Genome-wide analysis and prediction of genes involved in the biosynthesis of polysaccharides and bioactive secondary metabolites in high-temperature-tolerant wild Flammulina filiformis
Abstract Background Flammulina filiformis (previously known as Asian F. velutipes) is a popular commercial edible mushroom. Many bioactive compounds with medicinal effects, such as polysaccharides and sesquiterpenoids, have been isolated and identified from F. filiformis, but their biosynthesis and...
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BMC
2020-10-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-020-07108-6 |
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| author | Juan Chen Jia-Mei Li Yan-Jing Tang Ke Ma Bing Li Xu Zeng Xiao-Bin Liu Yang Li Zhu-Liang Yang Wei-Nan Xu Bao-Gui Xie Hong-Wei Liu Shun-Xing Guo |
| author_facet | Juan Chen Jia-Mei Li Yan-Jing Tang Ke Ma Bing Li Xu Zeng Xiao-Bin Liu Yang Li Zhu-Liang Yang Wei-Nan Xu Bao-Gui Xie Hong-Wei Liu Shun-Xing Guo |
| author_sort | Juan Chen |
| collection | DOAJ |
| description | Abstract Background Flammulina filiformis (previously known as Asian F. velutipes) is a popular commercial edible mushroom. Many bioactive compounds with medicinal effects, such as polysaccharides and sesquiterpenoids, have been isolated and identified from F. filiformis, but their biosynthesis and regulation at the molecular level remains unclear. In this study, we sequenced the genome of the wild strain F. filiformis Liu355, predicted its biosynthetic gene clusters (BGCs) and profiled the expression of these genes in wild and cultivar strains and in different developmental stages of the wild F. filiformis strain by a comparative transcriptomic analysis. Results We found that the genome of the F. filiformis was 35.01 Mb in length and harbored 10,396 gene models. Thirteen putative terpenoid gene clusters were predicted and 12 sesquiterpene synthase genes belonging to four different groups and two type I polyketide synthase gene clusters were identified in the F. filiformis genome. The number of genes related to terpenoid biosynthesis was higher in the wild strain (119 genes) than in the cultivar strain (81 genes). Most terpenoid biosynthesis genes were upregulated in the primordium and fruiting body of the wild strain, while the polyketide synthase genes were generally upregulated in the mycelium of the wild strain. Moreover, genes encoding UDP-glucose pyrophosphorylase and UDP-glucose dehydrogenase, which are involved in polysaccharide biosynthesis, had relatively high transcript levels both in the mycelium and fruiting body of the wild F. filiformis strain. Conclusions F. filiformis is enriched in a number of gene clusters involved in the biosynthesis of polysaccharides and terpenoid bioactive compounds and these genes usually display differential expression between wild and cultivar strains, even in different developmental stages. This study expands our knowledge of the biology of F. filiformis and provides valuable data for elucidating the regulation of secondary metabolites in this unique F. filiformis strain. |
| first_indexed | 2024-12-14T18:46:29Z |
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| id | doaj.art-f0f714549c5e4681b5e243890c25a273 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-14T18:46:29Z |
| publishDate | 2020-10-01 |
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| series | BMC Genomics |
| spelling | doaj.art-f0f714549c5e4681b5e243890c25a2732022-12-21T22:51:23ZengBMCBMC Genomics1471-21642020-10-0121111610.1186/s12864-020-07108-6Genome-wide analysis and prediction of genes involved in the biosynthesis of polysaccharides and bioactive secondary metabolites in high-temperature-tolerant wild Flammulina filiformisJuan Chen0Jia-Mei Li1Yan-Jing Tang2Ke Ma3Bing Li4Xu Zeng5Xiao-Bin Liu6Yang Li7Zhu-Liang Yang8Wei-Nan Xu9Bao-Gui Xie10Hong-Wei Liu11Shun-Xing Guo12Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical CollegeKey Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical CollegeKey Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical CollegeState Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of SciencesKey Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical CollegeKey Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical CollegeKey Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKey Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical CollegeKey Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesMycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry UniversityMycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry UniversityState Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of SciencesKey Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical CollegeAbstract Background Flammulina filiformis (previously known as Asian F. velutipes) is a popular commercial edible mushroom. Many bioactive compounds with medicinal effects, such as polysaccharides and sesquiterpenoids, have been isolated and identified from F. filiformis, but their biosynthesis and regulation at the molecular level remains unclear. In this study, we sequenced the genome of the wild strain F. filiformis Liu355, predicted its biosynthetic gene clusters (BGCs) and profiled the expression of these genes in wild and cultivar strains and in different developmental stages of the wild F. filiformis strain by a comparative transcriptomic analysis. Results We found that the genome of the F. filiformis was 35.01 Mb in length and harbored 10,396 gene models. Thirteen putative terpenoid gene clusters were predicted and 12 sesquiterpene synthase genes belonging to four different groups and two type I polyketide synthase gene clusters were identified in the F. filiformis genome. The number of genes related to terpenoid biosynthesis was higher in the wild strain (119 genes) than in the cultivar strain (81 genes). Most terpenoid biosynthesis genes were upregulated in the primordium and fruiting body of the wild strain, while the polyketide synthase genes were generally upregulated in the mycelium of the wild strain. Moreover, genes encoding UDP-glucose pyrophosphorylase and UDP-glucose dehydrogenase, which are involved in polysaccharide biosynthesis, had relatively high transcript levels both in the mycelium and fruiting body of the wild F. filiformis strain. Conclusions F. filiformis is enriched in a number of gene clusters involved in the biosynthesis of polysaccharides and terpenoid bioactive compounds and these genes usually display differential expression between wild and cultivar strains, even in different developmental stages. This study expands our knowledge of the biology of F. filiformis and provides valuable data for elucidating the regulation of secondary metabolites in this unique F. filiformis strain.http://link.springer.com/article/10.1186/s12864-020-07108-6Edible mushroomGene clusterGene expressionPolysaccharidesSesquiterpeneHigh-temperature-tolerance |
| spellingShingle | Juan Chen Jia-Mei Li Yan-Jing Tang Ke Ma Bing Li Xu Zeng Xiao-Bin Liu Yang Li Zhu-Liang Yang Wei-Nan Xu Bao-Gui Xie Hong-Wei Liu Shun-Xing Guo Genome-wide analysis and prediction of genes involved in the biosynthesis of polysaccharides and bioactive secondary metabolites in high-temperature-tolerant wild Flammulina filiformis BMC Genomics Edible mushroom Gene cluster Gene expression Polysaccharides Sesquiterpene High-temperature-tolerance |
| title | Genome-wide analysis and prediction of genes involved in the biosynthesis of polysaccharides and bioactive secondary metabolites in high-temperature-tolerant wild Flammulina filiformis |
| title_full | Genome-wide analysis and prediction of genes involved in the biosynthesis of polysaccharides and bioactive secondary metabolites in high-temperature-tolerant wild Flammulina filiformis |
| title_fullStr | Genome-wide analysis and prediction of genes involved in the biosynthesis of polysaccharides and bioactive secondary metabolites in high-temperature-tolerant wild Flammulina filiformis |
| title_full_unstemmed | Genome-wide analysis and prediction of genes involved in the biosynthesis of polysaccharides and bioactive secondary metabolites in high-temperature-tolerant wild Flammulina filiformis |
| title_short | Genome-wide analysis and prediction of genes involved in the biosynthesis of polysaccharides and bioactive secondary metabolites in high-temperature-tolerant wild Flammulina filiformis |
| title_sort | genome wide analysis and prediction of genes involved in the biosynthesis of polysaccharides and bioactive secondary metabolites in high temperature tolerant wild flammulina filiformis |
| topic | Edible mushroom Gene cluster Gene expression Polysaccharides Sesquiterpene High-temperature-tolerance |
| url | http://link.springer.com/article/10.1186/s12864-020-07108-6 |
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