Whole-Genome Sequencing and Comparative Genomics Analysis of the Wild Edible Mushroom (<i>Gomphus purpuraceus</i>) Provide Insights into Its Potential Food Application and Artificial Domestication
<i>Gomphus purpuraceus</i> (Iwade) Yokoyama is a species of wild fungi that grows in southwest China, considered an edible and medicinal fungus with potential commercial prospects. However, the detailed mechanisms related to the development of mycelium and the formation of the fruiting b...
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MDPI AG
2022-09-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/13/9/1628 |
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| author | Yangyang Geng Shixin Zhang Ningxian Yang Likang Qin |
| author_facet | Yangyang Geng Shixin Zhang Ningxian Yang Likang Qin |
| author_sort | Yangyang Geng |
| collection | DOAJ |
| description | <i>Gomphus purpuraceus</i> (Iwade) Yokoyama is a species of wild fungi that grows in southwest China, considered an edible and medicinal fungus with potential commercial prospects. However, the detailed mechanisms related to the development of mycelium and the formation of the fruiting body are unclear. To obtain a comprehensive overview of genetic features, whole-genome and comparative genomics analyses of <i>G. purpuraceus</i> were performed. High-quality DNA was extracted from the mycelium, which was isolated from a fresh fruiting body of <i>G. purpuraceus</i>. The DNA sample was subjected to sequencing using Illumina and Oxford Nanopore sequencing platforms. A genome assembly totaling 40.15 Mb in 50 contigs with an N50 length of 2.06 Mb was generated, and 8705 putative predicted genes were found. Subsequently, phylogenetic analysis revealed a close evolutionary relationship between <i>G. purpuraceus</i> and <i>Gomphus bonarii</i>. Moreover, a total of 403 carbohydrate-active enzymes (CAZymes) were identified in <i>G. purpuraceus</i>, which included 147 glycoside hydrolases (GHs), 85 glycosyl transferases (GTs), 8 polysaccharide lyases (PLs), 76 carbohydrate esterases (CEs), 57 auxiliary activities (AAs) and 30 carbohydrate-binding modules (CBMs). Compared with the other 13 fungi (<i>Laccaria bicolor</i>, <i>Russula virescens</i>, <i>Boletus edulis</i>, etc.), the number and distribution of CAZymes in <i>G. purpuraceus</i> were similar to other mycorrhizal fungi. Furthermore, the optimization of culture medium for <i>G. purpuraceus</i> showed the efficient utilization of disaccharides such as sucrose and maltose. The genome of <i>G. purpuraceus</i> provides new insights into its niche, food applications and potential artificial domestication. |
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| language | English |
| last_indexed | 2024-03-09T23:55:57Z |
| publishDate | 2022-09-01 |
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| series | Genes |
| spelling | doaj.art-e12c88b6b6b94f0ead96de479d3b4bb32023-11-23T16:25:24ZengMDPI AGGenes2073-44252022-09-01139162810.3390/genes13091628Whole-Genome Sequencing and Comparative Genomics Analysis of the Wild Edible Mushroom (<i>Gomphus purpuraceus</i>) Provide Insights into Its Potential Food Application and Artificial DomesticationYangyang Geng0Shixin Zhang1Ningxian Yang2Likang Qin3Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Hangtian West Road, Guiyang 550025, ChinaGuizhou Institute of Walnut, 214 Fuyuan South Road, Guiyang 550005, ChinaKey Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Hangtian West Road, Guiyang 550025, ChinaSchool of Liquor and Food Engineering, Guizhou University, Guiyang 550025, China<i>Gomphus purpuraceus</i> (Iwade) Yokoyama is a species of wild fungi that grows in southwest China, considered an edible and medicinal fungus with potential commercial prospects. However, the detailed mechanisms related to the development of mycelium and the formation of the fruiting body are unclear. To obtain a comprehensive overview of genetic features, whole-genome and comparative genomics analyses of <i>G. purpuraceus</i> were performed. High-quality DNA was extracted from the mycelium, which was isolated from a fresh fruiting body of <i>G. purpuraceus</i>. The DNA sample was subjected to sequencing using Illumina and Oxford Nanopore sequencing platforms. A genome assembly totaling 40.15 Mb in 50 contigs with an N50 length of 2.06 Mb was generated, and 8705 putative predicted genes were found. Subsequently, phylogenetic analysis revealed a close evolutionary relationship between <i>G. purpuraceus</i> and <i>Gomphus bonarii</i>. Moreover, a total of 403 carbohydrate-active enzymes (CAZymes) were identified in <i>G. purpuraceus</i>, which included 147 glycoside hydrolases (GHs), 85 glycosyl transferases (GTs), 8 polysaccharide lyases (PLs), 76 carbohydrate esterases (CEs), 57 auxiliary activities (AAs) and 30 carbohydrate-binding modules (CBMs). Compared with the other 13 fungi (<i>Laccaria bicolor</i>, <i>Russula virescens</i>, <i>Boletus edulis</i>, etc.), the number and distribution of CAZymes in <i>G. purpuraceus</i> were similar to other mycorrhizal fungi. Furthermore, the optimization of culture medium for <i>G. purpuraceus</i> showed the efficient utilization of disaccharides such as sucrose and maltose. The genome of <i>G. purpuraceus</i> provides new insights into its niche, food applications and potential artificial domestication.https://www.mdpi.com/2073-4425/13/9/1628<i>Gomphus purpuraceus</i> (Iwade) Yokoyamaedible fungiCAZymesphylogeneticsecondary metabolisms |
| spellingShingle | Yangyang Geng Shixin Zhang Ningxian Yang Likang Qin Whole-Genome Sequencing and Comparative Genomics Analysis of the Wild Edible Mushroom (<i>Gomphus purpuraceus</i>) Provide Insights into Its Potential Food Application and Artificial Domestication Genes <i>Gomphus purpuraceus</i> (Iwade) Yokoyama edible fungi CAZymes phylogenetic secondary metabolisms |
| title | Whole-Genome Sequencing and Comparative Genomics Analysis of the Wild Edible Mushroom (<i>Gomphus purpuraceus</i>) Provide Insights into Its Potential Food Application and Artificial Domestication |
| title_full | Whole-Genome Sequencing and Comparative Genomics Analysis of the Wild Edible Mushroom (<i>Gomphus purpuraceus</i>) Provide Insights into Its Potential Food Application and Artificial Domestication |
| title_fullStr | Whole-Genome Sequencing and Comparative Genomics Analysis of the Wild Edible Mushroom (<i>Gomphus purpuraceus</i>) Provide Insights into Its Potential Food Application and Artificial Domestication |
| title_full_unstemmed | Whole-Genome Sequencing and Comparative Genomics Analysis of the Wild Edible Mushroom (<i>Gomphus purpuraceus</i>) Provide Insights into Its Potential Food Application and Artificial Domestication |
| title_short | Whole-Genome Sequencing and Comparative Genomics Analysis of the Wild Edible Mushroom (<i>Gomphus purpuraceus</i>) Provide Insights into Its Potential Food Application and Artificial Domestication |
| title_sort | whole genome sequencing and comparative genomics analysis of the wild edible mushroom i gomphus purpuraceus i provide insights into its potential food application and artificial domestication |
| topic | <i>Gomphus purpuraceus</i> (Iwade) Yokoyama edible fungi CAZymes phylogenetic secondary metabolisms |
| url | https://www.mdpi.com/2073-4425/13/9/1628 |
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