Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Jan;61(1):83-93.
doi: 10.1007/s12275-022-00003-7. Epub 2023 Feb 1.

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

Mengpei Guo #  1 , Xiaolong Ma #  2 , Yan Zhou  3 , Yinbing Bian  4 , Gaolei Liu  1 , Yingli Cai  1 , Tianji Huang  5 , Hongxia Dong  1 , Dingjun Cai  1 , Xueji Wan  1 , Zhihong Wang  1 , Yang Xiao  4 , Heng Kang  4
Affiliations

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

Mengpei Guo et al. J Microbiol. 2023 Jan.

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.

Keywords: Comparative genomic analysis; Plant cell wall degrading enzymes; Stropharia rugosoannulata; Whole-genome sequencing.

PubMed Disclaimer

References

    1. Almagro Armenteros, J. J., Tsirigos, K. D., Sønderby, C. K., Petersen, T. N., Winther, O., Brunak, S., von Heijne, G., & Nielsen, H. (2019). SignalP 5.0 improves signal peptide predictions using deep neural networks. Nature Biotechnology, 37, 420–423.
    1. Anders, S., Pyl, P. T., & Huber, W. (2015). HTSeq—A Python framework to work with high-throughput sequencing data. Bioinformatics, 31, 166–169.
    1. Balabanova, L., Slepchenko, L., Son, O., & Tekutyeva, L. (2018). Biotechnology potential of marine fungi degrading plant and algae polymeric substrates. Frontiers in Microbiology, 9, 1527.
    1. Bian, J., Zhang, H., Meng, S., & Liu, Y. (2018). Chemotaxis of Caenorhabditis elegans toward volatile organic compounds from Stropharia rugosoannulata induced by amino acids. Journal of Nematology, 50, 3–8.
    1. Blin, K., Shaw, S., Steinke, K., Villebro, R., Ziemert, N., Lee, S. Y., Medema, M. H., & Weber, T. (2019). antiSMASH 5.0: Updates to the secondary metabolite genome mining pipeline. Nucleic Acids Research, 47, W81–W87.

Supplementary concepts

LinkOut - more resources