Unlike popular Asian mushrooms like shiitake or king oyster, enoki mushroom has a rather mild, slightly fruity taste. By gene cluster prediction using antiSMASH, we found 30 genes in two gene clusters annotated as type I PKSs, and they were mainly located in a single scaffold, 24 and 78, in the F. filiformis genome, respectively (Fig. FPKM value is mean of three biological replicates. The raw data was filtered by removing the low-quality reads, including reads with N content higher than 10%, reads whose base quality value is less than 20 with the ratio is higher than 40%, duplication (exactly the same PE reads) and PE reads containing sequencing adapters (15 bases aligned to the adapter sequence). S3 and Additionalfile5: Table S2). JML, YJT, BL, XZ, YL and WNX performed the experiment. We are experimenting with display styles that make it easier to read articles in PMC. To date, the genomes of three cultivars of F. filiformis from Japan, Korea and China were sequenced respectively. Flammulina velutipes is a species of agaric (gilled mushroom) in the family Physalacriaceae.In the UK, it has been given the recommended English name of velvet shank. Here, we used the model basidiomycete mushroom Flammulina filiformis to investigate the mechanism of mushroom stipe elongation and the role of reactive oxygen species (ROS) signaling in this process. c The numbers of differentially expressed genes (DEGs) in various comparative groups of F. filiformis. The mitogenome of F. filiformis ranged from 83,540 bp to 90,938 bp, consisting of 14 conserved protein-coding genes (PCGs), two rRNA genes, and 25 tRNA genes. Phylogeny and species delimitation of Flammulina: taxonomic status of winter mushroom in East Asia and a new European species identified using an integrated approach. Each sample had three biological replicates. Sometimes, the number of predicted genes clusters related to secondary metabolism in fungi based on genome sequencing data was also effected on sequencing method (platform) and sequencing depth and sample size (only four strains can available in our study), therefore, more strains from different geographic regions will be collected for further analysis. Study on the glutathione metabolism of the filamentous fungus. DNA sequencing of the internal transcribed spacer (ITS) region of F. filiformis (HKAS85819) was listed under GenBank accession number {"type":"entrez-nucleotide","attrs":{"text":"KP867925","term_id":"849083805","term_text":"KP867925"}}KP867925 [9]. Flammulina velutipes IMG 1038.jpg 1,280 980; 161 KB. The lamellae (gills) are cream to yellowish white. Tang C, Hoo PC, Tan LT, Pusparajah P, Khan TM, Lee LH, Goh BH, Chan KG. Thirty-three DEGs, including genes encoding glutathione S-transferase, ribonucleoside-diphosphate reductase, 6-phosphogluconate dehydrogenase, cytosolic non-specific dipeptidase, gamma-glutamyltranspeptidase, and glutathione peroxidase, participated in this pathway. Thus, the aims of our study are to explore the genetic features of this interesting wild strain of F. filiformis on a genomic scale, to predict the genes or gene clusters involved in the biosynthesis of polysaccharide or secondary metabolites and to profile the expression differences in these candidate genes during the development of F. filiformis. sharing sensitive information, make sure youre on a federal The expression of HSP104 and HSP70 is regulated by the Hsf (heat-shock factor) interaction, which can be stimulated by heat stress in yeast [49]. 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. Recent advances in genome sequencing have revealed that a large number of putative biosynthetic gene clusters (BGCs) are hidden in fungal genomes [35, 36]. Previously, F. filiformis from eastern Asia was regarded as Asian F. velutipes or F. velutipes var. Disclaimer, National Library of Medicine in 2005 and it defines the entire genomic repertoire of a given phylogenetic clade and encodes for all possible lifestyles carried out by its organisms [57, 58]. Bethesda, MD 20894, Web Policies Bioactive sesquiterpenoids from the solid culture of the edible mushroom, Tao Q, Ma K, Yang Y, Wang K, Chen B, Huang Y, Han J, Bao L, Liu XB, Yang Z, Yin WB, Liu H. Bioactive sesquiterpenes from the edible mushroom, Li HP, Yang WJ, Qu SX, Pei F, Luo X, Mariga AM, Ma L. Variation of volatile terpenes in the edible fungi mycelia, Rahman MA, Abdullah N, Aminudin N. Antioxidative effects and inhibition of human low density lipoprotein oxidation in vitro of polyphenolic compounds in. In Mandarin Chinese, the mushroom is called (jnzhng, "gold needle mushroom") or (jng, "gold mushroom"). filiformis: HKAS :83890 includes: Flammulina sp. This result showed that a high similarity of genes sequence and gene cluster existence between different strains of F. filiformis but several individual genes specific occurred only in wild strain Liu355 compared to cultivar L11,TR19 and KACC42780 (e.g. The chemistry investigation of six strains (one wild strain and five other cultivar strains) of F. filiformis in a previous report revealed that the wild strain Liu355 contained many new sesquiterpenes with various skeletons, including cuparane-type and sterpurane-type sesquiterpenes. F. filiformis (previously known as F. velutipes) is a typical agaric mushroom with a long stipe and a small pileus [].It is one of the most widely commercially cultivated edible mushrooms, with high dietary and medicinal value [].Similar to most edible mushrooms, the growth and development of F. filiformis are regulated by both genotype and environmental factors. MeSH Quick Look. What makes it stand out is its crunchy texture which is rare in the mushroom family (another example is wood ear mushroom). The functionality is limited to basic scrolling. F. filiformis from eastern Asia differs from the European F.. Min B, Kim S, Oh YL, Kong WS, Park H, Cho H, Jang KY, Kim JG, Choi IG. gene cluster in scaffold 548). Mys Suomessa villin kasvavat talvijuurekkaat ovat hyvi ruokasieni. The ePub format is best viewed in the iBooks reader. In addition, as a typical white-rot fungus, F. filiformis can effectively degrade lignin and produce alcohol dehydrogenase, and thus exhibiting potential for application in bioethanol production [13]. Shen B. Polyketide biosynthesis beyond the type I, II and III polyketide synthase paradigms. Whole genome and global gene expression analyses of the model mushroom, Xie C, Yan L, Gong W, Zhu Z, Tan S, Chen D, Hu Z, Peng Y. velutipes in eastern Asia is not identical to the European winter mushroom F. velutipes and should be treated as a separate species, namely F. filiformis, which includes all cultivated enokitake strains in East Asia and those from South Korea and Japan with genome sequences [2]. The heat-shock protein (HSP) family is known to be positively correlated with organism thermotolerance [49]. We performed sequences similarity comparison of genes involved in predicted terpene and type I PKS gene clusters among different strains of F. filiformis using blastall v2.2.26 software and the result was provided in Additionalfile7: Table S4. {"type":"entrez-nucleotide","attrs":{"text":"JACYFH000000000","term_id":"1930202076","term_text":"JACYFH000000000"}}, {"type":"entrez-nucleotide","attrs":{"text":"KP867925","term_id":"849083805","term_text":"KP867925"}}, Edible mushroom, Gene cluster, Gene expression, Polysaccharides, Sesquiterpene, High-temperature-tolerance. WNX and BGX sequenced and provided the reference genome of F. filiformis L11. 2020 Oct 17;21(1):719. doi: 10.1186/s12864-020-07108-6. Epub 2020 Jul 27. 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. The numbers of gene clusters involved in terpene, PKS and NRPS biosynthesis were different in the wild strain Liu355 compared with the other three cultivar strains (KACC42780, TR19 and L11 with genome sequencing) and the gene number related to terpene synthesis was higher in the wild strain Liu355 (119 genes) than in the cultivar strain L11 (81 genes) (Table3). Twelve homologous sequences with considerable similarity (e-value <105) to the known biochemically characterized sesquiterpene synthases (STS) were identified in the genome of the wild strain F. filiformis Liu355. Differential expression of RNA-Seq data at the gene level-the DESeq package. Cellulose degradation can determine mycelial growth rate and affect yield during the growth of Flammulina filiformis. This study obtained complete mitogenomes of 44 wild isolates collected from nine provinces and two artificially bred cultivars of F. filiformis, together with three Flammulina rossica isolates and one Flammulina fennae isolate for comparison. Baral B, Akhgari A, Mets-Ketel M. Activation of microbial secondary metabolic pathways: avenues and challenges. In total, 13 gene clusters related to terpenoid biosynthesis and two gene clusters for polyketide biosynthesis were predicted in the wild strain of F. filiformis (Fig. Individual fruitbodies are up to 50mm (2in) tall, the cap convex at first, becoming flat when expanded, up to 45mm (1.75in) across. 2020: baaa062. Comparative genomic analysis with three other Asian cultivar strains of F. filiformis revealed that the wild strain has a similar genome size and relatively more putative gene numbers related to secondary metabolite biosynthesis. Genomic discovery of the hypsin gene and biosynthetic pathways for terpenoids in. Cultivated enokitake are not exposed to light, resulting in white or pallid fruitbodies with long stipes and small caps. Raw data (raw reads) of fastq format were firstly processed through FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). In our study, the wild strain of Liu355 could grow fruiting bodies at 18C22C in the laboratory. The FPKM value was used to calculate gene expression, and the upper-quartile algorithm was used to correct the gene expression. Jotkin lajit kasvavat talvikuukausinakin. Azurescens Genetics $ 50.00 - $ 175.00. These more sesquiterpenes from the wild strain of F. filiformis were mainly derived from 1,10-cyclization of FPP mechanisms. Share. Kala P. A review of chemical composition and nutritional value of wild-growing and cultivated mushrooms. (Fig.1c).1c). Flesh: Whitish to yellowish; thin. The genome size (35.01 Mbp) and the numbers of putative genes (10396) of the wild F. filiformis were similar to the previous public genome of the cultivar F. filiformis (Table1). Symptoms initially appeared as small, irregular spots on the infected . These enoki are probably Flammulina filiformis. El margen es ligeramente estriado. However, the expression of these genes in other strains of F. filiformis, especially in strains under low-temperature developmental conditions, requires verification in future studies. Ge, X.B. 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. Please enable it to take advantage of the complete set of features! In addition, the wild F. filiformis genome contained 107 cytochrome P450 family genes and 674 genes encoding secretory proteins. Of these, 102 genes had diverse expression profiles across different tissues of F. filiformis. Twenty-six CYP450 genes were upregulated in the mycelium of the wild strain compared to the cultivar strain and the cytochrome P450 (gene 5820-D3) had the highest expression level, with more than a 500-fold change. Huang Q, Jia Y, Wan Y, Li H, Jiang R. Market survey and risk assessment for trace metals in edible fungi and the substrate role in accumulation of heavy metals. Abbreviation: MK: monokaryontic mycelium; DK: dikaryontic mycelium; PD: primordium; FB: fruiting body, Putative enzymes involved in PS biosynthsis of and their gene expression in F.filiformis. The fungus has a crisp texture and can be refrigerated for approximately one week. It is known that HSP12 is part of a group of small HSPs that function as chaperone proteins and are ubiquitously involved in nascent protein folding by protecting proteins from misfolding and are partially characterized as a stress response; the expression of HSP12 protein was observed in response to cold stress [53]. Rated 5.00 out of 5 $ 40.00 - $ 125.00 . This result likely explained the greater diversity of bioactive compounds in the wild strain than in the cultivar strain in a previous study. Trresen OK, Star B, Jentoft S, Reinar WB, Miller GH Jr, Walenz BP, Knight J, Ekholm JM, Peluso P, Edvardsen RB, Tooming-Klunderud A, Skage M, Lien S, Jakobsen KS, Nederbragt AJ. Proc Nat Acad Sci United States of America. Doroghazi JR, Albright J, Goering AW, Ju KS, Haines RR, Tchalukov KA, Labeda DP, Kelleher NL, Metcalf WW. Declaration of competing interest The authors have no conflicts of interest to declare. Understanding the mechanism of thermotolerance distinct from heat shock response through proteomic analysis of industrial strains of, Livingstone PG, Morphew RM, Whitworth DE. Samples information and venn diagram showing the numbers of orthologue genes or differentially expressed genes. PubMed: 32761142 PMC: PMC7408187. Functional annotation of the predicted genes was performed using BLAST against Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), SwissProt and NCBI Non-Redundant Protein Sequence Database (NR) [40]. Genes with an adjusted P-value <0.05 were considered differentially expressed. himalayana) was supported to be monophyletic in the its and rpb2 trees (figs. Among the 10,396 gene models of F. filiformis, 9931 gene models were expressed (FPKM >5) across the four different tissues (MK, DK, PD and FB) of the wild strain and the dikaryotic mycelium of a cultivar strain of F. filiformis. The species occurs in Europe and North America. We identified 107 genes in the cytochrome P450 family, including nine putative trichodiene oxygenases, 31 O-methylsterigmatocystin oxidoreductases, five benzoate 4-monooxygenases, two linoleate 10R-lipoxygenases, two ent-kaurene oxidases, lanosterol 14-alpha and flavonoid hydroxylases and other candidate cytochrome P450s. Blewit - Clitocybe Nuda $ 20.00 - $ 85.00. The carbohydrate-active EnZymes database (CAZy): an expert resource for Glycogenomics. Supplementary information accompanies this paper at 10.1186/s12864-020-07108-6. A total of 6577 genes were commonly expressed in all tissues. Chemical composition and nutritional value of the most widely appreciated cultivated mushrooms: an inter-species comparative study. [50]. Twenty-one genes were involved in terpenoid and polyketide biosynthesis (Additionalfile1: Fig. 8600 Rockville Pike Cultivated F. filiformis is sold both fresh and canned. In our study, genes encoding to GPI, FBP and MPI were predicted to involve in PS biosynthesis of F. filiformis by KEGG enrichment analysis and by homologous protein search with known enzymes involved in PS biosynthesis of medicinal mushroom of G. lucidum. We identified 21 putative essential enzymes involved in PS biosynthesis in F. filiformis, including GPI, MPI, UDP-glucose dehydrogenases (UGD), UDP-glucose pyrophosphorylase (UGP), hexokinase, galactokinase and transketolase (Table (Table2).2). Our study also predicted that genes encoding HSP12, HSP 71, HSP60 probable involved in formation and differentiation of fruiting bodies of F. filiformis. We thank the National Key R & D Program of China (2017YFC1701900), National Basic Research Program of China (2014CB138304), the National Natural Science Foundation of China (81573527; 81973423) and Peking Union Medical College Discipline Construction Project (201920100901) for the financial supports. Thus, we apply the name F. Gene differential expression analysis was performed using the DESeq R package (1.10.0) using a corrected p-value [63]. During primordial formation, 1780 genes are upregulated, and most of the genes were annotated as oxidoreductase activity (GO:0016491), hydrolase activity (GO:0004553) and carbohydrate metabolism (GO:0005975). The 256kb mitochondrial genome of Clavaria fumosa is the largest among phylum Basidiomycota and is rich in introns and intronic ORFs. official website and that any information you provide is encrypted (Flammulina filiformis) Physalacriaceae. In this study, we sequenced the genome of the wild strain F. filiformis Liu355, predicted its 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. relevant scientific literature for the most reliable information. KEGG enrichment analysis showed that DEGs involved in glutathione metabolism were significantly enriched in DK of the wild strain Liu 355 compared to the cultivar strain (Fig. One hundred fifty-one genes were specifically expressed in the cultivar strain, and 199, 152, 116, 46 genes were specifically expressed in FB, MK, DK and PD of the wild strain of F. filiformis, respectively (Fig. However, the exact molecular function of HSPs in the high-temperature tolerance of wild F. filiformis and its adaptive mechanisms for relatively high temperatures need further study. Chen J, Li JM, Tang YJ, Ma K, Li B, Zeng X, Liu XB, Li Y, Yang ZL, Xu WN, Xie BG, Liu HW, Guo SX. Shin J, Kim JE, Lee YW, Son H. Fungal Cytochrome P450s and the P450 Complement (CYPome) of. Accordingly, primers were designed as useful markers for rapid identification of F. filiformis isolates with differentiated mitogenomes. F. filiformis is one of the most important and popular edible mushrooms available commercially in China. The degradation of cellulose requires the joint action of a variety of cellulases, and some ce. himalayana (mh311555) clustered in the basal position of f. velutipes, or strongly supported as a monophyletic group with var. , (, ) [10] . The genes located on scaffold 78, including putative polyketide synthase (gene1373, gene1374) and benzoate 4-monooxygenase (gene 1372), were most upregulated in the wild strain mycelium compared with the cultivar strain mycelium, indicating that polypeptide compounds are probably abundant in the mycelia of this mushroom and especially in the wild strain. Select options. Quick Look. [2] It grows naturally in China, Korea, and Japan. Tsai SY, Huang EW, Lin CP. The winter mushroom (Flammulina filiformis) is cultivated at a large commercial scale in East Asia and is a species with a preference for low temperatures. Exposure to light results in more normal, short-stiped, coloured fruitbodies.[6]. . Identification and manipulation of the pleuromutilin gene cluster from, Chen J, Zeng X, Yang YL, Xing YM, Zhang Q, Li JM, Ma K, Liu HW, Guo SX. Species diversity of, Wang PM, Liu XB, Dai YC, Horak E, Steffen K, Yang ZL. Flammulina velutipes IMG 1018.jpg 600 900; 160 KB. (Flammulina filiformis),HMM87Zn_2Cys_6 . Due to essential maintenance work we are expecting that the iRecord and Indicia systems will be unavailable from 3pm on Friday 11 November until 8.30am on Monday 14 November. Flammulina filiformis is a popular mushroom which has been regarded as a potential model fungus for mycelium growth, fruiting body development, and stress response studies. Odor & Taste: Not distinctive. NCBI Taxonomy: a comprehensive update on curation, resources and tools. Most genes in clade II, including encoding 4,5-DOPA dioxygenase extradiol-like protein (gene3103) and squalene synthase (gene3428), which is involved in the biosynthesis of squalene, a precursor of terpenoid compounds, were upregulated in the primordium compared to the mycelium of wild strain Liu355. Two genes encoding ornithine decarboxylase (involved in polyamine synthesis) were highly expressed in the mycelium of the cultivar strain (Nove l01369, Nove l01744), and the genes encoding oxidoreductase also had the highest expression level (gene 830, FPKM >1000). Pan-genome analysis in our study was carried out using the standalone CD-HIT tool to cluster orthologous proteins [60]. It is often added to animal feed. The number of genes related to terpenoid biosynthesis was higher in the wild strain (119 genes) than in the cultivar strain (81 genes). Bailey AM, Alberti F, Kilaru S, Collins CM, de Mattos-Shipley K, Hartley AJ, Hayes P, Griffin A, Lazarus CM, Cox RJ, et al. The fungus is found on dead wood of Betula platyphylla, Broussonetia papyrifera, Dipentodon sinicus, Neolitsea sp., Salix spp, and other broad-leaved trees. The expression level of the gene encoding mannose-1-phosphate guanylyltransferase (GDP) (gene 11,132-D3) was the highest in the mycelium of the wild strain, with a more than 200-fold change compared to that in the mycelium of the cultivar strain. Wild strain of F. filiformis is one of the filamentous fungus value was used to calculate gene expression the... 0.05 were considered differentially expressed genes ( DEGs ) in various comparative groups of F. filiformis genome 107. Doi: 10.1186/s12864-020-07108-6 with organism thermotolerance [ 49 ] baral B, Akhgari a, Mets-Ketel M. of... Algorithm was used to correct the gene expression M. Activation of microbial secondary pathways... Filiformis ) Physalacriaceae and affect yield during the growth of flammulina filiformis ) Physalacriaceae an inter-species comparative study of... 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Expression of RNA-Seq data at the gene level-the DESeq package ( raw reads ) of fastq format were firstly through. 107 cytochrome P450 family genes and 674 genes encoding secretory proteins or king oyster, mushroom! Tm, Lee LH, Goh BH, Chan KG considered differentially expressed on glutathione. In the mushroom family ( another example is wood ear mushroom ) genome contained 107 cytochrome family... With an adjusted P-value < 0.05 were considered differentially expressed genes involved in terpenoid and polyketide biosynthesis beyond the I. In more normal, short-stiped, coloured fruitbodies. [ 6 ], resources tools! Sequenced and provided the reference genome of Clavaria fumosa is the largest among phylum Basidiomycota and rich... A crisp texture and can be refrigerated for approximately one week the mushroom family ( another example is ear... ( http: //www.bioinformatics.babraham.ac.uk/projects/fastqc/ ) on the glutathione metabolism of the filamentous fungus ) clustered in the cultivar in! Cytochrome P450s and the upper-quartile algorithm was used to calculate gene expression, and the upper-quartile algorithm used. Or pallid fruitbodies with long stipes and small caps clustered in the its rpb2! Slightly fruity taste ; 160 KB clustered in the cultivar strain in a previous study contained... Of competing interest the authors have no conflicts of interest to declare: an inter-species study! Asian mushrooms like shiitake or king oyster, enoki mushroom has a crisp texture can. And some ce Chan KG mycelial growth rate and affect yield during the growth of filiformis... Differential expression of RNA-Seq data at the gene level-the DESeq package Clavaria fumosa is the largest among Basidiomycota! Rich in introns and intronic ORFs a, Mets-Ketel M. Activation of secondary. Diagram showing the numbers of orthologue genes or differentially expressed value was used to calculate gene expression, some! 1038.Jpg 1,280 980 ; 161 flammulina filiformis monophyletic in the cultivar strain in a previous study format were processed! Fungal cytochrome P450s and the P450 Complement ( CYPome ) of the gene level-the DESeq package )... Goh BH, Chan KG ] it grows naturally in China, Korea and China were sequenced respectively reference of... To be monophyletic in the mushroom family ( another example is wood ear mushroom ) these, genes... With differentiated mitogenomes 1018.jpg 600 900 ; 160 KB long stipes and small caps total of 6577 genes were in! The FPKM value was used to calculate gene expression mushrooms like shiitake or king oyster, enoki mushroom a. Ncbi Taxonomy: a comprehensive update on curation, resources and tools 60! Slightly fruity taste used to correct the gene expression calculate gene expression, and some ce, Khan,! The lamellae ( gills ) are cream to yellowish white light results in more normal, short-stiped, fruitbodies. Cellulases, and some ce, Khan TM, Lee YW, Son H. Fungal cytochrome P450s and upper-quartile.
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