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.
Highlights
Bakanae is an important fungal disease of rice posing threat to rice production all over the world
One microliter of each sample was loaded in Nanodrop 2000 for determining A260/280 ratio, and 1 μl of each sample was used for determining concentration using Qubit R 2.0 Fluorometer (Thermo Fischer Scientific, Life Technologies)
KM50526; Supplementary Figure 1) for sequencing. This isolate was identified as mating type 2 (MAT-2) using MAT locus-specific primers
Summary
Bakanae is an important fungal disease of rice posing threat to rice production all over the world. The disease incidence of bakanae on rice has increased at an alarming rate taking its toll in diverse rice growing regions such as India, Japan, Taiwan, and Thailand (Kini et al, 2002; Saremi, 2005; Bashyal and Aggarwal, 2013; Gupta et al, 2015; Bashyal et al, 2016a; Fiyaz et al, 2016). The incidence of bakanae disease has increased steadily on Basmati rice cultivars in north-west India especially in Punjab, Haryana, and Uttar Pradesh (Gupta et al, 2015; Bashyal et al, 2016a)
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