<i>De novo</i> transcriptome sequencing of <i>Flammulina velutipes</i> uncover candidate genes associated with cold‐induced fruiting

Wu, Tuheng; Ye, Zhi‐Wei; Guo, Li‐Qiong; Yang, Xueqin; Lin, Jizhen

doi:10.1002/jobm.201800037

Cited by 9 publications

(8 citation statements)

References 33 publications

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“…The development of genomic and transcriptomic sequencing technologies has provided the powerful tools to understand the biology of edible mushrooms, including the effective utilization of cultivation substrates (lignocellulose) [28,29], the mechanism of fruiting body formation and development and adaption to adverse environments, such as high temperature environments or cold-stress conditions [30][31][32]. For example, genome sequencing of the cultivars of F. velutipes from Korea and Japan revealed their high capacity for lignocellulose degradation [28,33].…”

Section: F Filiformis Is One Of the Most Important And Popular Ediblmentioning

confidence: 99%

Genome-wide analysis and prediction of genes involved in the biosynthesis of polysaccharides and bioactive secondary metabolites in high-temperature-tolerant of wild Flammulina filiformis

Chen

Tang

et al. 2019

Preprint

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Background: Flammulina filiformis (=Asian “F.velutipes”) is a popular commercial edible mushroom. Many bioactive compounds with medicinal effects, such as polysaccharides and sesquiterpenoids, have been isolated and identified from F. filiformis, but their biosynthesis and regulation at the molecular level remains unclear. In this study, we sequenced the genome of the wild strain F. filiformis Liu355, predicated its the biosynthetic gene clusters (BGCs) and profiled the expression of these genes in wild and cultivar strains and in different developmental stages of the wild F. filiformis strain by a comparative transcriptomic analysis. Results: We found that the genome of the F. filiformis was 35.01 M bp in length and harbored 10396 gene models. Thirteen putative terpenoid gene clusters were predicted and 12 sesquiterpene synthase genes belonging to four different groups and two type I polyketide synthase gene clusters were identified in the F. filiformis genome. The number of genes related to terpenoid biosynthesis was higher in the wild strain (119 genes) than in the cultivar strain (81 genes). Most terpenoid biosynthesis genes were upregulated in the primordium and fruiting body of the wild strain, while the polyketide synthase genes were generally upregulated in the mycelium of the wild strain. Moreover, genes encoding UDP-glucose pyrophosphorylase and UDP-glucose dehydrogenase, which are involved in polysaccharide biosynthesis, had relatively high transcript levels both in the mycelium and fruiting body of the wild F. filiformis strain. Conclusions: F. filiformis is enriched in a number of gene clusters involved in the biosynthesis of polysaccharides and terpenoid bioactive compounds and these genes usually display differential expression between wild and cultivar strains, even in different developmental stages. This study expands our knowledge of the biology of F. filiformis and provides valuable data for elucidating the regulation of secondary metabolites in this unique F. filiformis strain.

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Section: F Filiformis Is One Of the Most Important And Popular Ediblmentioning

confidence: 99%

Genome-wide analysis and prediction of genes involved in the biosynthesis of polysaccharides and bioactive secondary metabolites in high-temperature-tolerant of wild Flammulina filiformis

Chen

Tang

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…Development of "omic" technology provided the powerful tools to understand the biology of edible mushroom including effective utilization for cultivation substrate (lignocellulose) [28,29], the mechanism of fruiting body's formation and development and adaption for environment such as high temperature or cold stress [30,31,32]. For example, genome sequencing of the cultivars of F.velutipes from Korea and Japan revealed the high capacity for lignocellulose degradation [28,33].…”

Section: F Filiformis Is One Of the Most Important And Popular Ediblmentioning

confidence: 99%

“…Transcriptomic sequencing revealed that histidine kinase and proteins involved in MAPK pathway (e.g. STE protein kinase, MAPK kinase kinase) and Ca 2+ signal transduction pathway (calcium-dependent protein kinase) were differentially expressed in F. velutipes [31].…”

Section: Heat Shock Protein Correspond To Temperature Change In F Fimentioning

confidence: 99%

Genomic-wide analysis and prediction of genes involved in biosynthesis of polysaccharide and bioactive secondary metabolites in high-temperature-tolerance of wild Flammulina filiformis

Chen

Tang

et al. 2019

Preprint

View full text Add to dashboard Cite

Background: Flammulina filiformis (=Asian “F.velutipes”) is a popular commercial edible mushroom. Many bioactive compounds such as polysaccharides and sesquiterpenoids with medicinal effects have been isolated and identified, but their biosynthesis and regulation in molecular level is unclear. In this study, we sequenced the genome of the wild strain F. filiformis Liu 355, predicated the biosynthetic gene clusters (BGCs) and profiled these genes expression between wild and cultivar strains and among different development stages of the wild strain of F. filiformis by a comparative transcriptomic analysis. Results: The results revealed that the genome of the F. filiformis was 35.01 M bp in length and annotated with 10396 gene models. 12 putative terpeniod gene clusters were predicted, 12 sesquiterpenes synthase genes belonged to four different groups and two type I PKS (polyketide synthase) gene clusters were identified from F. filiformis genome. The gene number related terpeniod biosynthesis is higher in wild strain (119 genes) than cultivar strain (81 genes) and most of them are up regulated in primodium and fruiting body of the wild strain, while PKS genes are usually up-regulated in the mycelium of wild strain. Moreover, genes encoding UDP-glucose pyrophosphorylase and UDP-glucose dehydrogenase involved in polysaccharide biosynthesis have relative high transcripts both in mycelium and fruiting bodies of F. filiformis. Conclusions: We identified candidate genes involved in the biosynthesis of polysaccharide and terpenoid bioactive compounds and profiled these genes expression during the development of F. filiformis. This study expends our knowledge for understanding the biology of F. filiformis and provides valuable data for elucidating the secondary metabolism regulation of the special strain of F. filiformis.

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“…Flammulina filiformis is not only a widely cultivated mushroom in East Asia, but also one of the five largest industrially cultivated mushrooms in the world [ 32 ]. It can be used as an ideal research material, due to its short growth cycle and simple cultivation method, and the availability of transcriptomic data and genome at different developmental stages [ 33 , 34 ].…”

Section: Introductionmentioning

confidence: 99%

Transcription factor FfMYB15 regulates the expression of cellulase gene FfCEL6B during mycelial growth of Flammulina filiformis

et al. 2022

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Background Cellulose degradation can determine mycelial growth rate and affect yield during the growth of Flammulina filiformis. The degradation of cellulose requires the joint action of a variety of cellulases, and some cellulase-related genes have been detected in mushrooms. However, little is known about the transcriptional regulatory mechanisms of cellulose degradation. Results In this study, FfMYB15 that may regulate the expression of cellulase gene FfCEL6B in F. filiformis was identified. RNA interference (RNAi) showed that FfCEL6B positively regulated mycelial growth. Gene expression analyses indicated that the expression patterns of FfCEL6B and FfMYB15 in mycelia cultured on the 0.9% cellulose medium for different times were similar with a correlation coefficient of 0.953. Subcellular localization and transcriptional activity analyses implied that FfMYB15 was located in the nucleus and was a transcriptional activator. Electrophoretic mobility shift assay (EMSA) and dual-luciferase assays demonstrated that FfMYB15 could bind and activate FfCEL6B promoter by recognizing MYB cis-acting element. Conclusions This study indicated that FfCEL6B played an active role in mycelial growth of F. filiformis and was regulated by FfMYB15.

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De novo transcriptome sequencing of Flammulina velutipes uncover candidate genes associated with cold‐induced fruiting

Cited by 9 publications

References 33 publications

Genome-wide analysis and prediction of genes involved in the biosynthesis of polysaccharides and bioactive secondary metabolites in high-temperature-tolerant of wild Flammulina filiformis

Genome-wide analysis and prediction of genes involved in the biosynthesis of polysaccharides and bioactive secondary metabolites in high-temperature-tolerant of wild Flammulina filiformis

Genomic-wide analysis and prediction of genes involved in biosynthesis of polysaccharide and bioactive secondary metabolites in high-temperature-tolerance of wild Flammulina filiformis

Transcription factor FfMYB15 regulates the expression of cellulase gene FfCEL6B during mycelial growth of Flammulina filiformis

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