensis, Samsoniella hepiali, and an AB067719-type fungus. The genotypes within AT-biased Cluster-A in the Bayesian tree occurred in all compartments of C. sinensis, but those within AT-biased Cluster-B were present in immature and mature stromata and SPFs but absent in the ascospores. Genotype #13 of O. sinensis was present in semi-ejected ascospores and Genotype #14 in fully ejected ascospores. GC-biased Genotypes #13-14 featured large DNA segment substitutions and genetic material recombination between the genomes of the parental fungi (H. sinensis and the AB067719-type fungus). These ascosporic offspring genotypes combined with varying abundances of S. hepiali in the 2 types of ascospores participated in the control of the development, maturation and ejection of the ascospores.ConclusionMultiple genotypes of O. sinensis coexist differentially in the stromata, SFPs and 2 types of C. sinensis ascospores, along with S. hepiali and the AB067719-type fungus. The fungal components in different combinations and their dynamic alterations in the compartments of C. sinensis during maturation play symbiotic roles in the lifecycle of natural C. sinensis.

Project description:ObjectiveTo examine multiple genotypes of Ophiocordyceps sinensis in a semi-quantitative manner in the stromal fertile portion (SFP) densely covered with numerous ascocarps and ascospores of natural Cordyceps sinensis and to outline the dynamic alterations of the coexisting O. sinensis genotypes in different developmental phases.MethodsMature Cordyceps sinensis specimens were harvested and continuously cultivated in our laboratory (altitude 2,254 m). The SFPs (with ascocarps) and fully and semi-ejected ascospores were collected for histological and molecular examinations. Biochip-based single nucleotide polymorphism (SNP) MALDI-TOF mass spectrometry (MS) was used to genotype multiple O. sinensis mutants in the SFPs and ascospores.ResultsMicroscopic analysis revealed distinct morphologies of the SFPs (with ascocarps) before and after ascospore ejection and SFP of developmental failure, which, along with the fully and semi-ejected ascospores, were subjected to SNP MS genotyping analysis. Mass spectra showed the coexistence of GC- and AT-biased genotypes of O. sinensis that were genetically and phylogenetically distinct in the SFPs before and after ejection and of developmental failure and in fully and semi-ejected ascospores. The intensity ratios of MS peaks were dynamically altered in the SFPs and the fully and semi-ejected ascospores. Mass spectra also showed transversion mutation alleles of unknown upstream and downstream sequences with altered intensities in the SFPs and ascospores. Genotype #5 of AT-biased Cluster-A maintained a high intensity in all SFPs and ascospores. An MS peak with a high intensity containing AT-biased Genotypes #6 and #15 in pre-ejection SFPs was significantly attenuated after ascospore ejection. The abundance of Genotypes #5‒6 and #16 of AT-biased Cluster-A was differentially altered in the fully and semi-ejected ascospores that were collected from the same Cordyceps sinensis specimens.ConclusionMultiple O. sinensis genotypes coexisted in different combinations with altered abundances in the SFPs prior to and after ejection, the SFP of developmental failure, and the two types of ascospores of Cordyceps sinensis, demonstrating their genomic independence. Metagenomic fungal members present in different combinations and with dynamic alterations play symbiotic roles in different compartments of natural Cordyceps sinensis.

Project description:Chinese cordyceps (GL) is a traditional medicinal fungus, with Ophiocordyceps sinensis (O. sinensis, BL) and Paecilomyces hepiali (P. hepiali, JSB) being fungi isolated from wild Chinese cordyceps. These three species share similar chemical composition and pharmacological effects. Existing studies have primarily compared the metabolites of Chinese cordyceps and O. sinensis, overlooking the assessment of antioxidant capacity in Chinese cordyceps, P. hepiali, and O. sinensis. In this study, LC-MS/MS was employed to analyze metabolites in GL, JSB, and BL. Utilizing principal component analysis (PCA), supervised orthogonal partial least squares discriminant analysis (OPLS-DA), and hierarchical cluster analysis (HCA), it was observed that the majority of differential metabolites (DMs) primarily accumulated in organic acids and derivatives, lipids and lipid-like molecules, and organoheterocyclic compounds. Antioxidant activity analysis indicated that GL exhibited the higher 2,2-diphenyl-1-picrylhydrazyl radical scavenging ability (DPPH•, scavenging rate is 81.87 ± 0.97%), hydroxyl free radical scavenging capacity (•OH, scavenging rate is 98.10 ± 0.60%), and superoxide anion radical scavenging capacity (O2•-, scavenging rate is 69.74 ± 4.36%), while JSB demonstrated the higher FRAP total antioxidant capacity of 8.26 μmol Trolox/g (p < 0.05). Correlation analysis revealed a positive correlation between DMs (fatty acyls and amino acids) and DPPH•, FRAP, •OH, and O2•- (p < 0.05). Additionally, glycerophospholipid DMs were found to be positively correlated with FRAP (p < 0.05). Through KEGG pathway analysis, it was determined that the accumulation of DMs in pathways such as cutin, suberine and wax biosynthesis has a higher impact on influencing the antioxidant activity of the samples. These results shed light on the antioxidant capacity and metabolic characteristics of Chinese cordyceps and its substitutes and offer valuable insights into how different DMs impact the strength of antioxidant activity, aiding in the advancement and application of Chinese cordyceps and its substitutes.

Dataset Information

A New High-Quality Draft Genome Assembly of the Chinese Cordyceps Ophiocordyceps sinensis.

Publications

A New High-Quality Draft Genome Assembly of the Chinese Cordyceps Ophiocordyceps sinensis.

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