De novo assembly and transcriptome analysis of sclerotial development in Wolfiporia cocos

Wu, Yayun; Zhu, Wenjun; Wei, Wei; Zhao, Xiaolong; Wang, Qi; Zeng, Wanyong; Zheng, Yanyan; Chen, Ping; Zhang, Shaopeng

doi:10.1016/j.gene.2016.05.020

Cited by 18 publications

(10 citation statements)

References 40 publications

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“…It was found that the types of SSR in W. cocos were rich and had high polymorphism potential. Wu et al [20] sequenced the transcriptome of early, middle, and mature stages of W. cocos sclerotia and found that gene expression patterns in the mature stage were significantly different from those in the other two stages. Shu et al [21] sequenced the transcriptome on mycelia and sclerotia of W. cocos and revealed that triterpenoids were only derived from the mevalonate pathway (MVA), and found that diphosphomevalonate decarboxylase (MVD), farnesyl diphosphate synthase (FDPS), hydroxymethyl glutaryl coenzyme A reductase (HMGCR), and lanosterol synthase (ERG7) gene expression was upregulated in the hyphal stage, and it was speculated that these genes were involved in triterpenoid biosynthesis in the hyphal stage.…”

Section: Introductionmentioning

confidence: 99%

Comparative Analysis of the Characteristics of Triterpenoid Transcriptome from Different Strains of Wolfiporia cocos

GuiPing

Zhao

2019

IJMS

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The dried sclerotia of Wolfiporia cocos (Schwein.) Ryvarden & Gilb., a traditional Chinese medicine, has triterpenoid as its main active component. Breeding high-yield triterpenoid in W. cocos is an important research topic at present. We screened out two monosporal strains from the same W. cocos 5.78, high-yielding DZAC-Wp-H-29 (H) and low-yielding DZAC-Wp-L-123 (L), and cultured mycelia for 17 days, 34 days, and 51 days, respectively. Transcriptome analysis results showed that triterpenoid synthesis is closely related to gene expression in triterpenoid synthesis pathways (hydroxymethyl glutaryl-CoA reductase (HMGCR), farnesyl diphosphate synthase (FDPS), 4-hydroxybenzoate polyprenyltransferase (COQ2), C-8 sterol isomerase (ERG2), sterol O-acyltransferase (ACAT), tyrosine aminotransferase (TAT), torulene dioxygenase (CAO2), and sterol-4alpha-carboxylate 3-dehydrogenase (erg26)), and is limited by the expression of enzyme M20 combined with domain protein peptide (Pm20d2), aryl-alcohol dehydrogenase (norA), ISWI chromatin-remodeling complex ATPase ISW2, GroES-like protein (adh), cytochrome P450 (ftmP450-1), and unknown proteins unigene0001029 and unigene0011374. In addition, maintaining high triterpenoid accumulation in W. cocos may require a stable membrane structure, so the accumulation ability may be related to the high synthesis ability of sterols. The low accumulation of triterpenoid in W. cocos may be due to the products of key enzymes increasing flow to other pathways.

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Section: Introductionmentioning

confidence: 99%

Comparative Analysis of the Characteristics of Triterpenoid Transcriptome from Different Strains of Wolfiporia cocos

GuiPing

Zhao

2019

IJMS

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“…Genes related to the oxidation-reduction process were differentially expressed during sclerotium formation in P. tuber-regium . Oxidation -reduction–related genes were differentially expressed in mycelium vs. sclerotium production in other mushroom-producing species, such as Polyporus umbellatus , W. cocos , and L. rhinocerotis ( Song et al, 2014 ; Yap et al, 2015 ; Wu et al, 2016 ; Li et al, 2017 ). The molecular mechanisms controlling sclerotium formation might include oxidative stress, signal transduction, and gene expression regulation ( Sun et al, 2020 ).…”

Section: Resultsmentioning

confidence: 99%

Genome and Comparative Transcriptome Dissection Provide Insights Into Molecular Mechanisms of Sclerotium Formation in Culinary-Medicinal Mushroom Pleurotus tuber-regium

Sun

Zhang

et al. 2022

Front. Microbiol.

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Pleurotus tuber-regium is an edible and medicinal sclerotium-producing mushroom. The sclerotia of this mushroom also serve as food and folk medicine. Based on the description of its monokaryon genome, sequenced with Illumina and PacBio sequencing technologies, comparative transcriptomic analysis using RNA sequencing (RNA-seq) was employed to study its mechanism of sclerotium formation. The de novo assembled genome is 35.82 Mb in size with a N50 scaffold size of 4.29 Mb and encodes 12,173 putative proteins. Expression analysis demonstrated that 1,146 and 1,249 genes were upregulated and downregulated with the formation of sclerotia, respectively. The differentially expressed genes were associated with substrate decomposition, the oxidation-reduction process, cell wall synthesis, and other biological processes in P. tuber-regium. These genomic and transcriptomic resources provide useful information for the mechanism underlying sclerotium formation in P. tuber-regium.

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“…Although sclerotial development has recently been studied ( Wu et al, 2016 ; Zhang et al, 2016 ), the mechanisms of sclerotial development and W. cocos -pine wood interactions remain largely unknown. This paucity of knowledge is also the case particularly for sclerotogenesis, which is regulated via PK signaling pathways.…”

Section: Discussionmentioning

confidence: 99%

The Kinome of Edible and Medicinal Fungus Wolfiporia cocos

et al. 2016

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Wolfiporia cocos is an edible and medicinal fungus that grows in association with pine trees, and its dried sclerotium, known as Fuling in China, has been used as a traditional medicine in East Asian countries for centuries. Nearly 10% of the traditional Chinese medicinal preparations contain W. cocos. Currently, the commercial production of Fuling is limited because of the lack of pine-based substrate and paucity of knowledge about the sclerotial development of the fungus. Since protein kinase (PKs) play significant roles in the regulation of growth, development, reproduction, and environmental responses in filamentous fungi, the kinome of W. cocos was analyzed by identifying the PKs genes, studying transcript profiles and assigning PKs to orthologous groups. Of the 10 putative PKs, 11 encode atypical PKs, and 13, 10, 2, 22, and 11 could encoded PKs from the AGC, CAMK, CK, CMGC, STE, and TLK Groups, respectively. The level of transcripts from PK genes associated with sclerotia formation in the mycelium and sclerotium stages were analyzed by qRT-PCR. Based on the functions of the orthologs in Sclerotinia sclerotiorum (a sclerotia-formation fungus) and Saccharomyces cerevisiae, the potential roles of these W. cocos PKs were assigned. To the best of our knowledge, our study is the first identification and functional discussion of the kinome in the edible and medicinal fungus W. cocos. Our study systematically suggests potential roles of W. cocos PKs and provide comprehensive and novel insights into W. cocos sclerotial development and other economically important traits. Additionally, based on our result, genetic engineering can be employed for over expression or interference of some significant PKs genes to promote sclerotial growth and the accumulation of active compounds.

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De novo assembly and transcriptome analysis of sclerotial development in Wolfiporia cocos

Cited by 18 publications

References 40 publications

Comparative Analysis of the Characteristics of Triterpenoid Transcriptome from Different Strains of Wolfiporia cocos

Comparative Analysis of the Characteristics of Triterpenoid Transcriptome from Different Strains of Wolfiporia cocos

Genome and Comparative Transcriptome Dissection Provide Insights Into Molecular Mechanisms of Sclerotium Formation in Culinary-Medicinal Mushroom Pleurotus tuber-regium

The Kinome of Edible and Medicinal Fungus Wolfiporia cocos

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