Identification of watermelon genes involved in the ZYMV interaction through a miRNA bioinformatics analysis and characterization ofATRIPandRBOHB

Abstract

AbstractSmall RNA sequencing of healthy and ZYMV-infected watermelon (21 dpi) was performed and bioinformatics analysis identified 353 miRNAs from which 22 known and 331 new miRNAs. Important information about their precursors, their length, the loci of which they originated on watermelon genome are provided. The ZYMV genome could be a target for mir396a-3p, miR8706a, and miR1886i-5p from the miRbase, but none of them was identified in the watermelon miRNAome. Furthermore, watermelon miRNAome does not contain a miRNA targeting ZYMV genome with an expectation score ≤ 3.5. There were 34 resistance genes (CC-NBS-LRR, TIR-NBS-LRR, TIR-NBS) predicted as targets of 32 miRNAs in healthy watermelon. For nine differentially expressed miRNAs the respective target genes (10 in total) were bioinformatically predicted. For cla-new_miR307 (upregulated upon ZYMV infection) and cla-miR166h-3p (downregulated upon ZYMV infection) the targets were predicted to beClaATRIPandClaRBOHB, respectively, withClaATRIPdownregulated andClaRBOHBupregulated upon ZYMV infection. ALSV-mediated VIGS ofClaATRIPrendered watermelon plants more resistant to ZYMV, whereas VIGS ofClaRBOHBresulted in higher levels of ZYMV titer in watermelon. These data suggest thatClaATRIPandClaRBOHBare a susceptibility and resistant gene, respectively. Our results provide new insights in watermelon miRNAome and could propose new strategies for generating resistant watermelon to ZYMV.HighlightsBioinformatics analysis in healthy and ZYMV-infected watermelon plants gave 353 miRNAs, 22 known and 331 new.The watermelon miRNAome identified in the present study does not appear to target the ZYMV genome (sense and reverse complement).The differential expression of ten genes of watermelon in relation to ZYMV infection was validated.The silencing of the two genes,ATRIPandRBOHB, through VIGS strongly suggested thatATRIPis a gene of susceptibility andRBOHBis a gene of resistance.