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De novo genome sequencing of mycoparasite Mycogone perniciosa strain MgR1 sheds new light on its biological complexity

  • Food Microbiology - Research Paper
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Abstract

Mycogone perniciosa is a mycoparasite causing Wet Bubble Diseases (WBD) of Agaricus bisporus. In the present study, the whole genome of M. perniciosa strain MgR1 was sequenced using Illumina NextSeq500 platform. This sequencing generated 8.03 Gb of high-quality data and a draft genome of 39 Mb was obtained through a de novo assembly of the high-quality reads. The draft genome resulted into prediction of 9276 genes from the 1597 scaffolds. NCBI-based homology analysis revealed the identification of 8660 genes. Notably, non-redundant protein database analysis of the M. perniciosa strain MgR1 revealed its close relation with the Trichoderma arundinaceum. Moreover, ITS-based phylogenetic analysis showed the highest similarity of M. perniciosa strain MgR1 with Hypomyces perniciosus strain CBS 322.22 and Mycogone perniciosa strain PPRI 5784. Annotation of the 3917 genes of M. perniciosa strain MgR1 grouped in three major categories viz. biological process (2583 genes), cellular component (2013 genes), and molecular function (2919 genes). UniGene analysis identified 2967 unique genes in M. perniciosa strain MgR1. In addition, prediction of the secretory and pathogenicity-related genes based on the fungal database indicates that 1512 genes (16% of predicted genes) encode for secretory proteins. Moreover, out of 9276 genes, 1296 genes were identified as pathogenesis-related proteins matching with 51 fungal and bacterial genera. Overall, the key pathogenic genes such as lysine M protein domain genes, G protein, hydrophobins, and cytochrome P450 were also observed. The draft genome of MgR1 provides an understanding of pathogenesis of WBD in A. bisporus and could be utilized to develop novel management strategies.

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Data availability

The whole genome shotgun project has been deposited at NCBI under the accession numbers PRJNA543984. The version described in this paper is version PRJNA543984. The NCBI accession number of bio-sample is SAMN11793478 and ID is 11793478.

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Funding

This work is funded by the ICAR- Directorate of Mushroom Research, Chambaghat, Solan, Himachal Pradesh, 173213 under an institutional project.

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  1. Directorate of Mushroom Research, ICAR, Himachal Pradesh, Chambaghat, Solan, 173213, India

    Anil Kumar, V. P. Sharma, Satish Kumar & Manoj Nath

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  1. Anil Kumar
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Material preparation, data collection, and analysis and preparation of the first draft were performed by Anil Kumar. All the co-authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

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Kumar, A., Sharma, V.P., Kumar, S. et al. De novo genome sequencing of mycoparasite Mycogone perniciosa strain MgR1 sheds new light on its biological complexity. Braz J Microbiol 52, 1545–1556 (2021). https://doi.org/10.1007/s42770-021-00535-x

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