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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.

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Background Fusarium fujikuroi causing bakanae is one of the most signi cant pathogen of rice and much responsible for yield losses thereby emerging as a major risk to food security. Methods In the present study transcriptomic analysis was conducted between two contrasting resistant (C101A51) and susceptible (Rasi) genotypes of rice with the combinations of C101A51 control (CC) vs C101A51 inoculated (CI); Rasi control (RC) vs Rasi inoculated (RI) and C101A51 inoculated (CI) vs Rasi inoculated (RI). ResultsIn CC vs CI commonly expressed genes were 12,764. Out of them 567 (4%) were signi cantly upregulated and 1399 (9%) genes were down regulated. For the RC vs RI 14, 333 (79%) genes were commonly expressed. For CI vs RI 13,662 (72%) genes commonly expressed. Cysteine proteinase inhibitor 10, disease resistance protein TAO1-like, oleosin 16 kDa-like, pathogenesis-related protein (PR1), (PR4), BTB/POZ and MATH domain-containing protein 5-like, alpha-amylase isozyme 3D-like (LOC4345814), were upregulated in resistant genotype C101A51.Whereas, GDSL esterase/lipase At5g33370, serine glyoxylate aminotransferase, CASP-like protein 2C1, WAT1related protein At4g08290, Cytoplasmic linker associated proteins, xyloglucan endotransglucosylase/hydrolase protein and β-D xylosidase 7 were upregulated in susceptible genotype Rasi. Gene ontology analysis showed functions related to defence response (GO:0006952), regulation of plant hypersensitive type response (GO:0010363), Potassium ion transmembrane activity (GO:0015079), chloroplast (GO:0009507), response to wounding (GO:0009611), xylan biosynthetic process (GO:0045492) were upregulated in resistant genotype C101A51 under inoculated conditions. Conclusions Real time PCR based validation of the selected DEGs showed that the qRT-PCR was consistent with the RNA-Seq results. This is the rst transcriptomic study against bakanae disease of rice in Indian genotypes and will be helpful for the development of bakanae management strategies.phenotype. BTB/POZ and MATH domain proteins are upregulated in resistant genotype C101A51. Generally, BTB domain participates in plant responses against biotic and abiotic stresses. He et al, [37] reported down regulation of BTB gene under Phytophthora capsici infection. Upregulation of this gene in resistant genotype may have role in defence against F. fujikuroi.Results of the selected DEGs showed that the qRT-PCR was consistent with the RNA-Seq results showing similar expression pattern of up-and down-regulated genes by using both, RNA-Seq and qRT-PCR, analyses. ConclusionsThe results showed that general expression of glucanases, peroxidases in both, resistant and susceptible, genotypes could represent the basic defence mechanism of rice against F. fujikuroi. What was found strikingly different in resistant genotype is the modulation of WRKY transcriptional factors, Cysteine proteinase inhibitor 10 (LOC4335551), disease resistance protein TAO1-like (LOC112939055), oleosin 16 kDa-like (LOC4336570), pathogenesis-related protein (PR1), pathogenesis-related...

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