Integrated Transcriptome and Metabolome Analysis Reveals Insights into Flavone and Flavonol Biosynthesis in Salicylic Acid-Induced <i>Citrus</i> Huanglongbing Tolerance

Salicylic acid (SA) exhibits positive effects against <i>Citrus</i> Huanglongbing (HLB), but how SA affects citrus resistance to HLB is currently unknown. This study conducted integrated transcriptome and metabolome analyses on SA-treated <i>Citrus sinensis</i> (HLB-sensitive) and <i>Poncirus trifoliata</i> (HLB-tolerant). The results indicated that the syntheses of flavones and flavonols were induced by SA, while the expression levels of associated genes and the contents of corresponding metabolites varied significantly between the two species after SA treatment or HLB infection. These differences may underpin the enhanced HLB management through SA treatment and the inherent HLB tolerance of <i>P. trifoliata</i>. Furthermore, two insertions of miniature inverted-repeat transposable element (MITE) were identified within the promoter of <i>PtrF3'H</i> in <i>P. trifoliata</i>, whereas none were found in the promoter of <i>CsF3'H</i> in <i>C. sinensis</i>. These MITE insertions notably enhanced the promoter activity of <i>PtrF3'H</i> in an SA-dependent manner. Our findings deepen the understanding of the correlation between SA response and HLB tolerance in <i>Citrus</i>.