Clean data were obtained by removing reads containing adapters, reads containing poly-N and low-quality reads from raw data through Trimmomatic (v.0.33) [41]. https://doi.org/10.1007/s11557-018-1409-2, DOI: https://doi.org/10.1007/s11557-018-1409-2. A: Volcano plots of differential expression analysis for each comparison group; B: Gene co-expression network of the young fruiting body cap module (module no. One study has suggested that enokitake mushroom consumption may cause increased activity of plasma creatine kinase, which has deleterious effects on both skeletal and cardiac muscle. Another option is to place the fresh enokitake mushrooms in an oven heated to 175F for two hours. The cyclic adenylate-dependent protein kinase A (cAMP/PKA) pathway is the main signaling pathway in response to environmental stress, and the PKAC is the terminal catalytic subunit of this pathway. (2020) Transcriptome data reveal conserved patterns of fruiting body development and response to heat stress in the mushroom-forming fungus Flammulina filiformis. The winter mushroom or enokitake, Flammulina filiformis (formerly known as F. velutipes) [29], is cultivated at large scales in East Asia [3032]. Dai, E. Horak & Zhu L. Yang, 2018 basionym: Flammulina velutipes var. Among them, dmc1, hop1 and hfm1 homologs were also up-regulated in mature cap (Fig 3; S2A Fig; S4 Table). When buying enokitake mushroom powder, make sure that the company youre going with is using only the fruiting body and shares their extraction process. If you want to have an abundant supply of enokitake mushrooms in an affordable way, then your best bet is to grow them yourself. The mushroom is well known for its use in Japanese cuisine, and the name enokitake is the Japanese term for it. https://doi.org/10.1128/genomeA.00505-16, Li J, He X, Liu XB, Yang ZL, Zhao ZW (2017) Species clarification of oyster mushrooms in China and their DNA barcoding. Both hardwood chips and/or sawdust are perfectly suitable to use when growing these mushrooms. Flammulina filiformis ( Dai and Yang, 2018 ), known as winter mushroom or enokitake, belongs to the family Physalacriaceae, Agaricales ( Ge et al., 2015 ). LGN acknowledges support from the European Research Council (grant no. Results In this . Interestingly, the second most up-regulated gene in primordium was restricted to the family Physalacriaceae, which indicated a role in primordium formation in this family (Table 1; Fig 3). The winter mushroom, or Enokitake, is economically important and commercially cultivated on a large scale in East Asia. Previous studies revealed molecular details in fruiting body development in Flammulina species at the transcriptome, proteome, single gene or protein level [20, 3539]. Additionally, this treatment with enokitake mushroom extract increased levels of certain antioxidants and neurotransmitters in the brain. and is widely cultivated in East Asia. S5 Fig. Gang Wu for their constructive comments and valuable suggestions. 18th ed. PubMed PLoS One 9:e93560, Prez-Butrn JL, Fernndez-Vicente J (2007) Una nueva especie de Flammulina P. Karsten, F. cephalariae (Agaricales) encontrada en Espaa. Total RNA of each sample was extracted using the RNAprep Pure toolkit, following the manufacturers protocol (TIANGEN, Beijing, China). The top 20 up-regulated genes induced in primordium relative to vegetative mycelium were listed in Table 1. The CAZymes genes annotated in F. filiformis. Conservation of genes was assessed based on the phylogeny, by assessing the presence/absence of genes across the panel of species. Genes with log2 (fold change) 1 and Padj 0.05 were considered as differentially expressed gene (DEG). All raw-sequence reads data were deposited in NCBI Sequence Read Archive (SRA, http://www.ncbi.nlm.nih.gov/Traces/sra) with accession number of PRJNA557510. Am J Hum Genet 68:978989, Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. While your coffee is still very hot, slowly pour your coffee over the mushroom powder, Brew your morning coffee like youre used to doing, Add it to your mug while your coffee is still very hot, Prepare your enokitake mushrooms by gently brushing off any debris or dirt with a vegetable brush. An old toothbrush works, too. PubMed The cyclic adenylate-dependent protein kinase A (cAMP/PKA) pathway is the main signaling pathway in response to environmental stress, and the PKAC is the terminal catalytic subunit of this pathway. Get Your Own Mushroom Grow Kit Here. CAS S5 Table. Until recently, the species was considered to be conspecific with the European Flammulina velutipes, but DNA sequencing has shown that the two are distinct. Phylogenetic tree inferred from maximum likelihood analysis based on the ITS alignment. The degradation of cellulose requires the joint action of a variety of cellulases, and some cellulase-related genes have been detected in mushrooms. These are compounds that can help neutralize harmful free radicals, thereby protecting your cells from damage and oxidative stress. A comprehensive understanding of fruiting body development of this mushroom would not only benefit its production, but can also help to uncover conserved molecular mechanisms of development in the Agaricomycetes. PubMed Differences in read mapability were not found between the M1 and XR strain which made the transcriptome comparable across these two strains (S3 Table). [view velutipes in East Asia, including those from South Korea and Japan with genome sequences labeled as such, are in fact F. filiformis. Lysine content is considered an important indicator of the quality of Flammulina filiformis.In this study, chitosan was used to improve lysine content of F. filiformis.Optimal design conditions were obtained using central combination design (CCD): treatment concentration was 14.61 g/mL, treatment time was 52.90 h, and the theoretical value of lysine content was 30.95 mg/g. Fungal Biol Biotechnol 3:113, Giraud T, Refrgier G, Le GM, de Vienne DM, Hood ME (2008) Speciation in fungi. [713]. The product should be organic and free from industrial pollutants. 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. Mol Phylogenet Evol 35:120, Methven A, Hughes KW, Petersen RH (2000) Flammulina velutipes RFLP patterns identify species and show biogeographical patterns within species. Liu & Zhu L. Yang) P.M. Wang, Y.C. Studies on these two model species using tools such as DNA-mediated transformation, RNA interference, and CRISPR/Cas9 etc. Inoculated bottles were incubated at 23 C under dark conditions for 30 days, and then the mycelium scratched to emulates disturbance and transferred to 23 C with 95% humidity for fruiting. Commercial scale cultivation of this mushroom requires a low temperature (15C) (since the wild strain commonly fruiting during late autumn to early spring), which costs large amounts of energy, especially during summer in East Asia [29, 33, 34]. Mycologia 106:649665, Gilmore BS, Alderman SC, Knaus BJ, Bassil NV, Martin RC, Dombrowski JE, Dung JK (2016) Simple sequence repeat markers that identify Claviceps species and strains. Purpura fulminans (PF) is a life-threatening condition characterized by intravascular coagulation and skin necrosis. Aquaporins were differentially expressed in mycorrhizal species [2, 26, 64], which provides additional support to the hypothesis that fruiting bodies and ectomycorrhizae have many shared gene expression patterns, possibly pointing to common developmental origins [2, 64, 66]. Yeast strains lacking Rad18 proteins may be highly sensitive to a wide variety of DNA damaging agents such as UVC-light, ROS stress and -radiation [8486]. 16 indicates developmental stages of basidia. Nevertheless, if you want to simplify the process even further, you can purchase a pre-made growing kit. [5] The fungus can be cultivated on a range of simple, lignocellulosic substrates including sawdust, wheat straw, and paddy straw. Syll Fung 5:11146, Selkoe KA, Toonen RJ (2006) Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers. In a study in mice with a viral respiratory infection, the proteins in enokitake mushrooms reduced airway inflammation. In the primordium stage, we found that genes encoding hydrophobins were (homologs of fv-hyd1, fv-hyd7 and S. commune sc3) significantly up-regulated relative to vegetative mycelium (Fig 3; S2A Fig; S4 Table). This is why its crucial to buy any coffee product from a trusted brand. Go enrichment of the DEGs in each successive developmental stage. Flammulina filiformis has been cultivated in China since 800 AD. Citation: Liu X-B, Xia E-H, Li M, Cui Y-Y, Wang P-M, Zhang J-X, et al. F-Box genes annotated in F. filiformis. Department of Biology, McMaster University, Hamilton, Ontario, Canada, Affiliations: your institution, http://www.biomedcentral.com/14712148/14/143, https://doi.org/10.1038/s41598-017-01682-8, https://doi.org/10.1371/journal.pone.0154794, http://wwwbioutkedu/mycology/Flammulina/defaulthtml. VM, P10-M1, P18-M1, YFBC, YFBS, FBC and FBS correspond to vegetative mycelium, primordium grown at 10C, primordium grown at 18C, young fruiting body cap, young fruiting body stipe, fruiting body cap and fruiting body stipe, of strain M1. 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. Then, the mycelium was inoculated in liquid cultures in 500ml Erlenmeyer flask containing 200ml enriched Potato Dextrose Broth (PDB) medium (0.05% KH2PO4, 0.05% MgSO4, 2% glucose, 0.2% yeast extract, 0.2% peptone), shaken at 150 r.p.m for 10 days at 23 C. In this study, 210 F-box encoding genes were annotated in F. filiformis, of which 80 were developmentally expressed and showed stage-specific expression patterns (Fig 2E; S8 Table). We obtained 39.463.6 million paired-end reads for 15 sample types in triplicates (45 libraries in total) (S3 Table). A re-analysis of this genes homologs in C. cinerea, R. mellea, and A. ostoyae revealed a conserved expression pattern in these species, which indicates that oxylipins may mediate sexual development in the Ascomycota and the Agaricomycetes. However, if you want to make your immune system more healthy and robust through dietary changes, consuming enokitake mushrooms may offer you added defense against infections. Based on our results, it seems likely that aquaporin-dependent water transport is a key process during mushroom development in saprotrophic fungi too, possibly in water transport along the stipe to facilitate water supply of the developing cap and gills [64]. Sci Rep 7:1493. https://doi.org/10.1038/s41598-017-01682-8, Article and the National Research, Development and Innovation office (Contract No. PubMed Central [3] Further molecular research using a combination of different sequences has shown that F. filiformis and F. velutipes are distinct and should be recognized as separate species.[2]. Key Laboratory of Microbial Resources, Ministry of Agriculture and Rural Affairs, Beijing, China, Affiliation: In this study, the Pkac gene was identified in F. filiformis, which was highly conserved in . Mushroom-forming fungi are widely distributed through Earths ecosystems. The red dots represent ribosomal protein encoding gene, blue dots represent other gene; E: Heatmap of the CAZyme and F-BOX gene expression in each developmental stage. nov. Persoonia 13:489494, Boyogueno ADB, Slippers B, Perez G, Wingfield MJ, Roux J (2012) High gene flow and outcrossing within populations of two cryptic fungal pathogens on a native and non-native host in Cameroon. A series of genes associated with mushroom formation, including the mating type genes, hydrophobins, and fruiting body specific genes have been identified [20, 31, 40]. qRT-PCR primers used in this study. In one animal study, certain compounds extracted from enokitake mushrooms offered protection against impairments in learning and memory caused by a medication associated with memory loss. Anyone you share the following link with will be able to read this content: Sorry, a shareable link is not currently available for this article. filiformis Z.W. 5 more], Twelve phylogenetic species were recognized, which was largely consistent with previous studies. Therefore, understanding fruiting body development is important also from the perspective of understanding major evolutionary transitions. One cup (65 g) of raw enokitake mushrooms contains: Enokitake mushrooms are especially high in niacin, a micronutrient that your body uses to regulate cholesterol and promote brain health. By signing up, you agree to our Terms & Privacy Policy, which includes the handling of your information in compliance with HIPAA regulations. aquaporins, eln3-homologs, hydrophobins, conserved transcription factors, oxylipin biosynthesis genes) that show conserved, dynamic expression during fruiting body development, and also uncovered signal for defense against high temperature in the heat tolerance strain (M1) (e.g. To validate the results of the RNA-seq analysis, 18 genes were randomly selected for quantitative real-time PCR (qRT-PCR). Flammulina filiformis ( Dai and Yang, 2018 ), known as winter mushroom or enokitake, belongs to the family Physalacriaceae, Agaricales ( Ge et al., 2015 ). IJMS | Free Full-Text | Comparative Transcriptomics of Flammulina filiformis Suggests a High CO2 Concentration Inhibits Early Pileus Expansion by Decreasing Cell Division Control Pathways Journals IJMS Volume 20 Issue 23 10.3390/ijms20235923 announcement format_quote question_answer Discuss in SciProfiles Endorse settings Order Article Reprints "Enoki" redirects here. Mycol Prog 9:469484, Rodrigues AM, de Hoog GS, de Camargo ZP (2014) Genotyping species of the Sporothrix schenckii complex by PCR-RFLP of calmodulin. Measure and add a serving of enokitake mushroom powder to your mug following your package directions. Pore-forming proteins have been studied in Pleurotus species, which exhibit cytotoxicity toward insect cells via pore formation in cell membranes to defend predation [52, 53]. A re-analysis of the data published by Sipos et al. Heat the sesame oil in a medium-sized non-stick skillet over medium heat. However, the phylogeny and species delimitation of the winter mushroom genus ( Flammulina) have not been fully clarified. A new species, Flammulina. Cultivated specimens are not exposed to light, which results in white or pallid fruit bodies with long stipes and small caps. We need further research to determine if enokitake mushrooms can combat cancer growth in humans when consumed in normal food amounts. By using an extract powder, you will consume a much lower dosage to get the same medicinal benefits. Am J Hum Genet 73:11621169, Stephens M, Smith NJ, Donnelly P (2001) A new statistical method for haplotype reconstruction from population data. This study investigated fruiting body development in F. filiformis by comparing transcriptomes of 4 developmental stages, and compared the developmental genes to a 200-genome dataset to . construct the phylogenetic tree of Ste12-like proteins of Flammulina filiformis and other fungi by comparison of the amino acid sequences, and show that the Ste12-like proteins contain the conserved amino acid sequences with three typical motifs, namely motif 1, 2, and 3. Shop High Quality Mushroom Supplements Here, and Use Code HEALINGMAPS For a Discount. Add soy sauce and ginger; toss to coat. Fungal Divers 69:93115, Wu G, Li YC, Zhu XT, Zhao K, Han LH, Cui YY, Li F, Xu JP, Yang ZL (2016) One hundred noteworthy boletes from China. Fungal Divers 81:25188, Xie BG, Jiang YJ, Wu WL (2004) Fruit-body color inheritance of Flammulina velutipes. Moreover, antioxidants may help prevent many chronic conditions, including heart disease, different types of cancer, and type 2 diabetes. Volcano plots of differential expression analysis of each comparison group of M1 and XR strain grown at 10C and 18C. The temperature range should be around 50-55 degrees Fahrenheit (10-12 degrees Celsius). You can keep your enokitake mushroom tea in the fridge and reheat it later or serve it chilled. Plant Biosyst 143:528542, Earl DA, Von Holdt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the evanno method. Instead, the genes homologous to S. pombe hsp20 were up-regulated in XR strain in all developmental stages at 18C, they play different roles than hsp70 and hsp90, which are probably required to prevent misfolded protein aggregation and their degradation under heat stress [80]. A large number (74) of ribosomal protein encoding genes, and homologs of genes involved in cell differentiation and cell wall formation in S. pombe (agn1 and rae1), Candida albicans (ada2), and S. cerevisiae (ecm3) were hub genes in the young fruiting body cap module of the WGCNA analysis or were up-regulated relative to the primordium stage (Figs 2D and 3; S2A and S2B Fig; S4 Table). F. filiformis has been cultivated in China since 800 AD. Due to the presence of antioxidants and other health-promoting compounds, enokitake mushrooms may offer immune-boosting properties. Previous studies revealed that the knockout of this gene in C. neoformans resulted in a severe defect in basidium formation [7173]. A new species, Flammulina finlandica, was also unexpectedly discovered in Northern Europe. To investigate the metabolic energy differences between Flammulina filiformis packaged with nanocomposite (NP) and conventional polyethylene (CP) bags, tandem mass tags (TMT) labeling combined with two-dimensional liquid chromatography-tandem mass spectrometry technique and biochemical analysis were applied. Furthermore, the fruiting body is a complex multicellular structure [6], whose complexity level resembles that of multicellular plants and animals. Copyright: 2020 Liu et al. Overview of the sampling and differential expression analyses used in this study. The stipe (stem) is smooth, pale yellow at the apex, yellow-brown to dark brown towards the base, and lacking a ring. GO enrichment of the genes up-regulated in each developmental stage grown at 18C relative to 10C in M1 and XR strain respectively. Transcriptome data reveal conserved patterns of fruiting body development and response to heat stress in the mushroom-forming fungus Flammulina filiformis Xiao-Bin Liu, En-Hua Xia, Meng Li, Yang-Yang Cui, Pan-Meng Wang, Jin-Xia Zhang, Bao-Gui Xie, Jian-Ping Xu, Jun-Jie Yan, Jing Li x Published: October 16, 2020 (S5 Fig; S9 Table). Enokitake mushrooms are typically grown in the dark, producing pallid fruit bodies with long and narrow stipes and undeveloped caps. This study investigated fruiting body development in F. filiformis by comparing transcriptomes of 4 developmental stages, and compared the developmental genes to a 200-genome dataset to identify conserved genes involved in fruiting body development, and examined the response of heat sensitive and -resistant strains to heat stress. G3 6:36353645, White TJ, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. Aquaporins are integral membrane proteins responsible for water and solute transport, and also involved in mycorrhizal formation and plant-fungal interactions during symbiosis establishment [26, 61]. Development of Multiple Nucleotide Polymorphism Molecular Markers for Enoki Mushroom ( Flammulina filiformis) Cultivars Identification by Fei Liu 1, Shi-Hui Wang 1,2, Ding-Hong Jia 3, Hao Tan 3, Bo Wang 3,* and Rui-Lin Zhao 1,4,* 1 State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China 2 However, the molecular response to heat stress, in particular those of the well-known heat shock protein coding gene hsp70, hsp90 and other molecular chaperons etc., in F. filiformis remains unknown. [2], Basidiocarps are agaricoid and grow in clusters. Bioinformatics 25:14511452, Liu XB, Feng B, Li J, Yan C, Yang ZL (2016) Genetic diversity and breeding history of winter mushroom (Flammulina velutipes) in China uncovered by genomic SSR markers. Certain CAZymes were shown or assumed to participate in cell wall remodeling during fungal tissue differentiation [13, 49, 7577]. In addition, these mushrooms are rich in thiamine, which regulates the function of your nerve cells. Mol Ecol 11(1):16, Zhao YE, Wu LP (2012) RAPDSCAR marker and genetic relationship analysis of three Demodex species (Acari: Demodicidae). Meng Li, All of the genes were annotated using local BLASTX programs against the Nr, SwissPort, GO and PFAM databases. The researchers reported that pairing enokitake mushroom extract with ginsenosides compounds found in ginseng can improve brain function in rats with Alzheimers disease. Gene expression patterns in fruiting body development of, Synoptic summary of key genes at different stages of development of. Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China, Affiliation: Ms. Ming-Li Li (Kunming Institute of Zoology, Chinese Academy of Sciences), Dr. Botond Hegeds and Dr. Balzs Blint (Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged), Dr. Ti-Cao Zhang (Yunnan University of Chinese Medicine), Dr. Peter Langfelder (University of California), Dr. Yong-Ping Fu (Jilin Agricultural University) and Dr. Robin Ohm (Utrecht University) were acknowledged for their kind help in data analyses. This mushroom has a tetrapolar mating system that consists of homeodomain . S1 Table. Enokitake mushroom extract powder. The mushroom is well known for its use in Japanese cuisine, and the name enokitake is the Japanese term for it. Thus, these genes may also play a key role in fruiting body development in Agaricomycetes. Measure out 1 g of mushroom powder. DEGs in each developmental stage. Add the mushrooms to a food dehydrator until all the moisture is removed. However, you should know that when studies refer to the golden needle mushroom or winter mushroom as Flammulina velutipes, the now accepted species name is Flammulina filiformis. However, there are some important things to keep in mind. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturers instructions. These aggregates continuously develop into primordia, which further differentiate into mature fruiting bodies [713]. Dai, E. Horak . PubMedGoogle Scholar. Ge, X.B. During this phase, the spores will inoculate the substrate and white mycelium will grow. J Med Plants Stud 1:19, Hahn C (2016) Bestimmungsschlssel zu ausgewhlten Gattungen der Agaricales 2: Die Gattung Flammulina. These data highlighted novel genes involved in complex multicellular development in fungi and aid further studies on gene function and efforts to improve the productivity and heat tolerance in mushroom-forming fungi.
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flammulina filiformis
