Fungal Genome De Novo Sequencing Promotes The Discovery And Research of Plant Pathogenic Fungi

Fungal genome de novo sequencing is a technology to assemble the microbial genome sequence from scratch without reference genome, annotate the genome in combination with database, and carry out relevant downstream analysis based on it. Fungal genome sequencing provides strong support for the study of fungi. After obtaining the whole genome sequence of fungi, bioinformatics analysis technology can be used to make gene prediction and functional annotation of the sequence, which can provide molecular biological basis for the study of the specific biological characteristics of fungi (pathogenic mechanism, host interaction mechanism, metabolic mechanism, etc.). Combined with comparative genome analysis, it can provide theoretical guidance for the study of character variation, functional differences and genetic evolutionary relationships among fungi. Fungal whole genome sequencing has become an indispensable tool for fungal genome research.

Comparative genome reveals the mechanism of plant disease resistance

Rice blast, caused by the ascomycete pathogen Magnaporthe oryzae, is a major fungal disease and imposes a constant threat to stable rice production worldwide. Researchers identified the Magnaporthe oryzae, avirulence effector AvrPi9 cognate to rice blast resistance gene Pi9 by comparative genomics of requisite strains derived from a sequential planting method. In this study, a pathogenic strain R01-1 was selected, and a non-toxic strain R88-002, which was the closest relative to the pathogenic strain, was selected. The two strains were sequenced and assembled, and comparative genomics was used to try to find the core genes associated with the pathogenesis of griseomycin. The AvrPi9 gene in R01-1 was found to have an insertion of a repeat sequence, resulting in the failure of the AvRPi9-mediated nontoxic mechanism. RT-PCR showed that AvrPi9 gene was highly expressed at the early stage of infection, which indicated that AvRPI9 gene played an important role in the process of infection. Further analysis also showed that different AvrPi9 genotypes were associated with specific virulence traits of the strains. This study describes the isolation and characterization of fungi by the means of comparative genomics and genetic studies.

The First T2T chromosome-level genome assembly of Stagonospora tainanensis

The sexual morph Leptosphaeria taiwanensis Yen and Chi and its asexual morph Stagonospora tainanensis W. H. Hsieh is an important necrotrophic fungal phytopathogen, which causes sugarcane leaf blight, resulting in loss of cane tonnage and sucrose in susceptible sugarcane varieties. This study employed Nanopore sequencing and Illumina sequencing together to finish a near telomere-to-telomere chromosome-level genome assembly and RNA-seq based gene annotation of this necrotrophic infecting fungus S. tainanensis strain StFZ01. It can provide a more precise understanding of the pathogen and the fungal pathogenicity and can offer a series of putative proteins in the fungal pathogenesis, such as effectors, and it is thus beneficial for developing a new disease management strategy and for sugarcane improvement of leaf blight resistance. this study presented the first T2T chromosome-level genome assembly and high-quality gene annotation of the pathogenic fungus S. tainanensis strain StFZ01 causing sugarcane leaf blight, integrating with Nanopore sequencing and Illumina sequencing. The well annotated repeats and genes, such as CAZys and effectors will play as the reference genome for designing species-specific molecular markers and identifying pathogenicity-related genes in the future.

What's exciting is that the virulence mechanism of pathogenic fungi was investigated also based on comparative genomes. The detailed analysis of comparative genomes, combined with subsequent sufficient experimental verification, comprehensively revealed the action mechanism of key genes in the pathogenic process of strains from multiple perspectives. Future fungal genomics sequencing will reveal more mysteries for us.

References:

1. Wu, Jun et al. "Comparative genomics identifies the Magnaporthe oryzae avirulence effector AvrPi9 that triggers Pi9-mediated blast resistance in rice." The New phytologist vol. 206,4 (2015): 1463-75.
2. Xu, Fu et al. "The First Telomere-to-Telomere Chromosome-Level Genome Assembly of Stagonospora tainanensis Causing Sugarcane Leaf Blight." Journal of fungi (Basel, Switzerland) vol. 8,10 1088. 16 Oct. 2022