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Guo M, Ma X, Zhou Y, Bian Y, Liu G, Cai Y, Huang T, Dong H, Cai D, Wan X, Wang Z, Xiao Y, Kang H. Genome Sequencing Highlights the Plant Cell Wall Degrading Capacity of Edible Mushroom Stropharia rugosoannulata. J Microbiol 2023; 61:83-93. [PMID: 36723791 DOI: 10.1007/s12275-022-00003-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/04/2022] [Indexed: 02/02/2023]
Abstract
The basidiomycetous edible mushroom Stropharia rugosoannulata has excellent nutrition, medicine, bioremediation, and biocontrol properties. S. rugosoannulata has been widely and easily cultivated using agricultural by-products showing strong lignocellulose degradation capacity. However, the unavailable high-quality genome information has hindered the research on gene function and molecular breeding of S. rugosoannulata. This study provided a high-quality genome assembly and annotation from S. rugosoannulata monokaryotic strain QGU27 based on combined Illumina-Nanopore data. The genome size was about 47.97 Mb and consisted of 20 scaffolds, with an N50 of 3.73 Mb and a GC content of 47.9%. The repetitive sequences accounted for 17.41% of the genome, mostly long terminal repeats (LTRs). A total of 15,726 coding gene sequences were putatively identified with the BUSCO score of 98.7%. There are 142 genes encoding plant cell wall degrading enzymes (PCWDEs) in the genome, and 52, 39, 30, 11, 8, and 2 genes related to lignin, cellulose, hemicellulose, pectin, chitin, and cutin degradation, respectively. Comparative genomic analysis revealed that S. rugosoannulata is superior in utilizing aldehyde-containing lignins and is possible to utilize algae during the cultivation.
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Affiliation(s)
- Mengpei Guo
- Institute of Vegetable, Wuhan Academy of Agricultural Sciences, Wuhan, 430065, Hubei, People's Republic of China
| | - Xiaolong Ma
- Institute of Vegetable, Wuhan Academy of Agricultural Sciences, Wuhan, 430065, Hubei, People's Republic of China.
| | - Yan Zhou
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China.
| | - Yinbing Bian
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Gaolei Liu
- Institute of Vegetable, Wuhan Academy of Agricultural Sciences, Wuhan, 430065, Hubei, People's Republic of China
| | - Yingli Cai
- Institute of Vegetable, Wuhan Academy of Agricultural Sciences, Wuhan, 430065, Hubei, People's Republic of China
| | - Tianji Huang
- Hubei Changjiu Fungi Co. Ltd., Suizhou, 431525, Hubei, People's Republic of China
| | - Hongxia Dong
- Institute of Vegetable, Wuhan Academy of Agricultural Sciences, Wuhan, 430065, Hubei, People's Republic of China
| | - Dingjun Cai
- Institute of Vegetable, Wuhan Academy of Agricultural Sciences, Wuhan, 430065, Hubei, People's Republic of China
| | - Xueji Wan
- Institute of Vegetable, Wuhan Academy of Agricultural Sciences, Wuhan, 430065, Hubei, People's Republic of China
| | - Zhihong Wang
- Institute of Vegetable, Wuhan Academy of Agricultural Sciences, Wuhan, 430065, Hubei, People's Republic of China
| | - Yang Xiao
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Heng Kang
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
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Tang S, Fan T, Jin L, Lei P, Shao C, Wu S, Yang Y, He Y, Ren R, Xu J. Soil microbial diversity and functional capacity associated with the production of edible mushroom Stropharia rugosoannulata in croplands. PeerJ 2022; 10:e14130. [PMID: 36213510 PMCID: PMC9536307 DOI: 10.7717/peerj.14130] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/06/2022] [Indexed: 01/21/2023] Open
Abstract
In recent years, a rare edible mushroom Stropharia rugosoannulata has become popular. S. rugosoannulata has the characteristics of easy cultivation, low cost, high output value, and low labor requirement, making its economic benefits significantly superior to those of other planting industries. Accumulating research demonstrates that cultivating edible fungus is advantageous for farming soil. The present experiment used idle croplands in winter for S. rugosoannulata cultivation. We explored the effects of S. rugosoannulata cultivation on soil properties and soil microbial community structure in paddy and dry fields, respectively. We cultivated S. rugosoannulata in the fields after planting chili and rice, respectively. The results showed that Chili-S. rugosoannulata and Rice-S. rugosoannulata planting patterns increased the yield, quality and amino acid content of S. rugosoannulata. By analyzing the soil properties, we found that the Chili-S. rugosoannulata and Rice-S. rugosoannulata cropping patterns increased the total nitrogen, available phosphorus, soil organic carbon, and available potassium content of the soil. We used 16s amplicons for bacteria and internal transcribed spacer (ITS) region for fungi to analyze the microbial communities in rhizosphere soils. Notably, S. rugosoannulata cultivation significantly increased the abundance of beneficial microorganisms such as Chloroflexi, Cladosporium and Mortierella and reduce the abundance of Botryotrichumin and Archaeorhizomyces. We consider S. rugosoannulata cultivation in cropland can improve soil properties, regulate the community structure of soil microorganisms, increase the expression abundance of beneficial organisms and ultimately improve the S. rugosoannulata yield and lay a good foundation for a new round of crops after this edible mushroom cultivation.
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Affiliation(s)
- Shaojun Tang
- Hunan Institute of Microbiology, Changsha, china
| | - Tingting Fan
- College of Forestry, Central South University of Forestry & Technology, Changsha, China
| | - Lei Jin
- Hunan Institute of Microbiology, Changsha, china
| | - Pin Lei
- Hunan Institute of Microbiology, Changsha, china
| | - Chenxia Shao
- Hunan Institute of Microbiology, Changsha, china
| | - Shenlian Wu
- Hunan Institute of Microbiology, Changsha, china
| | - Yi Yang
- Hunan Institute of Microbiology, Changsha, china
| | - Yuelin He
- Hunan Institute of Microbiology, Changsha, china
| | - Rui Ren
- Hunan Institute of Microbiology, Changsha, china
| | - Jun Xu
- Hunan Institute of Microbiology, Changsha, china
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Wang C, Zhang X, Zeng Z, Song F, Lin Z, Chen L, Cai Z. Transcriptome Analysis Explored the Differential Genes’ Expression During the Development of the Stropharia rugosoannulata Fruiting Body. Front Genet 2022; 13:924050. [PMID: 35903349 PMCID: PMC9318406 DOI: 10.3389/fgene.2022.924050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
Stropharia rugosoannulata (S. rugosoannulata) is a fungus with great edible and nutritional values; however, the development mechanism of its fruiting body has not been studied. Thus, this study aimed to analyze the differentially expressed genes (DEGs) in four stages; primordia stage (Sra1), young mushroom stage (Sra2), picking stage (Sra3), and opening umbrella stage (Sra4). Therefore, total RNA was extracted for further RNA-sequencing analysis. In three pairwise comparison groups (PCGs), Sra1 vs. Sra2, Sra2 vs. Sra3, and Sra3 vs. Sra4, a total of 3,112 DEGs were identified among the three PCGs. A GO analysis of the DEGs showed that there were 21 terms significantly enriched in Sra1 vs. Sra2 PCG. There was no significantly enriched GO term in the other two PCGs. Furthermore, KEGG pathway analysis showed that these DEGs were mainly enriched in glucose and amino acid metabolisms. Moreover we found that intron retention (IR) and the alternative 3′ splice site (A3SS) accounted for more than 80%. The development of the S. rugosoannulata fruiting body mainly involved glucose and amino acid metabolisms. IR and A3SS were the two main types of ASE, which played an important role in the development and maturation of the S. rugosoannulata fruiting body.
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Affiliation(s)
- Cui Wang
- Department of Health and Food, Fujian Vocational College of Bioengineering, Fuzhou, China
| | - Xunjie Zhang
- Department of Health and Food, Fujian Vocational College of Bioengineering, Fuzhou, China
| | - Zhiheng Zeng
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Feifei Song
- Department of Health and Food, Fujian Vocational College of Bioengineering, Fuzhou, China
| | - Zhen Lin
- Department of Health and Food, Fujian Vocational College of Bioengineering, Fuzhou, China
| | - Liangjun Chen
- Department of Health and Food, Fujian Vocational College of Bioengineering, Fuzhou, China
| | - Zhixin Cai
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, China
- *Correspondence: Zhixin Cai,
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