174 results on '"Won Sik Kong"'
Search Results
2. An origin identification model for labeling of shiitake (Lentinula edodes)
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Ill-Min Chung, Yun-Ju Kim, Chang Kwon, Hee-Sung Moon, Jae-Gu Han, Won-Sik Kong, and Seung-Hyun Kim
- Subjects
Nutrition. Foods and food supply ,TX341-641 ,Food processing and manufacture ,TP368-456 - Abstract
Abstract With the increasing globalization of the food trade across countries and continents, reliable identification of the geographical origin of products is critical. In this study, we describe the limitations of the current origin labeling system for non-soil-based agricultural products and suggest alternative strategies for the identification of the geographical origin of such products. An origin identification model based on stable isotope ratio analysis combined with discriminant analysis is used to evaluate the similarities and dissimilarities between domestic and foreign shiitake mushrooms, including Chinese inoculated sawdust blocks and Chinese origin. The results show a classification sensitivity of 92.0%, classification specificity of 91.5%, and overall accuracy of 93.5%. In particular, δ15N was the most important isotope marker for the identification of the origin of shiitake mushrooms. Hence, the current origin labeling system for mushroom species has to be revised to establish fair trade and avoid improper origin labeling in the global shiitake market.
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- 2021
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3. Evaluating Genetic Diversity of Agaricus bisporus Accessions through Phylogenetic Analysis Using Single-Nucleotide Polymorphism (SNP) Markers
- Author
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Youn-Lee Oh, In-Geol Choi, Won-Sik Kong, Kab-Yeul Jang, Min ji Oh, and Ji-Hoon Im
- Subjects
principal coordinate analysis ,genetic diversity ,wild germplasm ,button mushroom ,Botany ,QK1-989 - Abstract
Agaricus bisporus, commonly known as the button mushroom, is widely cultivated throughout the world. To breed new strains with more desirable traits and improved adaptability, diverse germplasm, including wild accessions, is a valuable genetic resource. To better understand the genetic diversity available in A. bisporus and identify previously unknown diversity within accessions, a phylogenetic analysis of 360 Agaricus spp. accessions using single-nucleotide polymorphism genotyping was performed. Genetic relationships were compared using principal coordinate analysis (PCoA) among accessions with known origins and accessions with limited collection data. The accessions clustered into four groups based on the PCoA with regard to genetic relationships. A subset of 67 strains, which comprised a core collection where repetitive and uninformative accessions were not included, clustered into 7 groups following analysis. Two of the 170 accessions with limited collection data were identified as wild germplasm. The core collection allowed for the accurate analysis of A. bisporus genetic relationships, and accessions with an unknown pedigree were effectively grouped, allowing for origin identification, by PCoA analysis in this study.
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- 2021
- Full Text
- View/download PDF
4. Mycoremediation: An Elimination of Metal and Non-metal Inclusions from Polluted Soil
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Raman, Jegadeesh, primary, Kab-Yeul, Jang, additional, Lakshmanan, Hariprasath, additional, Won-Sik, Kong, additional, and Gajendran, Babu, additional
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- 2021
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5. Molecular Characterization of 170 New gDNA-SSR Markers for Genetic Diversity in Button Mushroom (Agaricus bisporus)
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Hyejin An, Ick-Hyun Jo, Youn-Lee Oh, Kab-Yeul Jang, Won-Sik Kong, Jwa-Kyung Sung, Yoon-Sup So, and Jong-Wook Chung
- Subjects
button mushroom ,cluster analysis ,genetic diversity ,simple sequence repeat marker ,Botany ,QK1-989 - Abstract
We designed 170 new simple sequence repeat (SSR) markers based on the whole-genome sequence data of button mushroom (Agaricus bisporus), and selected 121 polymorphic markers. A total of 121 polymorphic markers, the average major allele frequency (MAF) and the average number of alleles (NA) were 0.50 and 5.47, respectively. The average number of genotypes (NG), observed heterozygosity (HO), expected heterozygosity (HE), and polymorphic information content (PIC) were 6.177, 0.227, 0.619, and 0.569, respectively. Pearson’s correlation coefficient showed that MAF was negatively correlated with NG (−0.683), NA (−0.600), HO (−0.584), and PIC (−0.941). NG, NA, HO, and PIC were positively correlated with other polymorphic parameters except for MAF. UPGMA clustering showed that 26 A. bisporus accessions were classified into 3 groups, and each accession was differentiated. The 121 SSR markers should facilitate the use of molecular markers in button mushroom breeding and genetic studies.
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- 2019
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6. Development of a Molecular Marker Linked to the A4 Locus and the Structure of HD Genes in Pleurotus eryngii
- Author
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Song Hee Lee, Asjad Ali, Byeongsuk Ha, Min-Keun Kim, Won-Sik Kong, and Jae-San Ryu
- Subjects
Mating-type gene ,A4 locus ,Pleurotus eryngii ,SCAR marker ,homeodomain ,Botany ,QK1-989 - Abstract
Allelic differences in A and B mating-type loci are a prerequisite for the progression of mating in the genus Pleurotus eryngii; thus, the crossing is hampered by this biological barrier in inbreeding. Molecular markers linked to mating types of P. eryngii KNR2312 were investigated with randomly amplified polymorphic DNA to enhance crossing efficiency. An A4-linked sequence was identified and used to find the adjacent genomic region with the entire motif of the A locus from a contig sequenced by PacBio. The sequence-characterized amplified region marker 7-2299 distinguished A4 mating-type monokaryons from KNR2312 and other strains. A BLAST search of flanked sequences revealed that the A4 locus had a general feature consisting of the putative HD1 and HD2 genes. Both putative HD transcription factors contain a homeodomain sequence and a nuclear localization sequence; however, valid dimerization motifs were found only in the HD1 protein. The ACAAT motif, which was reported to have relevance to sex determination, was found in the intergenic region. The SCAR marker could be applicable in the classification of mating types in the P. eryngii breeding program, and the A4 locus could be the basis for a multi-allele detection marker.
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- 2019
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7. Genomic discovery of the hypsin gene and biosynthetic pathways for terpenoids in Hypsizygus marmoreus
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Byoungnam Min, Seunghwan Kim, Youn-Lee Oh, Won-Sik Kong, Hongjae Park, Heejung Cho, Kab-Yeul Jang, Jeong-Gu Kim, and In-Geol Choi
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Hypsizygus marmoreus ,Beech mushroom ,Fungal genome ,Hypsin ,Marmorin ,Hypsiziprenol A9 ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Hypsizygus marmoreus (Beech mushroom) is a popular ingredient in Asian cuisine. The medicinal effects of its bioactive compounds such as hypsin and hypsiziprenol have been reported, but the genetic basis or biosynthesis of these components is unknown. Results In this study, we sequenced a reference strain of H. marmoreus (Haemi 51,987–8). We evaluated various assembly strategies, and as a result the Allpaths and PBJelly produced the best assembly. The resulting genome was 42.7 Mbp in length and annotated with 16,627 gene models. A putative gene (Hypma_04324) encoding the antifungal and antiproliferative hypsin protein with 75% sequence identity with the previously known N-terminal sequence was identified. Carbohydrate active enzyme analysis displayed the typical feature of white-rot fungi where auxiliary activity and carbohydrate-binding modules were enriched. The genome annotation revealed four terpene synthase genes responsible for terpenoid biosynthesis. From the gene tree analysis, we identified that terpene synthase genes can be classified into six clades. Four terpene synthase genes of H. marmoreus belonged to four different groups that implies they may be involved in the synthesis of different structures of terpenes. A terpene synthase gene cluster was well-conserved in Agaricomycetes genomes, which contained known biosynthesis and regulatory genes. Conclusions Genome sequence analysis of this mushroom led to the discovery of the hypsin gene. Comparative genome analysis revealed the conserved gene cluster for terpenoid biosynthesis in the genome. These discoveries will further our understanding of the biosynthesis of medicinal bioactive molecules in this edible mushroom.
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- 2018
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8. Unusual genome expansion and transcription suppression in ectomycorrhizal Tricholoma matsutake by insertions of transposable elements.
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Byoungnam Min, Hyeokjun Yoon, Julius Park, Youn-Lee Oh, Won-Sik Kong, Jong-Guk Kim, and In-Geol Choi
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Medicine ,Science - Abstract
Genome sequencing of Tricholoma matsutake revealed its unusually large size as 189.0 Mbp, which is a consequence of extraordinarily high transposable element (TE) content. We identified that 702 genes were surrounded by TEs, and 83.2% of these genes were not transcribed at any developmental stage. This observation indicated that the insertion of TEs alters the transcription of the genes neighboring these TEs. Repeat-induced point mutation, such as C to T hypermutation with a bias over "CpG" dinucleotides, was also recognized in this genome, representing a typical defense mechanism against TEs during evolution. Many transcription factor genes were activated in both the primordia and fruiting body stages, which indicates that many regulatory processes are shared during the developmental stages. Small secreted protein genes (
- Published
- 2020
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9. Development of Polymorphic Simple Sequence Repeat Markers using High-Throughput Sequencing in Button Mushroom (Agaricus bisporus)
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Hwa-Yong Lee, Sebastin Raveendar, Hyejin An, Youn-Lee Oh, Kab-Yeul Jang, Won-Sik Kong, Hojin Ryu, Yoon-Sup So, and Jong-Wook Chung
- Subjects
Agaricus bisporus ,button mushroom ,SSR ,illumina sequencing ,Botany ,QK1-989 - Abstract
The white button mushroom (Agaricus bisporus) is one of the most widely cultivated species of edible mushroom. Despite its economic importance, relatively little is known about the genetic diversity of this species. Illumina paired-end sequencing produced 43,871,558 clean reads and 69,174 contigs were generated from five offspring. These contigs were subsequently assembled into 57,594 unigenes. The unigenes were annotated with reference genome in which 6,559 unigenes were associated with clusters, indicating orthologous genes. Gene ontology classification assigned many unigenes. Based on genome data of the five offspring, 44 polymorphic simple sequence repeat (SSR) markers were developed. The major allele frequency ranged from 0.42 to 0.92. The number of genotypes and the number of alleles ranged from 1 to 4, and from 2 to 4, respectively. The observed heterozygosity and the expected heterozygosity ranged from 0.00 to 1.00, and from 0.15 to 0.64, respectively. The polymorphic information content value ranged from 0.14 to 0.57. The genetic distances and UPGMA clustering discriminated offspring strains. The SSR markers developed in this study can be applied in polymorphism analyses of button mushroom and for cultivar discrimination.
- Published
- 2018
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10. Genome-Wide Comparison of Carbohydrate-Active Enzymes (CAZymes) Repertoire of Flammulina ononidis
- Author
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Young-Jin Park and Won-Sik Kong
- Subjects
Flammulina ononidis ,genome ,carbohydrate-active enzyme ,Botany ,QK1-989 - Abstract
Whole-genome sequencing of Flammulina ononidis, a wood-rotting basidiomycete, was performed to identify genes associated with carbohydrate-active enzymes (CAZymes). A total of 12,586 gene structures with an average length of 2009 bp were predicted by the AUGUSTUS tool from a total 35,524,258 bp length of de novo genome assembly (49.76% GC). Orthologous analysis with other fungal species revealed that 7051 groups contained at least one F. ononidis gene. In addition, 11,252 (89.5%) of 12,586 genes for F. ononidis proteins had orthologs among the Dikarya, and F. ononidis contained 8 species-specific genes, of which 5 genes were paralogous. CAZyme prediction revealed 524 CAZyme genes, including 228 for glycoside hydrolases, 21 for polysaccharide lyases, 87 for glycosyltransferases, 61 for carbohydrate esterases, 87 with auxiliary activities, and 40 for carbohydrate-binding modules in the F. ononidis genome. This genome information including CAZyme repertoire will be useful to understand lignocellulolytic machinery of this white rot fungus F. ononidis.
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- 2018
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11. Comparative Analysis of Carbohydrate Active Enzymes in the Flammulina velutipes var. lupinicola Genome
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Hye-Won Yu, Ji-Hoon Im, Won-Sik Kong, and Young-Jin Park
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carbohydrate-active enzyme ,Flammulina velutipes var. lupinicola ,whole genome sequencing ,Biology (General) ,QH301-705.5 - Abstract
The purpose of this study was to determine the genome sequence of Flammulina velutipes var. lupinicola based on next-generation sequencing (NGS) and to identify the genes encoding carbohydrate-active enzymes (CAZymes) in the genome. The optimal assembly (71 kmer) based on ABySS de novo assembly revealed a total length of 33,223,357 bp (49.53% GC content). A total of 15,337 gene structures were identified in the F.velutipes var. lupinicola genome using ab initio gene prediction method with Funannotate pipeline. Analysis of the orthologs revealed that 11,966 (96.6%) out of the 15,337 predicted genes belonged to the orthogroups and 170 genes were specific for F. velutipes var. lupinicola. CAZymes are divided into six classes: auxiliary activities (AAs), glycosyltransferases (GTs), carbohydrate esterases (CEs), polysaccharide lyases (PLs), glycoside hydrolases (GHs), and carbohydrate-binding modules (CBMs). A total of 551 genes encoding CAZymes were identified in the F. velutipes var. lupinicola genome by analyzing the dbCAN meta server database (HMMER, Hotpep, and DIAMOND searches), which consisted of 54–95 AAs, 145–188 GHs, 55–73 GTs, 6–19 PLs, 13–59 CEs, and 7–67 CBMs. CAZymes can be widely used to produce bio-based products (food, paper, textiles, animal feed, and biofuels). Therefore, information about the CAZyme repertoire of the F. velutipes var. lupinicola genome will help in understanding the lignocellulosic machinery and in-depth studies will provide opportunities for using this fungus for biotechnological and industrial applications.
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- 2020
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12. Fatty Acids and Stable Isotope Ratios in Shiitake Mushrooms (Lentinula edodes) Indicate the Origin of the Cultivation Substrate Used: A Preliminary Case Study in Korea
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Ill-Min Chung, So-Yeon Kim, Jae-Gu Han, Won-Sik Kong, Mun Yhung Jung, and Seung-Hyun Kim
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shiitake mushroom ,cultivation substrate ,harvesting cycle ,fatty acid ,stable isotope ratio ,Chemical technology ,TP1-1185 - Abstract
Shiitake mushroom (Lentinula edodes) is commonly consumed worldwide and is cultivated in many farms in Korea using Chinese substrates owing to a lack of knowledge on how to prepare sawdust-based substrate blocks (bag cultivation). Consequently, issues related to the origin of the Korean or Chinese substrate used in shiitake mushrooms produced using bag cultivation have been reported. Here, we investigated differences in fatty acids (FAs) and stable isotope ratios (SIRs) in shiitake mushrooms cultivated using Korean and Chinese substrates under similar conditions (strain, temperature, humidity, etc.) and depending on the harvesting cycle. The total FA level decreased significantly by 5.49 mg∙g−1 as the harvesting cycle increased (p < 0.0001); however, no differences were found in FAs between shiitake mushrooms cultivated using Korean and Chinese substrates. Linoleic acid was the most abundant FA, accounting for 77–81% of the total FAs during four harvesting cycles. Moreover, the SIRs differed significantly between the Korean and Chinese substrates, and the harvesting cycles resulted in smaller maximum differences in SIR values compared to those of the cultivation substrate origins. Our findings contribute to the identification of the geographical origin of shiitake mushrooms and may have potential applications in international shiitake-mushroom markets.
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- 2020
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13. Genomic Insights into the Fungal Lignocellulolytic Machinery of Flammulina rossica
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Young-Jin Park, Chang-Soo Lee, and Won-Sik Kong
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basidiomycete ,carbohydrate active enzyme ,flammulina rossica ,fungi ,genome ,Biology (General) ,QH301-705.5 - Abstract
Next-generation sequencing (NGS) of the Flammulina rossica (wood-rotting basidiomycete) genome was performed to identify its carbohydrate-active enzymes (CAZymes). De novo genome assembly (31 kmer) revealed a total length of 35,646,506 bp (49.79% GC content). In total, 12,588 gene models of F. rossica were predicted using an ab initio gene prediction tool (AUGUSTUS). Orthologous analysis with other fungal species revealed that 7433 groups contained at least one F. rossica gene. Additionally, 12,033 (95.6%) of 12,588 genes for F. rossica proteins had orthologs among the Dikarya, and F. rossica contained 12 species-specific genes. CAZyme annotation in the F. rossica genome revealed 511 genes predicted to encode CAZymes including 102 auxiliary activities, 236 glycoside hydrolases, 94 glycosyltransferases, 19 polysaccharide lyases, 56 carbohydrate esterases, and 21 carbohydrate binding-modules. Among the 511 genes, several genes were predicted to simultaneously encode two different CAZymes such as glycoside hydrolases (GH) as well as carbohydrate-binding module (CBM). The genome information of F. rossica offers opportunities to understand the wood-degrading machinery of this fungus and will be useful for biotechnological and industrial applications.
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- 2019
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14. Evaluating Genetic Diversity of Agaricus bisporus Accessions through Phylogenetic Analysis Using Single-Nucleotide Polymorphism (SNP) Markers
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Won-Sik Kong, In Geol Choi, Im Ji Hoon, Min ji Oh, Kab Yeul Jang, and Youn Lee Oh
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Germplasm ,Genetics ,0303 health sciences ,Genetic diversity ,Phylogenetic tree ,button mushroom ,Single-nucleotide polymorphism ,genetic diversity ,Biology ,biology.organism_classification ,principal coordinate analysis ,Microbiology ,lcsh:QK1-989 ,030308 mycology & parasitology ,03 medical and health sciences ,Infectious Diseases ,Agaricus ,Snp markers ,lcsh:Botany ,wild germplasm ,Genotyping ,Agaricus bisporus ,030304 developmental biology - Abstract
Agaricus bisporus, commonly known as the button mushroom, is widely cultivated throughout the world. To breed new strains with more desirable traits and improved adaptability, diverse germplasm, including wild accessions, is a valuable genetic resource. To better understand the genetic diversity available in A. bisporus and identify previously unknown diversity within accessions, a phylogenetic analysis of 360 Agaricus spp. accessions using single- nucleotide polymorphism genotyping was performed. Genetic relationships were compared using principal coordinate analysis (PCoA) among accessions with known origins and accessions with limited collection data. The accessions clustered into four groups based on the PCoA with regard to genetic relationships. A subset of 67 strains, which comprised a core collection where repetitive and uninformative accessions were not included, clustered into 7 groups following analysis. Two of the 170 accessions with limited collection data were identified as wild germplasm. The core collection allowed for the accurate analysis of A. bisporus genetic relationships, and accessions with an unknown pedigree were effectively grouped, allowing for origin identification, by PCoA analysis in this study.
- Published
- 2020
15. Bioactive Sterol Derivatives Isolated from the Pleurotus djamor var. Roseus Induced Apoptosis in Cancer Cell Lines
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Kong Won-Sik Kong, Jang Kab-Yeul Jang, Nanjian Raaman, Raman Jagadeesh, Gajandran Babu, Hariprasath Lakshmanan, and Oh Min-Ji Oh
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Pharmacology ,Pleurotus ,biology ,Chemistry ,Thiobarbituric acid ,Pleurotus djamor ,Hematology ,biology.organism_classification ,Sterol ,Lipid peroxidation ,Edible mushroom ,Palmitic acid ,chemistry.chemical_compound ,Column chromatography ,Biochemistry ,Cardiology and Cardiovascular Medicine - Abstract
Objective: The aim of the present study is to isolate and characterize the bioactive compounds from Pleurotus djamor against human breast cancer (MDA-MD-231) and mouse T cell lymphoma (EL4) cell lines. Materials and methods: Sequential fractionization and column chromatography methods were involved in compound isolation. The structures of the isolated compound were determined by NMR, GC/MS, and X-ray crystallography studies. Results: The isolated compounds 1- 4 [D-mannitol (C1), ergosta-5,7,22-trien-3β-ol (C2), 5,8- epidioxy-ergosta-6-22-dien-3β-ol (C3), and palmitic acid (C4)] are white crystal and amorphous powder in nature. All these compounds were isolated from this mushroom for the first time. In vitro lipid peroxidation activities of isolated compounds were determined by ferric thiocyanate (FTC) and thiobarbituric acid (TBA) method. The sterol derivatives C2 and C3 compounds displayed strong antioxidant activity and were not significantly different (p Conclusion: The compound C3 has exhibited better cytotoxic activity against MDA-MD-231 and EL4 cells. The present finding and data might provide new insights into the possible therapeutic and pharmaceutical use for the design of anti-cancer drugs from this edible mushroom.
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- 2020
16. Genome Sequencing and Carbohydrate-Active Enzyme (CAZyme) Repertoire of the White Rot Fungus Flammulina elastica
- Author
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Young-Jin Park, Yong-Un Jeong, and Won-Sik Kong
- Subjects
carbohydrate active enzyme ,Flammulina elastica ,whole genome sequencing ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
Next-generation sequencing (NGS) of the Flammulina elastica (wood-rotting basidiomycete) genome was performed to identify carbohydrate-active enzymes (CAZymes). The resulting assembly (31 kmer) revealed a total length of 35,045,521 bp (49.7% GC content). Using the AUGUSTUS tool, 12,536 total gene structures were predicted by ab initio gene prediction. An analysis of orthologs revealed that 6806 groups contained at least one F. elastica protein. Among the 12,536 predicted genes, F. elastica contained 24 species-specific genes, of which 17 genes were paralogous. CAZymes are divided into five classes: glycoside hydrolases (GHs), carbohydrate esterases (CEs), polysaccharide lyases (PLs), glycosyltransferases (GTs), and auxiliary activities (AA). In the present study, annotation of the predicted amino acid sequences from F. elastica genes using the dbCAN CAZyme database revealed 508 CAZymes, including 82 AAs, 218 GHs, 89 GTs, 18 PLs, 59 CEs, and 42 carbohydrate binding modules in the F. elastica genome. Although the CAZyme repertoire of F. elastica was similar to those of other fungal species, the total number of GTs in F. elastica was larger than those of other basidiomycetes. This genome information elucidates newly identified wood-degrading machinery in F. elastica, offers opportunities to better understand this fungus, and presents possibilities for more detailed studies on lignocellulosic biomass degradation that may lead to future biotechnological and industrial applications.
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- 2018
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17. Development of a Molecular Marker Linked to the A4 Locus and the Structure of HD Genes in Pleurotus eryngii
- Author
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Jae-San Ryu, Byeongsuk Ha, Won-Sik Kong, Asjad Ali, Song Hee Lee, and Min Keun Kim
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Mating type ,Locus (genetics) ,Biology ,Microbiology ,Pleurotus eryngii ,030308 mycology & parasitology ,03 medical and health sciences ,chemistry.chemical_compound ,Intergenic region ,Molecular marker ,lcsh:Botany ,Mating-type gene ,Allele ,Gene ,030304 developmental biology ,Genetics ,0303 health sciences ,Contig ,biology.organism_classification ,lcsh:QK1-989 ,Infectious Diseases ,chemistry ,homeodomain ,A4 locus ,SCAR marker - Abstract
Allelic differences in A and B mating-type loci are a prerequisite for the progression of mating in the genus Pleurotus eryngii; thus, the crossing is hampered by this biological barrier in inbreeding. Molecular markers linked to mating types of P. eryngii KNR2312 were investigated with randomly amplified polymorphic DNA to enhance crossing efficiency. An A4-linked sequence was identified and used to find the adjacent genomic region with the entire motif of the A locus from a contig sequenced by PacBio. The sequence-characterized amplified region marker 7-2299 distinguished A4 mating-type monokaryons from KNR2312 and other strains. A BLAST search of flanked sequences revealed that the A4 locus had a general feature consisting of the putative HD1 and HD2 genes. Both putative HD transcription factors contain a homeodomain sequence and a nuclear localization sequence; however, valid dimerization motifs were found only in the HD1 protein. The ACAAT motif, which was reported to have relevance to sex determination, was found in the intergenic region. The SCAR marker could be applicable in the classification of mating types in the P. eryngii breeding program, and the A4 locus could be the basis for a multi-allele detection marker.
- Published
- 2019
18. Characterization of Volatile Profiles of Six Popular Edible Mushrooms Using Headspace-Solid-Phase Microextraction Coupled with Gas Chromatography Combined with Chemometric Analysis
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Mun Yhung Jung, Won-Sik Kong, Seung Hyun Kim, Da Eun Lee, Jae-Gu Han, Hong Yu Cheng, and Il-Min Chung
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0303 health sciences ,Oyster ,Mushroom ,biology ,Food industry ,030309 nutrition & dietetics ,business.industry ,04 agricultural and veterinary sciences ,biology.organism_classification ,Solid-phase microextraction ,040401 food science ,Hexanal ,03 medical and health sciences ,chemistry.chemical_compound ,0404 agricultural biotechnology ,chemistry ,biology.animal ,Food science ,Gas chromatography ,business ,Canonical discriminant analysis ,Beech ,Food Science - Abstract
The classification of six mushroom species (white beech, brown beech, button, oyster, king oyster, and enoki mushrooms) was successfully achieved using canonical discriminant analysis (CDA) on volatile metabolite data sets obtained by headspace-solid-phase microextraction gas chromatography (HS-SPME-GC). Twenty-seven major volatile compounds in six edible mushrooms were positively identified by HS-SPME-GC mass spectroscopy. The total volatile content was highest in brown beech mushroom (P < 0.05). Significant difference in volatile profile was observed between brown beach and white beech mushrooms. Button mushroom contained significantly higher contents of benzaldehyde and benzyl alcohol than the other mushrooms (P < 0.05). Oyster mushroom contained 1-octen-3-ol as the most prevalent volatile, representing 67% out of total volatiles. Hexanal (35.0%) and 1-octen-3-ol (22.5%) were the most abundant volatiles found in king oyster. Hexanal (29.1%) was the most prevalent volatile in enoki mushroom only. Several volatile pairs with very high positive correlation in their levels were identified, representing the highest correlation coefficient (r = 0.970) for the pair of t-2-octenal and 2,4-octandienal. CDA was much more efficient than principal component analysis for the differentiation of mushroom species. PRACTICAL APPLICATION: The present study provided the important information on the volatile metabolite profiles of popular six commercial mushroom species. The present data will be useful for the quality control of mushrooms cultivated in farms and mushroom products processed in food industry. The strategy of canonical discriminant analysis in combination with HS-SPME-GC could be expanded for the determining the authentication of mushroom species.
- Published
- 2019
19. Identification of degenerate nuclei and development of a SCAR marker for Flammulina velutipes.
- Author
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Sun Young Kim, Kyung-Hee Kim, Chak Han Im, Asjad Ali, Chang Yun Lee, Won-Sik Kong, and Jae-San Ryu
- Subjects
Medicine ,Science - Abstract
Flammulina velutipes is one of the major edible mushrooms in the world. Recently, abnormalities that have a negative impact on crop production have been reported in this mushroom. These symptoms include slow vegetative growth, a compact mycelial mat, and few or even no fruiting bodies. The morphologies and fruiting capabilities of monokaryons of wild-type and degenerate strains that arose through arthrospore formation were investigated through test crossing. Only one monokaryotic group of the degenerate strains and its hybrid strains showed abnormal phenotypes. Because the monokaryotic arthrospore has the same nucleus as the parent strain, these results indicated that only one aberrant nucleus of the two nuclei in the degenerate strain was responsible for the degeneracy. A sequence-characterized amplified region marker that is linked to the degenerate monokaryon was identified based on a polymorphic sequence that was generated using random primers. Comparative analyses revealed the presence of a degenerate-specific genomic region in a telomere, which arose via the transfer of a genomic fragment harboring a putative helicase gene. Our findings have narrowed down the potential molecular targets responsible for this phenotype for future studies and have provided a marker for the detection of degenerate strains.
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- 2014
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20. Identification and functional analysis of pheromone and receptor genes in the B3 mating locus of Pleurotus eryngii.
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Kyung-Hee Kim, Young Min Kang, Chak Han Im, Asjad Ali, Sun Young Kim, Hee-Jeong Je, Min-Keun Kim, Hyun Su Rho, Hyun Sook Lee, Won-Sik Kong, and Jae-San Ryu
- Subjects
Medicine ,Science - Abstract
Pleurotus eryngii has recently become a major cultivated mushroom; it uses tetrapolar heterothallism as a part of its reproductive process. Sexual development progresses only when the A and B mating types are compatible. Such mating incompatibility occasionally limits the efficiency of breeding programs in which crossing within loci-shared strains or backcrossing strategies are employed. Therefore, understanding the mating system in edible mushroom fungi will help provide a short cut in the development of new strains. We isolated and identified pheromone and receptor genes in the B3 locus of P. eryngii and performed a functional analysis of the genes in the mating process by transformation. A genomic DNA library was constructed to map the entire mating-type locus. The B3 locus was found to contain four pheromone precursor genes and four receptor genes. Remarkably, receptor PESTE3.3.1 has just 34 amino acid residues in its C-terminal cytoplasmic region; therefore, it seems likely to be a receptor-like gene. Real-time quantitative RT-PCR (real-time qRT-PCR) revealed that most pheromone and receptor genes showed significantly higher expression in monokaryotic cells than dikaryotic cells. The pheromone genes PEphb3.1 and PEphb3.3 and the receptor gene PESTE3.3.1 were transformed into P5 (A3B4). The transformants were mated with a tester strain (A4B4), and the progeny showed clamp connections and a normal fruiting body, which indicates the proposed role of these genes in mating and fruiting processes. This result also confirms that PESTE3.3.1 is a receptor gene. In this study, we identified pheromone and receptor genes in the B3 locus of P. eryngii and found that some of those genes appear to play a role in the mating and fruiting processes. These results might help elucidate the mechanism of fruiting differentiation and improve breeding efficiency.
- Published
- 2014
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21. Whole genome and global gene expression analyses of the model mushroom Flammulina velutipes reveal a high capacity for lignocellulose degradation.
- Author
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Young-Jin Park, Jeong Hun Baek, Seonwook Lee, Changhoon Kim, Hwanseok Rhee, Hyungtae Kim, Jeong-Sun Seo, Hae-Ran Park, Dae-Eun Yoon, Jae-Young Nam, Hong-Il Kim, Jong-Guk Kim, Hyeokjun Yoon, Hee-Wan Kang, Jae-Yong Cho, Eun-Sung Song, Gi-Ho Sung, Young-Bok Yoo, Chang-Soo Lee, Byoung-Moo Lee, and Won-Sik Kong
- Subjects
Medicine ,Science - Abstract
Flammulina velutipes is a fungus with health and medicinal benefits that has been used for consumption and cultivation in East Asia. F. velutipes is also known to degrade lignocellulose and produce ethanol. The overlapping interests of mushroom production and wood bioconversion make F. velutipes an attractive new model for fungal wood related studies. Here, we present the complete sequence of the F. velutipes genome. This is the first sequenced genome for a commercially produced edible mushroom that also degrades wood. The 35.6-Mb genome contained 12,218 predicted protein-encoding genes and 287 tRNA genes assembled into 11 scaffolds corresponding with the 11 chromosomes of strain KACC42780. The 88.4-kb mitochondrial genome contained 35 genes. Well-developed wood degrading machinery with strong potential for lignin degradation (69 auxiliary activities, formerly FOLymes) and carbohydrate degradation (392 CAZymes), along with 58 alcohol dehydrogenase genes were highly expressed in the mycelium, demonstrating the potential application of this organism to bioethanol production. Thus, the newly uncovered wood degrading capacity and sequential nature of this process in F. velutipes, offer interesting possibilities for more detailed studies on either lignin or (hemi-) cellulose degradation in complex wood substrates. The mutual interest in wood degradation by the mushroom industry and (ligno-)cellulose biomass related industries further increase the significance of F. velutipes as a new model.
- Published
- 2014
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22. Improved accuracy of geographical origin identification of shiitake grown in sawdust medium: A compound-specific isotope model-based pilot study
- Author
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Seung-Hyun Kim, Yun-Ju Kim, Hee-Sung Moon, Jae-Gu Han, Ill-Min Chung, Christopher T. Yarnes, and Won-Sik Kong
- Subjects
Carbon Isotopes ,China ,Isotope ,Geography ,Discriminant model ,Compound specific ,Pilot Projects ,General Medicine ,Biology ,Analytical Chemistry ,visual_art ,Origin identification ,Republic of Korea ,visual_art.visual_art_medium ,Food science ,Sawdust ,Food Science ,Isotope analysis - Abstract
In countries like South Korea and the USA, origin labeling of shiitake grown using imported Chinese-inoculated medium is an issue. Therefore, we evaluated the use of compound-specific isotope analysis (CSIA) for the accurate identification of the geographical origin of shiitake (Korean, Chinese-inoculated medium, and Chinese); Chinese-inoculated medium shiitake were cultivated in Korea using inoculated sawdust medium from China. The CSIA-discriminant model showed an overall accuracy of 100% in the geographical classification of the original set and 96.4% for the cross-validated set. Glutamate and aspartate δ15N values were the most important variables for differentiating shiitake based on their origins. Compared to that observed upon using the bulk stable isotope analysis, the CSIA model was associated with significantly improved predictability of origin identification. Our findings elucidate the importance of isotope signatures in developing a reliable origin labeling method for shiitake cultured on the sawdust medium for the global market.
- Published
- 2021
23. Fatty Acids and Stable Isotope Ratios in Shiitake Mushrooms (Lentinula edodes) Indicate the Origin of the Cultivation Substrate Used: A Preliminary Case Study in Korea
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Won-Sik Kong, Ill-Min Chung, So-Yeon Kim, Jae-Gu Han, Mun Yhung Jung, and Seung-Hyun Kim
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Health (social science) ,Linoleic acid ,cultivation substrate ,Plant Science ,lcsh:Chemical technology ,01 natural sciences ,Health Professions (miscellaneous) ,Microbiology ,Article ,chemistry.chemical_compound ,harvesting cycle ,0404 agricultural biotechnology ,lcsh:TP1-1185 ,Food science ,shiitake mushroom ,chemistry.chemical_classification ,Mushroom ,biology ,Stable isotope ratio ,010401 analytical chemistry ,Fatty acid ,Substrate (chemistry) ,04 agricultural and veterinary sciences ,biology.organism_classification ,040401 food science ,0104 chemical sciences ,stable isotope ratio ,Lentinula ,chemistry ,visual_art ,visual_art.visual_art_medium ,Sawdust ,fatty acid ,Food Science ,Shiitake mushrooms - Abstract
Shiitake mushroom (Lentinula edodes) is commonly consumed worldwide and is cultivated in many farms in Korea using Chinese substrates owing to a lack of knowledge on how to prepare sawdust-based substrate blocks (bag cultivation). Consequently, issues related to the origin of the Korean or Chinese substrate used in shiitake mushrooms produced using bag cultivation have been reported. Here, we investigated differences in fatty acids (FAs) and stable isotope ratios (SIRs) in shiitake mushrooms cultivated using Korean and Chinese substrates under similar conditions (strain, temperature, humidity, etc.) and depending on the harvesting cycle. The total FA level decreased significantly by 5.49 mg∙g&minus, 1 as the harvesting cycle increased (p <, 0.0001), however, no differences were found in FAs between shiitake mushrooms cultivated using Korean and Chinese substrates. Linoleic acid was the most abundant FA, accounting for 77&ndash, 81% of the total FAs during four harvesting cycles. Moreover, the SIRs differed significantly between the Korean and Chinese substrates, and the harvesting cycles resulted in smaller maximum differences in SIR values compared to those of the cultivation substrate origins. Our findings contribute to the identification of the geographical origin of shiitake mushrooms and may have potential applications in international shiitake-mushroom markets.
- Published
- 2020
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24. Interspecific hybridization between Ganoderma lingzhi and G. applanatum through protoplast fusion
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Jegadeesh Raman, Youn-Lee Oh, Kab-Yeul Jang, Minji Oh, Won-Sik Kong, Hariprasath Lakshmanan, and Ji-Hoon Im
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Dietary Fiber ,Physiology ,Ganoderma ,Biology ,Polysaccharide ,Applied Microbiology and Biotechnology ,Polyethylene Glycols ,Quercus ,Glucans ,Mycelium ,Glucan ,chemistry.chemical_classification ,Mushroom ,Protoplasts ,Dendrogram ,General Medicine ,Protoplast ,biology.organism_classification ,DNA Fingerprinting ,RAPD ,Culture Media ,Random Amplified Polymorphic DNA Technique ,Horticulture ,chemistry ,Hybridization, Genetic ,Biotechnology - Abstract
Interspecific hybridization between Ganoderma lingzhi and G. applanatum was attempted through polyethylene glycol (PEG) induced fusion technique. The protoplast isolation procedure was simplified, and we obtained a significant number of protoplasts from both Ganoderma species. The number of protoplasts obtained was 5.27 ± 0.31 × 107/mL in G. lingzhi and 5.57 ± 0.49 × 106/mL in G. applanatum. Osmotic stabilizer NaCl (0.4 M) at pH 5.8 and enzymolysis time 3.5 h have supported high frequency of protoplast regeneration. G. lingzhi and G. applanatum regeneration frequency was 1.73 ± 0.04% and 0.23 ± 0.02%, respectively. 40% of PEG induced high number of protoplast fusion the regeneration frequency was 0.09% on a minimal medium. Two hundred fifty-two fusant colonies were isolated from the following four individual experiments. Among them, ten fusants showed the mycelial morphological difference compared to their parents and other fusant isolates. The fruiting body could be generated on oak sawdust and wheat bran substrate, and a few of them showed recombined morphology of the parental strains. The highest yield and biological efficacy (BE) were recorded in GF248, while least in GF244. The hybridity of the fusant was established based on mycelia, fruiting morphology, and PCR fingerprinting. ISSR and RAPD profile analysis of ten fusants and parents depicted that fusants contained polymorphic bands, which specified the rearrangement and deletion of DNA in the fusants. A Dendrogram was constructed based on the RAPD profile, and the clustering data exhibited two major clusters: cluster I included the G. lingzhi and Cluster II, including the G. applanatum and fusant lines. Total polysaccharide (α, β and total glucan) content was compared with fusants and parental strains. The present study highlighted the efficient methods for protoplast isolation from Ganoderma species. PEG-induced fusants showed high polymorphic frequency index, while the phenotypic characters showed high similarity to G. applanatum. A significant difference was observed in the mushroom yield and its total polysaccharide between the fusants and parental strains.
- Published
- 2020
25. Unusual genome expansion and transcription suppression in ectomycorrhizal Tricholoma matsutake by insertions of transposable elements
- Author
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Youn Lee Oh, Julius Park, Hyeokjun Yoon, Byoungnam Min, In Geol Choi, Jong Guk Kim, and Won-Sik Kong
- Subjects
Transcription, Genetic ,Gene Expression ,Genome ,Biochemistry ,Gene Expression Regulation, Fungal ,Mycorrhizae ,Mobile Genetic Elements ,Genetics ,0303 health sciences ,Multidisciplinary ,food and beverages ,Genomics ,Medicine ,Genome, Fungal ,Research Article ,Transposable element ,Gene prediction ,Science ,Mycology ,Biology ,03 medical and health sciences ,Genetic Elements ,Ascomycota ,Protein Domains ,DNA-binding proteins ,Fungal Genetics ,Gene Regulation ,Symbiosis ,Gene Prediction ,Gene ,Genome size ,Fungal Genomics ,030304 developmental biology ,Whole genome sequencing ,Whole Genome Sequencing ,Biology and life sciences ,030306 microbiology ,Basidiomycota ,Tricholoma ,Transposable Elements ,Correction ,Computational Biology ,Proteins ,Molecular Sequence Annotation ,Comparative Genomics ,Genome Analysis ,Genomic Libraries ,Regulatory Proteins ,DNA Transposable Elements ,Transcription Factor Gene ,Transcription Factors - Abstract
Genome sequencing of Tricholoma matsutake revealed its unusually large size as 189.0 Mbp, which is a consequence of extraordinarily high transposable element (TE) content. We identified that 702 genes were surrounded by TEs, and 83.2% of these genes were not transcribed at any developmental stage. This observation indicated that the insertion of TEs alters the transcription of the genes neighboring these TEs. Repeat-induced point mutation, such as C to T hypermutation with a bias over "CpG" dinucleotides, was also recognized in this genome, representing a typical defense mechanism against TEs during evolution. Many transcription factor genes were activated in both the primordia and fruiting body stages, which indicates that many regulatory processes are shared during the developmental stages. Small secreted protein genes (
- Published
- 2020
26. Development of Polymorphic Simple Sequence Repeat Markers using High-Throughput Sequencing in Button Mushroom (Agaricus bisporus)
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Yoon-Sup So, Jong-Wook Chung, Sebastin Raveendar, Won-Sik Kong, Hwa-Yong Lee, Hojin Ryu, Hyejin An, Youn-Lee Oh, and Kab-Yeul Jang
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0106 biological sciences ,0301 basic medicine ,Biology ,01 natural sciences ,Microbiology ,DNA sequencing ,Loss of heterozygosity ,03 medical and health sciences ,lcsh:Botany ,Research Articles ,Illumina dye sequencing ,Genetics ,Genetic diversity ,Contig ,UPGMA ,food and beverages ,button mushroom ,Agaricus bisporus ,SSR ,lcsh:QK1-989 ,030104 developmental biology ,Infectious Diseases ,illumina sequencing ,010606 plant biology & botany ,Reference genome - Abstract
The white button mushroom (Agaricus bisporus) is one of the most widely cultivated species of edible mushroom. Despite its economic importance, relatively little is known about the genetic diversity of this species. Illumina paired-end sequencing produced 43,871,558 clean reads and 69,174 contigs were generated from five offspring. These contigs were subsequently assembled into 57,594 unigenes. The unigenes were annotated with reference genome in which 6,559 unigenes were associated with clusters, indicating orthologous genes. Gene ontology classification assigned many unigenes. Based on genome data of the five offspring, 44 polymorphic simple sequence repeat (SSR) markers were developed. The major allele frequency ranged from 0.42 to 0.92. The number of genotypes and the number of alleles ranged from 1 to 4, and from 2 to 4, respectively. The observed heterozygosity and the expected heterozygosity ranged from 0.00 to 1.00, and from 0.15 to 0.64, respectively. The polymorphic information content value ranged from 0.14 to 0.57. The genetic distances and UPGMA clustering discriminated offspring strains. The SSR markers developed in this study can be applied in polymorphism analyses of button mushroom and for cultivar discrimination.
- Published
- 2018
27. Genome Sequencing and Genome-Wide Identification of Carbohydrate-Active Enzymes (CAZymes) in the White Rot Fungus Flammulina fennae
- Author
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Won-Sik Kong, Chang-Soo Lee, and Young-Jin Park
- Subjects
Genetics ,Identification (biology) ,Biology ,White rot fungus ,Applied Microbiology and Biotechnology ,Microbiology ,Flammulina fennae ,Carbohydrate active enzymes ,Genome ,DNA sequencing ,Biotechnology - Published
- 2018
28. Comparative genomics of the mating-type loci of the mushroom Flammulina velutipes reveals widespread synteny and recent inversions.
- Author
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Arend F van Peer, Soon-Young Park, Pyung-Gyun Shin, Kab-Yeul Jang, Young-Bok Yoo, Young-Jin Park, Byoung-Moo Lee, Gi-Ho Sung, Timothy Y James, and Won-Sik Kong
- Subjects
Medicine ,Science - Abstract
Mating-type loci of mushroom fungi contain master regulatory genes that control recognition between compatible nuclei, maintenance of compatible nuclei as heterokaryons, and fruiting body development. Regions near mating-type loci in fungi often show adapted recombination, facilitating the generation of novel mating types and reducing the production of self-compatible mating types. Compared to other fungi, mushroom fungi have complex mating-type systems, showing both loci with redundant function (subloci) and subloci with many alleles. The genomic organization of mating-type loci has been solved in very few mushroom species, which complicates proper interpretation of mating-type evolution and use of those genes in breeding programs.We report a complete genetic structure of the mating-type loci from the tetrapolar, edible mushroom Flammulina velutipes mating type A3B3. Two matB3 subloci, matB3a that contains a unique pheromone and matB3b, were mapped 177 Kb apart on scaffold 1. The matA locus of F. velutipes contains three homeodomain genes distributed over 73 Kb distant matA3a and matA3b subloci. The conserved matA region in Agaricales approaches 350 Kb and contains conserved recombination hotspots showing major rearrangements in F. velutipes and Schizophyllum commune. Important evolutionary differences were indicated; separation of the matA subloci in F. velutipes was diverged from the Coprinopsis cinerea arrangement via two large inversions whereas separation in S. commune emerged through transposition of gene clusters.In our study we determined that the Agaricales have very large scale synteny at matA (∼350 Kb) and that this synteny is maintained even when parts of this region are separated through chromosomal rearrangements. Four conserved recombination hotspots allow reshuffling of large fragments of this region. Next to this, it was revealed that large distance subloci can exist in matB as well. Finally, the genes that were linked to specific mating types will serve as molecular markers in breeding.
- Published
- 2011
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29. Characteristics of 'Baekseung', a new cultivar Flammulina velutipes
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Won-Sik Kong, Kab Yeul Jang, and Sung-I Woo
- Subjects
Horticulture ,Cultivar ,Biology ,biology.organism_classification ,Flammulina - Published
- 2017
30. Detection of fungi in imported supplemental substrates for mushroom cultivation media
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Kim Jun Young, Kim Bo-young, Won-Sik Kong, Kim Seong Hwan, and Lee Chan Jung
- Subjects
Mushroom ,010504 meteorology & atmospheric sciences ,Botany ,Environmental science ,010501 environmental sciences ,01 natural sciences ,0105 earth and related environmental sciences - Published
- 2016
31. Inhibitory effect of Panax ginseng and Pleurotus osteratus complex on expression of cytokine genes induced by extract of Dermatophagoides pteronissinus in human monocytic THP-1 and EoL-1 cells
- Author
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Kyeong Hun Park, Eun Suk Lee, Young Ock Kim, Kyung Sun Myung, Won-Sik Kong, Chun Geon Park, Hong Woo Park, and Yong Ik Jin
- Subjects
0301 basic medicine ,Innate immune system ,biology ,business.industry ,Atopic dermatitis ,CCL2 ,medicine.disease ,030207 dermatology & venereal diseases ,03 medical and health sciences ,Ginseng ,030104 developmental biology ,0302 clinical medicine ,Immunology ,biology.protein ,Medicine ,THP1 cell line ,Acute monocytic leukemia ,Interleukin 8 ,business ,Interleukin 6 - Abstract
A recent study reported that Pleurotus ostreatus has the potential to be used as a β-glucan- based cream for supportive complementary therapy of atopic dermatitis. KH054 is a new herbal prescription consisting of P. ostreatus and Panax ginseng. The effects of atopic dermatitis-induced materials on the expression of cytokine genes in human monocytes (THP-1, EoL- 1) have been examined. Some reports demonstrated that P. ginseng augments the activity of natural killer cells, which plays an important role in innate immunity against infection and tumor development. Monocyte chemotactic protein 1 (MCP-1), interleukin (IL)-6, and IL-8 have important roles in mediating the infiltration of various cells into the skin of atopic dermatitis and psoriasis. The present study investigated whether KH054 on induced IL-6, IL-8, and MCP-1 secretion by house dust mite (Dermatophagoides pteronissinus) in THP-1 (human acute monocytic leukemia) and EoL-1 (Human eosinophilic leukemia) cell. D. pteronissinus functions in the pathogenesis of allergic diseases, including atopic dermatitis and asthma. The inhibitory effect of KH054 on the induction of IL-6, IL-8, and MCP-1 secretion by D. pteronissinus extract in THP-1 and EoL-1 cells was examined. KH054 potently suppressed the elevated production of IL-6 and IL-8 induced by D. pteronissinus treatment in THP-1 and EoL-1 cells. Based on the present results, KH054 may be useful for developing functional foods to treat atopic dermatitis.
- Published
- 2016
32. Introduction of the representative mushroom cultivars and groundbreaking cultivation techniques in Korea
- Author
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Pyung-Gyun Shin, Sung-I Woo, Won-Sik Kong, Youn-Lee Oh, Kab-Yeul Jang, Minji Oh, and Ji-hoow Im
- Subjects
0301 basic medicine ,Mushroom ,Oyster ,biology ,business.industry ,030108 mycology & parasitology ,biology.organism_classification ,Domestic market ,03 medical and health sciences ,Agricultural science ,030104 developmental biology ,Agronomy ,Agriculture ,biology.animal ,Pleurotus eryngii ,Business ,Pleurotus ostreatus ,Productivity ,Agaricus bisporus - Abstract
The production scale of mushrooms in Korea is approximately 600 billion won, which is 1.6% of Korea’s gross agricultural output. In Korea, ca. 190,000 tons of mushrooms are harvested annually. Although the numbers of mushroom farms and cultivators are constantly decreasing, total mushroom yields are increasing owing to large- scale cultivation facilities and automation. The recent expansion of the well-being trend has caused an increase in mushroom consumption in Korea: the annual per capita mushroom was 3.9 kg (’13), whichis a little higher than that in Europe. Thus, mushroom export, mainly Flammulina velutipes and Pleurotus ostreatus, has increased since the mid-2000s. Recently, however, it is slightly reduced. Nevertheless, Vietnam, Hong Kong, the United States, and the Netherlands continue to export mushrooms, and Korea has increased its export to Australia, Canada, Southeast Asia, etc. Canned Agaricus bisporus, the first export of the Korean mushroom industry, reached it speak sales in 1977-1978. When Korea initiated trade with China in 1980, the international prices of mushrooms fell sharply, leading to shrinkage of the domestic markets. Spurred by the high demand to develop substitute goods for A. bisporus, the oyster mushroom (P. ostreatus) gained attention since it seemed to suit the taste of Korean consumers. Although the log cultivation technique for oyster mushroom was developed in the early 1970s, it required a great deal of labor. Thus, we developed the shelf cultivation technique, which is easier to manage and allows for mass production. In this technique, the growing shelf is made mafrom fermented rice straw, whichis the only P. ostreatus medium in the world and isused only in South Korea. After then, the use of cotton wastes as an additional material of medium, the productivity. Currently, we are developing a standard cultivation technique and environmental control system that can stably produce mushrooms throughout the year. The increase of oyster mushroom production may boostthe domestic market and contribute to industrial development. In addition, oyster mushroom production technology played a role in forming the basis for the development of bottle cultivation, which made mass production . In particular, bottle cultivation using liquid spawn could allow for the export of F. velutipes and Pleurotus eryngii. In addition, the white varieties of F. velutipes were second developed in the world after Japan. We also developed the new A. bisporus cultivar ‘Saeah’, which is easy to grow in Korea. In hopes to advance the mushroom industry, we will continue to develop cultivars with international competitive power and to improve cultivation techniques.
- Published
- 2016
33. Ribosomal Intergenic Spacer 1 Based Characterization of Button Mushroom (Agaricus bisporus) Strains
- Author
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Min Ah Choi, Seong Hwan Kim, Won-Sik Kong, Youn-Lee Oh, Dae Wook Kim, Hyuk Woo Kwon, and Min Woo Hyun
- Subjects
0301 basic medicine ,Genetics ,Mushroom ,biology ,Phylogenetic tree ,Strain (biology) ,Nucleic acid sequence ,Agaricus bisporus ,Ribosomal RNA ,biology.organism_classification ,Microbiology ,Dikaryotic strain ,Research Note ,03 medical and health sciences ,030104 developmental biology ,Infectious Diseases ,Agaricus ,Genetic variation ,Ribosomal intergenic spacer 1 - Abstract
Breeding the button mushroom requires genetic information about its strains. This study was undertaken to genetically characterize four domestically bred button mushroom strains (Saea, Saejung, Saedo, Saeyeon cultivars) and to assess the possibility of using the intergenic spacer 1 (IGS1) region of rDNA as a genetically variable region in the genetic characterization. For the experiment, 34 strains of Agaricus bisporus, two strains of A. bitorquis, and one strain of A. silvaticus, from 17 countries were used. Nucleotide sequence analysis of IGS1 rDNA in these 37 Agaricus strains confirmed that genetic variations exist, not only among the four domestic strains, but also between the four domestic strains and foreign strains. Crossing two different haploid strains of A. bisporus seems to generate genetic variation in the IGS1 region in their off-spring haploid strains. Phylogenetic analysis based on the IGS1 sequence revealed all A. bisporus strains could be differentiated from A. silvaticus and A. bitorquis strains. Five genetic groups were resolved among A. bisporus strains. Saejung and Saeyeon cultivars formed a separate genetic group. Our results suggest that IGS1 could be complementarily applied in the polymorphism analysis of button mushroom.
- Published
- 2016
34. Bioactive Sterol Derivatives Isolated from the
- Author
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Raman, Jagadeesh, Gajandran, Babu, Hariprasath, Lakshmanan, Oh Min-Ji, Oh, Jang Kab-Yeul, Jang, Kong Won-Sik, Kong, and Nanjian, Raaman
- Subjects
Sterols ,Cell Line, Tumor ,Neoplasms ,Humans ,Antineoplastic Agents ,Apoptosis ,Lipid Peroxidation ,Pleurotus - Abstract
The aim of the present study is to isolate and characterize the bioactive compounds from Pleurotus djamor against human breast cancer (MDA-MD-231) and mouse T cell lymphoma (EL4) cell lines.Sequential fractionization and column chromatography methods were involved in compound isolation. The structures of the isolated compound were determined by NMR, GC/MS, and X-ray crystallography studies.The isolated compounds 1- 4 [D-mannitol (C1), ergosta-5,7,22-trien-3β-ol (C2), 5,8- epidioxy-ergosta-6-22-dien-3β-ol (C3), and palmitic acid (C4)] are white crystal and amorphous powder in nature. All these compounds were isolated from this mushroom for the first time. In vitro lipid peroxidation activities of isolated compounds were determined by ferric thiocyanate (FTC) and thiobarbituric acid (TBA) method. The sterol derivatives C2 and C3 compounds displayed strong antioxidant activity and were not significantly different (p0.05) to α-tocopherol. This finding elaborates on the isolation of a cytotoxic compound C2 and C3 from P. djamor via a rapid elution method.The compound C3 has exhibited better cytotoxic activity against MDA-MD-231 and EL4 cells. The present finding and data might provide new insights into the possible therapeutic and pharmaceutical use for the design of anti-cancer drugs from this edible mushroom.
- Published
- 2019
35. Unusual genome expansion and transcription suppression in ectomycorrhizal Tricholoma matsutake by repetitive insertions of transposable elements
- Author
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Won-Sik Kong, Julius Park, Jong Guk Kim, Byoungnam Min, In Geol Choi, Hyeokjun Yoon, and Youn Lee Oh
- Subjects
Genetics ,Transposable element ,Whole genome sequencing ,Transcription (biology) ,Point mutation ,Somatic hypermutation ,Biology ,Transcription Factor Gene ,Gene ,Genome - Abstract
Genome sequence of Tricholoma matsutake was revealed as the one of the large fungal genomes published up to date at 189.0 Mbp with 15,305 predicted genes. The unusual size of this fungal genome contained frequent colonization of transposable elements (TEs) occupying more than half of the entire genome. We identified that 702 genes were surrounded by TEs and 83.2% of those genes were never transcribed at any development stage. This observation corroborated that the insertion of transposable elements alters the transcription of the genes neighboring TEs.Repeat-induced point mutation such as C to T hypermutation with a bias over ’CpG’ dinucleotides was also recognized in this genome, representing a typical defense mechanism against TEs during evolution. Many transcription factor genes were activated in both primordia and fruiting body, which indicates that many regulatory processes are shared during developmental stages. Small secreted protein genes (T. matsutake genome contained four copies of this domain. Three of the IstB-like genes were overexpressed in hyphae. In the CAZyme analysis, reduced CAZyme genes were found as other ectomycorrhizal genomes including a lot of loss of glycoside hydrolase genes. Also, auxiliary activity genes were dominantly transcribed in primordia. The T. matsutake genome sequence provides insight into the large genome size and clues to understand unusual fungal genome expansion.
- Published
- 2019
36. Potential geo-discriminative tools to trace the origins of the dried slices of shiitake (Lentinula edodes) using stable isotope ratios and OPLS-DA
- Author
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Yeon-Ju An, Hee-Youn Chi, Jae Kwang Kim, Ill-Min Chung, Won-Sik Kong, Jae-Gu Han, So-Yeon Kim, Mun Yhung Jung, Chang Kwon, Seung-Hyun Kim, and Yu-Jin Yang
- Subjects
Carbon Isotopes ,China ,Food trade ,biology ,Nitrogen Isotopes ,Stable isotope ratio ,010401 analytical chemistry ,Shiitake Mushrooms ,Discriminant Analysis ,04 agricultural and veterinary sciences ,General Medicine ,biology.organism_classification ,040401 food science ,01 natural sciences ,Mass Spectrometry ,0104 chemical sciences ,Analytical Chemistry ,0404 agricultural biotechnology ,Lentinula ,Republic of Korea ,Sulfur Isotopes ,Environmental science ,Food science ,Food Analysis ,Food Science - Abstract
The Lentinus edodes species, known as shiitake, has a history of extensive use in many cuisines in several East Asian countries owing to its unique and pleasant flavor and texture. As international food trade increases, reliable discrimination of geographical origin is becoming increasingly crucial in Korea to identify cheaper imported Chinese shiitake. Herein, stable isotope ratios (i.e., δ13C, δ15N, δ18O, and δ34S) were measured with a stable isotope ratio mass spectrometer, and a geographical discrimination method using orthogonal projection to latent structure-discriminant analysis was developed. The externally validated discrimination method showed excellent predictability (Q2cum = 0.881) and illustrated that δ18O and δ15N were important isotope markers for the geographical discrimination of dried shiitake slices. This study extends the knowledge of geographical differences between China and Korea evidenced by the shiitake isotope signatures, thereby contributing to potential geographical authentication with broader applications for international shiitake markets.
- Published
- 2019
37. Genomic discovery of the hypsin gene and biosynthetic pathways for terpenoids in Hypsizygus marmoreus
- Author
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Jeong Gu Kim, Kab Yeul Jang, Heejung Cho, Byoungnam Min, Seunghwan Kim, In Geol Choi, Won-Sik Kong, Youn Lee Oh, and Hongjae Park
- Subjects
0301 basic medicine ,Secondary Metabolism ,Genome ,Medical and Health Sciences ,Repetitive Sequences ,Putative gene ,Gene cluster ,Phylogeny ,Regulator gene ,Genetics ,Marmorin ,Genome project ,Genomics ,Hypsiziprenol A9 ,Biological Sciences ,Fungal ,Fungal genome ,Carbohydrate Metabolism ,Beech mushroom ,DNA microarray ,Genome, Fungal ,Sequence Analysis ,Research Article ,Biotechnology ,lcsh:QH426-470 ,Evolution ,Bioinformatics ,lcsh:Biotechnology ,Biology ,Evolution, Molecular ,Fungal Proteins ,03 medical and health sciences ,lcsh:TP248.13-248.65 ,Information and Computing Sciences ,Amino Acid Sequence ,Gene ,Repetitive Sequences, Nucleic Acid ,Nucleic Acid ,Terpenes ,fungi ,Human Genome ,Molecular ,Hypsizygus marmoreus ,Sequence Analysis, DNA ,DNA ,Biosynthetic Pathways ,lcsh:Genetics ,030104 developmental biology ,Hypsin ,Generic health relevance ,Agaricales - Abstract
Background Hypsizygus marmoreus (Beech mushroom) is a popular ingredient in Asian cuisine. The medicinal effects of its bioactive compounds such as hypsin and hypsiziprenol have been reported, but the genetic basis or biosynthesis of these components is unknown. Results In this study, we sequenced a reference strain of H. marmoreus (Haemi 51,987–8). We evaluated various assembly strategies, and as a result the Allpaths and PBJelly produced the best assembly. The resulting genome was 42.7 Mbp in length and annotated with 16,627 gene models. A putative gene (Hypma_04324) encoding the antifungal and antiproliferative hypsin protein with 75% sequence identity with the previously known N-terminal sequence was identified. Carbohydrate active enzyme analysis displayed the typical feature of white-rot fungi where auxiliary activity and carbohydrate-binding modules were enriched. The genome annotation revealed four terpene synthase genes responsible for terpenoid biosynthesis. From the gene tree analysis, we identified that terpene synthase genes can be classified into six clades. Four terpene synthase genes of H. marmoreus belonged to four different groups that implies they may be involved in the synthesis of different structures of terpenes. A terpene synthase gene cluster was well-conserved in Agaricomycetes genomes, which contained known biosynthesis and regulatory genes. Conclusions Genome sequence analysis of this mushroom led to the discovery of the hypsin gene. Comparative genome analysis revealed the conserved gene cluster for terpenoid biosynthesis in the genome. These discoveries will further our understanding of the biosynthesis of medicinal bioactive molecules in this edible mushroom. Electronic supplementary material The online version of this article (10.1186/s12864-018-5159-y) contains supplementary material, which is available to authorized users.
- Published
- 2018
38. Characteristics and breeding of a new cultivar of Pleurotus ostreatus that is tolerant to envirochanges
- Author
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Minji Oh, Won-Sik Kong, Pyung-Gyun Shin, Young-Bok Yoo, Eun-Sun Kim, Youn-Lee Oh, and Kab-Yeul Jang
- Subjects
0301 basic medicine ,03 medical and health sciences ,Horticulture ,030104 developmental biology ,030109 nutrition & dietetics ,Cultivar ,Pleurotus ostreatus ,Biology ,biology.organism_classification - Published
- 2016
39. Two-Step Solution Heat Treatment of AlSiCu Alloy for Improvement of Mechanical Properties
- Author
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Won Sik Kong, Chung Seok Kim, and Sang Guy Park
- Subjects
Materials science ,Mechanical Engineering ,Metallurgy ,Alloy ,Intermetallic ,chemistry.chemical_element ,engineering.material ,Condensed Matter Physics ,Microstructure ,Matrix (chemical analysis) ,Dendrite (crystal) ,chemistry ,Mechanics of Materials ,Aluminium ,Casting (metalworking) ,engineering ,General Materials Science ,Eutectic system - Abstract
This paper investigated the effects of two-step solution heat treatment of aluminum alloy for lightweight automotive on mechanical properties. Solution heat treatments in this study are applied to improve of mechanical properties through a single-step and two-step solution heat treatment. The microstructure of AlSiCu casting specimen represents a typical dendrite structure having a secondary dendrite arm spacing (SDAS) of 40 um. In addition to the Al matrix, a large amount of coarsen eutectic Si, Al2Cu intermetallic phases and Fe-rich phases are identified. After solution heat treatment, the mechanical properties of two-step solution heat treatment alloy show higher values than as-cast and a single-step solution specimens. Consequentially, the two-step solution heat treatment could be used in automotive parts to improve mechanical properties.
- Published
- 2016
40. Effect of Sensitization Treatment on Corrosion Properties in Austenitic Stainless Steel 304
- Author
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Chung Seok Kim, Won Sik Kong, and Seung Jae Moon
- Subjects
Materials science ,Scanning electron microscope ,chemistry.chemical_element ,02 engineering and technology ,engineering.material ,01 natural sciences ,Corrosion ,Chromium ,0103 physical sciences ,medicine ,General Materials Science ,Austenitic stainless steel ,Sensitization ,010302 applied physics ,020502 materials ,Mechanical Engineering ,Metallurgy ,Intergranular corrosion ,Condensed Matter Physics ,Microstructure ,medicine.anatomical_structure ,0205 materials engineering ,chemistry ,Mechanics of Materials ,engineering ,Deformation (engineering) - Abstract
Chromium depletion in AISI304 stainless steel can lead to intergranular corrosion due to temperature conditions and degree of deformation, and consequently to materials failure. The aim of this work is to study the effect of sensitization treatment on the corrosion resistance in AISI304 stainless steel after solution heat treatment at 1,000°C. Sensitization treatments were carried out at 670°C for 1 h, 2h, 5h and 10h in the electrical furnace. The intergranular corrosion resistance of the sensitized specimens was evaluated by double loop electrochemical potentiokinetic reactivation test. The microstructure of the specimens before and after the corrosion tests was observed through optical and scanning electron microscope. Solution treatment shows the dual structure, however, aging for 5 hours depicts the ditch structure. The ratio of current density increased as a function of aging time resulted in increase in the degree of sensitization.
- Published
- 2016
41. Thermal Aging of Dissimilar-Metal Weld Joints for Reactor Pressurized Vessels at Elevated Temperature
- Author
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Won Sik Kong and Chung Seok Kim
- Subjects
Materials science ,Mechanical Engineering ,Gas tungsten arc welding ,Alloy ,Alloy steel ,Metallurgy ,Welding ,engineering.material ,Condensed Matter Physics ,Microstructure ,law.invention ,Mechanics of Materials ,law ,Residual stress ,engineering ,General Materials Science ,Inconel ,Base metal - Abstract
The purpose of this study is to investigate the thermal aging of dissimilar metal welds for reactor pressurized vessels in the primary system of nuclear power plants. The influences of long-term aging of dissimilar-metal welds on microstructural and mechanical characteristics have been studied qualitatively and quantitatively. The dissimilar-metal welds composed of SA 508 Cl.3 low alloy steel and AISI 316L stainless steel are prepared after buttering alloy 82 on the SA 508 side by the gas tungsten arc welding process using Inconel 82 welding consumable. The test specimens are heat-treated at 600°C for 10000 hours at each predetermined aging time to simulate the degraded microstructure of dissimilar-metal welds subjected to high temperature and pressure. The long-term aging tests are interrupted at various stages to obtain the different level of degraded specimens. The microstructural changes in base metals and weld metal have been evaluated by the optical and electron microscope in relation with twins, grains, precipitates, and phase transformation. The residual stress and mechanical softening were also discussed in terms of microstructural changes during long-term aging.
- Published
- 2016
42. Taxonomic Position and Species Identity of the Cultivated Yeongji ‘Ganoderma lucidum’ in Korea
- Author
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Won-Sik Kong, Jae-Han Cho, Young-Jin Park, Chang-Soo Lee, Hong-Il Kim, and O-Chul Kwon
- Subjects
0301 basic medicine ,Ganoderma lingzhi ,Phylogenetic tree ,Traditional medicine ,Ganoderma ,Ganoderma sichuanense ,ITS rDNA ,Biology ,biology.organism_classification ,Microbiology ,03 medical and health sciences ,030104 developmental biology ,Infectious Diseases ,Phylogenetics ,Botany ,Taxonomy (biology) ,Internal transcribed spacer ,History of use ,Phylogeny ,Research Article ,Taxonomy ,Ganoderma lucidum - Abstract
Ganoderma lucidum has a long history of use as a traditional medicine in Asian countries. However, the taxonomy of Ganoderma species remains controversial, since they were initially classified on the basis of their morphological characteristics. Recently, it was proposed that G. lucidum from China be renamed as G. sichuanense or G. lingzhi. In the present study, phylogenetic analysis using the internal transcribed spacer region rDNA sequences of the Ganoderma species indicated that all strains of the Korean 'G. lucidum' clustered into one group together with G. sichuanense and G. lingzhi from China. However, strains from Europe and North American, which were regarded as true G. lucidum, were positioned in a clearly different group. In addition, the average size of the basidiospores from the Korean cultivated Yeongji strains was similar to that of G. lingzhi. Based on these results, we propose that the Korean cultivated Yeongji strains of 'G. lucidum' should be renamed as G. lingzhi.
- Published
- 2016
43. Development of medium for Pleurotus eryngii cultivation using Kojongsi persimmon peels
- Author
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Won-Sik Kong, Hye Soo Kim, Jong-Chun Cheong, Soo-Jeong Cho, Hyun Sook Kwon, Hong Chul Kim, and Chul Hwan Kim
- Subjects
Mushroom ,biology ,Stipe (botany) ,Untreated control ,Chemistry ,visual_art ,Botany ,visual_art.visual_art_medium ,Pleurotus eryngii ,Food science ,Sawdust ,biology.organism_classification ,Mycelium - Abstract
This study was carried out to investigated the avaiability of dried Koojongsi persimmon peels (KPP) as a useful mushroom medium using Pleurotus eryngii ASI 2312. Mushroom cultivation medium used in this study was mixed with medium mixture, corn cob and sawdust (220:65:15, v/v). Dried KPP was replaced mushroom cultivation medium (control) with 5, 10, 15, 20, 30, 40, 50% dried KPP. The T-N content of dried KPP treatments decreased to increase replaced ratio of the dried KPP and C/N ratio was increased to increase replaced ratio of the dried KPP. But T-C content of dried KPP treatments was similar to untreated control. The average cultivating periods of mycelium on dried KPP treatments was delayed to increase replaced ratio of the dried KPP and cultivating periods was delayed over 30% dried KPP treatments. The length of stipe of dried KPP treatments was longer than that of the untreated control to increase replaced ratio of the dried KPP and thickness of stipes was tend to be thinner than that of the untreated control to increase replaced ratio of the dried KPP. The moisture, carbohydrate, crude protein and crude ash content of mycelial were similar to untreated control, but crude fatty acid was increased to increase replaced ratio of the dried KPP. The content of 10% and 15% treatments were higher than untreatment control. The results based on cultivation yield and content indicated that optimal mixture ratio dried KPP was 15%.
- Published
- 2015
44. Effect of Conversion Rate of γ-Aminobutyric acid (GABA) by Yogurt Fermentation with Addition of Nanoparticle Winter Mushroom and Hydroponic Ginseng
- Author
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Won-Sik Kong, Hee-Cheong Kim, Youn-Lee Oh, Young-Bok Yoo, and Pyung-Gyun Shin
- Subjects
Mushroom ,animal structures ,Chemistry ,Decarboxylation ,Monosodium glutamate ,fungi ,Glutamate decarboxylase ,food and beverages ,Industrial fermentation ,Aminobutyric acid ,Ginseng ,chemistry.chemical_compound ,nervous system ,Biochemistry ,Fermentation ,Food science - Abstract
Aminobutyric acid (GABA) is basically neurotrasmitter produced by the decarboxylation of L-glutamic acid catalyzed by glutamic acid decarboxylase (GAD), which was known to convert monosodium glutamate (MSG) to GABA. To investigate enhancement of reversion rate of GABA, the yogurt fermentation with addition of nanoparticle winter mushroom and hydroponic ginseng was used. The conversion rate was revealed to nanoparticle winter mushroom and hydroponic ginseng fermenter (88%) > winter mushroom fermenter (52%) > nanoparticle winter mushroom fermenter (44%). The results showed that nanoparticle winter mushroom and hydroponic ginseng supplemented substrates for enhancement of GABA may be used more effectively as one of potential sources of functional foods.
- Published
- 2015
45. Isolation and Characterization of Bacillus subtilis CA105 from Spent Mushroom (Pleurotus ostreatus) Substrates
- Author
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Chan-Jung Lee, Hyun Sook Kwon, Won-Sik Kong, Soo Jeong Cho, Hye Soo Kim, and Chul Hwan Kim
- Subjects
Mushroom ,biology ,fungi ,Xylanase ,biology.protein ,Pleurotus ostreatus ,Agar diffusion test ,Bacillus subtilis ,Cellulase ,biology.organism_classification ,16S ribosomal RNA ,Bacteria ,Microbiology - Abstract
In order to isolate compost-promoting bacteria with high activity of cellulase and xylanase, spent mushroom substrates with sawdust were collected from mushroom cultivation farm, Jinju, Gyeongnam in Korea. Among of the isolates, one strain, designated CA105 was selected by agar diffusion method. The strain CA105 was identified as members of the Bacillus subtilis by biochemical characteristics using VITEK 2 system. Comparative 16S rRNA gene sequence analysis showed that isolate CA105 formed a distinct phylogenetic tree within the genus Bacillus and was most closely related to Bacillus subtilis with 16S rRNA gene sequence similarity of 98.9%. On the basis of its physiological properties, biochemical characteristics and phylogenetic distinctiveness, isolate CA105 was classified within the genus Bacillus subtilis, for which the name Bacillus subtilis CA105 is proposed. The cellulase and xylanase activity of B. subtilis CA105 was slightly increased according to bacterial population from exponential phase to stationary phase in growth curve for Bacillus sp. CA105.
- Published
- 2015
46. Characterization of Volatile Profiles of Six Popular Edible Mushrooms Using Headspace-Solid-Phase Microextraction Coupled with Gas Chromatography Combined with Chemometric Analysis
- Author
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Mun Yhung, Jung, Da Eun, Lee, Hong Yu, Cheng, Il-Min, Chung, Seung-Hyun, Kim, Jae-Gu, Han, and Won-Sik, Kong
- Subjects
Principal Component Analysis ,Volatile Organic Compounds ,Plant Extracts ,Vegetables ,Discriminant Analysis ,Agaricales ,Gas Chromatography-Mass Spectrometry ,Solid Phase Microextraction - Abstract
The classification of six mushroom species (white beech, brown beech, button, oyster, king oyster, and enoki mushrooms) was successfully achieved using canonical discriminant analysis (CDA) on volatile metabolite data sets obtained by headspace-solid-phase microextraction gas chromatography (HS-SPME-GC). Twenty-seven major volatile compounds in six edible mushrooms were positively identified by HS-SPME-GC mass spectroscopy. The total volatile content was highest in brown beech mushroom (P0.05). Significant difference in volatile profile was observed between brown beach and white beech mushrooms. Button mushroom contained significantly higher contents of benzaldehyde and benzyl alcohol than the other mushrooms (P0.05). Oyster mushroom contained 1-octen-3-ol as the most prevalent volatile, representing 67% out of total volatiles. Hexanal (35.0%) and 1-octen-3-ol (22.5%) were the most abundant volatiles found in king oyster. Hexanal (29.1%) was the most prevalent volatile in enoki mushroom only. Several volatile pairs with very high positive correlation in their levels were identified, representing the highest correlation coefficient (r = 0.970) for the pair of t-2-octenal and 2,4-octandienal. CDA was much more efficient than principal component analysis for the differentiation of mushroom species. PRACTICAL APPLICATION: The present study provided the important information on the volatile metabolite profiles of popular six commercial mushroom species. The present data will be useful for the quality control of mushrooms cultivated in farms and mushroom products processed in food industry. The strategy of canonical discriminant analysis in combination with HS-SPME-GC could be expanded for the determining the authentication of mushroom species.
- Published
- 2018
47. Genome Sequencing and Carbohydrate-Active Enzyme (CAZyme) Repertoire of the White Rot Fungus Flammulina elastica
- Author
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Yong-Un Jeong, Young-Jin Park, and Won-Sik Kong
- Subjects
0301 basic medicine ,Glycoside Hydrolases ,Gene prediction ,Computational biology ,Genome ,Catalysis ,DNA sequencing ,Article ,lcsh:Chemistry ,Inorganic Chemistry ,Fungal Proteins ,03 medical and health sciences ,Databases, Genetic ,Glycoside hydrolase ,carbohydrate active enzyme ,Physical and Theoretical Chemistry ,Flammulina elastica ,lcsh:QH301-705.5 ,Molecular Biology ,Gene ,Spectroscopy ,Phylogeny ,Flammulina ,Polysaccharide-Lyases ,Whole genome sequencing ,whole genome sequencing ,biology ,Organic Chemistry ,Glycosyltransferases ,General Medicine ,Sequence Analysis, DNA ,biology.organism_classification ,Computer Science Applications ,030104 developmental biology ,lcsh:Biology (General) ,lcsh:QD1-999 ,Genome, Fungal ,GC-content - Abstract
Next-generation sequencing (NGS) of the Flammulina elastica (wood-rotting basidiomycete) genome was performed to identify carbohydrate-active enzymes (CAZymes). The resulting assembly (31 kmer) revealed a total length of 35,045,521 bp (49.7% GC content). Using the AUGUSTUS tool, 12,536 total gene structures were predicted by ab initio gene prediction. An analysis of orthologs revealed that 6806 groups contained at least one F. elastica protein. Among the 12,536 predicted genes, F. elastica contained 24 species-specific genes, of which 17 genes were paralogous. CAZymes are divided into five classes: glycoside hydrolases (GHs), carbohydrate esterases (CEs), polysaccharide lyases (PLs), glycosyltransferases (GTs), and auxiliary activities (AA). In the present study, annotation of the predicted amino acid sequences from F. elastica genes using the dbCAN CAZyme database revealed 508 CAZymes, including 82 AAs, 218 GHs, 89 GTs, 18 PLs, 59 CEs, and 42 carbohydrate binding modules in the F. elastica genome. Although the CAZyme repertoire of F. elastica was similar to those of other fungal species, the total number of GTs in F. elastica was larger than those of other basidiomycetes. This genome information elucidates newly identified wood-degrading machinery in F. elastica, offers opportunities to better understand this fungus, and presents possibilities for more detailed studies on lignocellulosic biomass degradation that may lead to future biotechnological and industrial applications.
- Published
- 2018
48. Regional discrimination of Agaricus bisporus mushroom using the natural stable isotope ratios
- Author
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Ji-Hee Lee, Mun Yhung Jung, Seung-Hyun Kim, Ill-Min Chung, Jae-Gu Han, Won-Sik Kong, Jae Kwang Kim, Min-Jeong An, and Yeon-Ju An
- Subjects
Farms ,Agaricus ,Biology ,Oxygen Isotopes ,01 natural sciences ,Mass Spectrometry ,Analytical Chemistry ,0404 agricultural biotechnology ,Isotopes ,Republic of Korea ,Sulfur Isotopes ,Cultivar ,Mushroom ,Carbon Isotopes ,δ13C ,Nitrogen Isotopes ,Stable isotope ratio ,010401 analytical chemistry ,04 agricultural and veterinary sciences ,General Medicine ,biology.organism_classification ,040401 food science ,Isotopes of nitrogen ,0104 chemical sciences ,Horticulture ,Isotopes of carbon ,Agaricus bisporus ,Food Science - Abstract
This study was aimed to verify the regional traceability of Agaricus bisporus mushroom using unique δ13C, δ15N, δ18O, and δ34S features combined with chemometric approaches. Ten cultivars from 15 mushroom farms in six regions of Korea were measured their isotopic signatures by stable isotope ratio mass spectrometer. The δ13C, δ15N, δ18O, and δ34S values were significantly different among mushrooms collected from six cultivation regions (P
- Published
- 2018
49. Anti-inflammatory effect of lovastatin is mediated via the modulation of NF-κB and inhibition of HDAC1 and the PI3K/Akt/mTOR pathway in RAW264.7 macrophages
- Author
-
Ji-Hyun Lee, Hyung-Wook Choi, Minji Oh, Gun-Do Kim, Pyung-Gyun Shin, Won-Sik Kong, Woo-Suk Choi, Yong-Bae Seo, and Min-Jae Kang
- Subjects
Lipopolysaccharides ,0301 basic medicine ,Anti-Inflammatory Agents ,Nitric Oxide Synthase Type II ,Histone Deacetylase 1 ,Nitric oxide ,Mice ,Phosphatidylinositol 3-Kinases ,03 medical and health sciences ,chemistry.chemical_compound ,polycyclic compounds ,Genetics ,medicine ,Animals ,Humans ,Lovastatin ,Protein kinase B ,PI3K/AKT/mTOR pathway ,Inflammation ,biology ,Tumor Necrosis Factor-alpha ,Macrophages ,TOR Serine-Threonine Kinases ,NF-kappa B ,nutritional and metabolic diseases ,NF-κB ,General Medicine ,Molecular biology ,Nitric oxide synthase ,RAW 264.7 Cells ,030104 developmental biology ,Gene Expression Regulation ,chemistry ,biology.protein ,Phosphorylation ,lipids (amino acids, peptides, and proteins) ,Tumor necrosis factor alpha ,Proto-Oncogene Proteins c-akt ,medicine.drug - Abstract
Lovastatin is a 3-hydroxy-3-methylglutaryl-CoA reductase inhibitor that is clinically used for the prevention of cardiovascular diseases. Although it has been reported that lovastatin has anti-inflammatory properties in several studies, how lovastatin regulates the inflammation is still unclear. To evaluate the effect of lovastatin on nitric oxide production (NO) in RAW264.7 macrophages, NO production assay was performed. Also, cell viability was measured to confirm cytotoxicity. Level of tumor necrosis factor-α (TNF-α) transcription was measured by reverse transcription polymerase chain reaction (RT-PCR) from total RNA in RAW264.7 cells. Western blot analysis and immunofluorescence staining were used to investigate the regulation of lovastatin on the expression, phosphorylation, and nuclear translocation of cellular proteins. The results of the present study revealed that lovastatin reduced nitric oxide production via the reduction of inducible nitric oxide synthase (iNOS) expression in lipopolysaccharide (LPS)-stimulated RAW264.7 macrophage cells. The mRNA level of TNF-α was reduced in presence of lovastatin. In addition, lovastatin downregulated histone deacetylase 1 (HDAC1), resulting in the accumulation of acetylated histone H3 and heat shock protein 70. Furthermore, the expression of phosphoinositide 3-kinase catalytic subunits α and β was reduced under lovastatin treatment, and the phosphorylation of Akt and mammalian target of rapamycin was consequently inhibited. Lovastatin also inhibited the phosphorylation of inhibitor of nuclear factor (NF)-κBα and the translocation of NF-κB into the nucleus. Therefore, the present study demonstrates that lovastatin inhibits the expression of pro-inflammatory mediators, including iNOS and TNF-α, through the suppression of HDAC1 expression, PI3K/Akt phosphorylation and NF-κB translocation in LPS-stimulated RAW264.7 macrophage cells.
- Published
- 2017
50. Selection of parental monokaryons from Korean Hypsizigus marmoreus by protoplast regeneration
- Author
-
Youn-Lee Oh, Kab-Yeul Jang, Min ji Oh, Eun-Sun Kim, Pyung-Gyun Shin, Won-Sik Kong, and In Geol Choi
- Subjects
Mushroom ,food.ingredient ,Strain (chemistry) ,fungi ,food and beverages ,Biology ,Protoplast ,Edible mushroom ,Horticulture ,food ,Botany ,Agar ,Cultivar ,Clamp connection ,Mycelium - Abstract
Hypsizigus marmoreus is commercially the most important edible mushroom in Japan. This mushroom is usually cultivated for a longer period (about 85~120 days) than other mushroom. In order to develop a new cultivar that has a shortened cultivation period, the genome analysis of this strain has been considered. This study aims to obtain parental monokaryotic strains reproducing 'Haemi' cultivar in Hypsizigus marmoreus for reference genome sequencing. The mycelia were cultured in MCM and MYG media for various incubation periods. Homogenized mycelia were treated with commercial cell wall degrading enzymes to maximize protoplasts production yield from Hypsizigus marmoreus. The greatest number of protoplasts was obtained from mycelia cultured in MCM media for 3 days using Novozyme enzyme. The isolated protoplasts were grown in regeneration agar media after two weeks. Regenerated colonies were picked and moved on separated dishes for microscopic observation. Neohaplonts regenerated from dikayotic strains were identified by the absence of clamp connections. We confirmed that one of monokaryotic strains is a parental strain by crossing with an original compatible strain of 'Haemi' cultivar. This parental strain will be used for reference genome sequence analysis.
- Published
- 2015
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