Whole Genome Sequence of an Edible Mushroom <i>Oudemansiella raphanipes</i> (Changgengu)
<i>Oudemansiella raphanipes</i>, considered as a well-known culinary edible mushroom with a high content of natural bioactive substances, is widely cultivated in China with the commercial name Changgengu. However, due to the lack of genomic data, molecular and genetic study on <i>O...
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MDPI AG
2023-02-01
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| Series: | Journal of Fungi |
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| Online Access: | https://www.mdpi.com/2309-608X/9/2/266 |
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| author | Liping Zhu Xia Gao Meihua Zhang Chunhui Hu Wujie Yang Lizhong Guo Song Yang Hailong Yu Hao Yu |
| author_facet | Liping Zhu Xia Gao Meihua Zhang Chunhui Hu Wujie Yang Lizhong Guo Song Yang Hailong Yu Hao Yu |
| author_sort | Liping Zhu |
| collection | DOAJ |
| description | <i>Oudemansiella raphanipes</i>, considered as a well-known culinary edible mushroom with a high content of natural bioactive substances, is widely cultivated in China with the commercial name Changgengu. However, due to the lack of genomic data, molecular and genetic study on <i>O. raphanipes</i> is rare. To obtain a comprehensive overview of genetic characteristics and enhance the value of <i>O. raphanipes</i>, two mating-compatible monokaryons isolated from the dikaryon were applied for de novo genome sequencing and assembly using Nanopore and /or Illumina sequencing platforms. One of the monokaryons, <i>O. raphanipes</i> CGG-A-s1, was annotated with 21,308 protein-coding genes, of which 56 were predicted to be involved in the biosynthesis of secondary metabolites such as terpene, type I PKS, NRPS, and siderophore. Phylogenetic and comparative analysis of multiple fungi genomes revealed a close evolutionary relationship between <i>O. raphanipes</i> and <i>Mucidula mucid</i> based on single-copy orthologous protein genes. Significant collinearity was detected between <i>O. raphanipes</i> and <i>Flammulina velutipes</i> on the synteny of inter-species genomes. 664 CAZyme genes in CGG-A-s1 were identified with GHs and AAs families significantly elevated when compared with the other 25 sequenced fungi, indicating a strong wood degradation ability. Furthermore, the mating type locus analysis revealed that CGG-A-s1 and CGG-A-s2 were conserved in the gene organization of the mating <i>A</i> locus but various in that of the mating <i>B</i> locus. The genome resource of <i>O. raphanipes</i> will provide new insights into its development of genetic studies and commercial production of high-quality varieties. |
| first_indexed | 2024-03-11T08:36:02Z |
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| issn | 2309-608X |
| language | English |
| last_indexed | 2024-03-11T08:36:02Z |
| publishDate | 2023-02-01 |
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| series | Journal of Fungi |
| spelling | doaj.art-bbdf159911944e64aa2d1f2573903a1a2023-11-16T21:31:23ZengMDPI AGJournal of Fungi2309-608X2023-02-019226610.3390/jof9020266Whole Genome Sequence of an Edible Mushroom <i>Oudemansiella raphanipes</i> (Changgengu)Liping Zhu0Xia Gao1Meihua Zhang2Chunhui Hu3Wujie Yang4Lizhong Guo5Song Yang6Hailong Yu7Hao Yu8Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao 266109, ChinaShandong Agricultural Technology Extending Station, Jinan 250100, ChinaShandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao 266109, ChinaShandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao 266109, ChinaShandong Agricultural Technology Extending Station, Jinan 250100, ChinaShandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao 266109, ChinaShandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao 266109, ChinaInstitute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Shanghai 201403, ChinaShandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao 266109, China<i>Oudemansiella raphanipes</i>, considered as a well-known culinary edible mushroom with a high content of natural bioactive substances, is widely cultivated in China with the commercial name Changgengu. However, due to the lack of genomic data, molecular and genetic study on <i>O. raphanipes</i> is rare. To obtain a comprehensive overview of genetic characteristics and enhance the value of <i>O. raphanipes</i>, two mating-compatible monokaryons isolated from the dikaryon were applied for de novo genome sequencing and assembly using Nanopore and /or Illumina sequencing platforms. One of the monokaryons, <i>O. raphanipes</i> CGG-A-s1, was annotated with 21,308 protein-coding genes, of which 56 were predicted to be involved in the biosynthesis of secondary metabolites such as terpene, type I PKS, NRPS, and siderophore. Phylogenetic and comparative analysis of multiple fungi genomes revealed a close evolutionary relationship between <i>O. raphanipes</i> and <i>Mucidula mucid</i> based on single-copy orthologous protein genes. Significant collinearity was detected between <i>O. raphanipes</i> and <i>Flammulina velutipes</i> on the synteny of inter-species genomes. 664 CAZyme genes in CGG-A-s1 were identified with GHs and AAs families significantly elevated when compared with the other 25 sequenced fungi, indicating a strong wood degradation ability. Furthermore, the mating type locus analysis revealed that CGG-A-s1 and CGG-A-s2 were conserved in the gene organization of the mating <i>A</i> locus but various in that of the mating <i>B</i> locus. The genome resource of <i>O. raphanipes</i> will provide new insights into its development of genetic studies and commercial production of high-quality varieties.https://www.mdpi.com/2309-608X/9/2/266<i>Oudemansiella raphanipes</i>genomemonokaryonsecondary metabolitesCAZymephylogenetic analysis |
| spellingShingle | Liping Zhu Xia Gao Meihua Zhang Chunhui Hu Wujie Yang Lizhong Guo Song Yang Hailong Yu Hao Yu Whole Genome Sequence of an Edible Mushroom <i>Oudemansiella raphanipes</i> (Changgengu) Journal of Fungi <i>Oudemansiella raphanipes</i> genome monokaryon secondary metabolites CAZyme phylogenetic analysis |
| title | Whole Genome Sequence of an Edible Mushroom <i>Oudemansiella raphanipes</i> (Changgengu) |
| title_full | Whole Genome Sequence of an Edible Mushroom <i>Oudemansiella raphanipes</i> (Changgengu) |
| title_fullStr | Whole Genome Sequence of an Edible Mushroom <i>Oudemansiella raphanipes</i> (Changgengu) |
| title_full_unstemmed | Whole Genome Sequence of an Edible Mushroom <i>Oudemansiella raphanipes</i> (Changgengu) |
| title_short | Whole Genome Sequence of an Edible Mushroom <i>Oudemansiella raphanipes</i> (Changgengu) |
| title_sort | whole genome sequence of an edible mushroom i oudemansiella raphanipes i changgengu |
| topic | <i>Oudemansiella raphanipes</i> genome monokaryon secondary metabolites CAZyme phylogenetic analysis |
| url | https://www.mdpi.com/2309-608X/9/2/266 |
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