Whole Genome Sequencing of Fusarium fujikuroi Provides Insight into the Role of Secretory Proteins and Cell Wall Degrading Enzymes in Causing Bakanae Disease of Rice

Abstract

Fusarium fujikuroi causing bakanae disease has emerged as one of the major pathogen of rice across the world. The study aims to comparative genomic analysis of Fusarium fujikuroi isolates and identification of the secretary proteins of the fungus involved in rice pathogenesis. In the present study, F. fujikuroi isolate “F250” was sequenced with an assembly size of 42.47 Mb providing coverage of 96.89% on reference IMI58289 genome. A total of 13,603 protein-coding genes were predicted from genome assembly. The average gene density in the F. fujikuroi genome was 315.10 genes per Mb with an average gene length of 1.67 kb. Additionally, 134,374 single nucleotide polymorphisms (SNPs) are identified against IMI58289 isolate, with an average SNP density of 3.11 per kb of genome. Repetitive elements represent approximately 270,550 bp, which is 0.63% of the total genome. In total, 3,109 simple sequence repeats (SSRs), including 302 compound SSRs are identified in the 8,656 scaffolds. Comparative analysis of the isolates of F. fujikuroi revealed that they shared a total of 12,240 common clusters with F250 showing higher similarity with IMI58289. A total of 1,194 secretory proteins were identified in its genome among which there were 356 genes encoding carbohydrate active enzymes (CAZymes) capable for degradation of complex polysaccharides. Out of them glycoside hydrolase (GH) families were most prevalent (41%) followed by carbohydrate esterase (CE). Out of them CE8 (4 genes), PL1 (10 genes), PL3 (5 genes), and GH28 (8 genes) were prominent plant cell wall degrading enzymes families in F250 secretome. Besides this, 585 genes essential for the pathogen–host interactions were also identified. Selected genes were validated through quantitative real-time PCR analyses in resistant and susceptible genotypes of rice at different days of inoculation. The data offers a better understanding of F. fujikuroi genome and will help us enhance our knowledge on Fusarium fujikuroi–rice interactions.

Genomic Features of Cladobotryum dendroides, Which Causes Cobweb Disease in Edible Mushrooms, and Identification of Genes Related to Pathogenicity and Mycoparasitism

“…At the beginning of infection, pathogens primarily use CAZymes to destroy the polysaccharide component of the host cell wall [32]. We identified 327 C. dendroides genes across the six categories of CAZymes.…”

The Gibberellin Producer Fusarium fujikuroi: Methods and Technologies in the Current Toolkit

“…These genome sequences can be used as efficient and essential tools for identification of Fusarium species, gene/enzyme mining, evolutionary, and phylogenetic analysis etc. (Ward et al, 2002;O'Donnell et al, 2013;Bashyal et al, 2017). There are currently 68 Fusarium species with their genome sequences available in the NCBI (National Center of Biotechnology Information, United States) database.…”

“…Bashyal et al analyzed the F. fujikuroi genome and predicted that there were 1194 secretory proteins, of which 38% proteins might relate to the virulence. Moreover, out of secretory proteins, 5% were polysaccharide lyases, 7% were glycosyl transferases, 20% were carbohydrate esterases, and 41% were glycosyl hydrolases (Bashyal et al, 2017). It is interesting to exploit further experimentally the specialized pathogenicity genes, especially some secreted cell wall degrading enzymes and mycotoxins in F. fujikuroi (Desmond et al, 2008).…”

“…A prerequisite to characterize the molecular biology is having efficient analysis tools. After a number of F. fujikuroi genome sequences are available (Jeong et al, 2013;Wiemann et al, 2013;Bashyal et al, 2017;Niehaus et al, 2017), it is more eager than ever to develop molecular tools. However, unlike many other fungi, such as the baker's yeast and some phylogenetically close Aspergillus spp., F. fujikuroi is critically short of molecular tools.…”

Activation of silent secondary metabolite gene clusters by nucleosome map-guided positioning of the synthetic transcription factor VPR-dCas9

“…and Fusarium spp. have a high gene density (~ 1 gene/ 3,000 bps (Bashyal et al, 2017;Cuomo et al, 2007;Galagan et al, 2005)) when compared to other eukaryotes like human (~ 1 gene/ 150,000 bps (Ezkurdia et al, 2014;Piovesan et al, 2019)), Mus musculus (~ 1 gene / 83,000 bps (Weitzman, 2002)), Caenorhabditis elegans (~ 1 gene/ 5,000 bps (Consortium, 1998)), Drosophila melanogaster (~ 1 gene/ 9,000 bps (Adams et al, 2000)),…”