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Genome Sequencing Highlights the Plant Cell Wall Degrading Capacity of Edible Mushroom Stropharia rugosoannulata

  • Microbial Genetics, Genomics and Molecular Biology (eukaryote)
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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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Data Availability

Raw sequencing data have been submitted to NCBI SRA (http://www.ncbi.nlm.nih.gov/sra) under BioProject PRJNA854204. Genome assembly has been deposited at GenBank (https://www.ncbi.nlm.nih.gov/genome/) under the accession JANCIK000000000 and NMDC (https://nmdc.cn/) under the accession NMDC60045022. Genome annotation is available at figshare: https://doi.org/10.6084/m9.figshare.20324016.

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Acknowledgements

This study was financially supported by Innovation Project of Wuhan Academy of Agricultural Sciences (Grant No. XKCX202201-6), Key R & D Project of Hubei Province (Grant No. 2021BBA254), and Hubei Agriculture Research System of Edible Fungi (Grant No. HBHZDZB-2021-023). The authors also thank Dr. Lianfu Chen (http://www.chenlianfu.com/) for sharing his bioinformatic pipelines and scripts.

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  1. Mengpei Guo and Xiaolong Ma contributed equally to this work.

Authors and Affiliations

  1. Institute of Vegetable, Wuhan Academy of Agricultural Sciences, Wuhan, 430065, Hubei, People’s Republic of China

    Mengpei Guo, Xiaolong Ma, Gaolei Liu, Yingli Cai, Hongxia Dong, Dingjun Cai, Xueji Wan & Zhihong Wang

  2. Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People’s Republic of China

    Yan Zhou, Yinbing Bian, Yang Xiao & Heng Kang

  3. Hubei Changjiu Fungi Co. Ltd., Suizhou, 431525, Hubei, People’s Republic of China

    Tianji Huang

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  1. Mengpei Guo
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Guo, M., Ma, X., Zhou, Y. et al. Genome Sequencing Highlights the Plant Cell Wall Degrading Capacity of Edible Mushroom Stropharia rugosoannulata. J Microbiol. 61, 83–93 (2023). https://doi.org/10.1007/s12275-022-00003-7

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