Bacterial wilt in mulberry(Morus atropurpurea Roxb.),caused by Ralstonia solanacearum,is one of the most important production constraints in many tropical and subtropical areas.In our previous work,we investigated gene expression changes in mulberry at the early stages of R.solanacearum infection.Now we are investigating transcriptional changes in mulberry that occur during the entire R.solanacearum infection process.Analysis of gene expression changes in two mulberry cultivars,following infection with R.solanacearum,revealed that expression of a series of genes associated with flavonoid biosynthesis was significantly responsive to infection at all sample time points.Specifically,the expression of genes encoding key enzymes involved in flavonoid biosynthesis—such as chalcone synthase,chalcone isomerase,and flavonoid 3-hydroxylase—was altered.We obtained full-length sequences of these three genes and additional transcriptional and phytochemical evidence to verify this result using qPCR and aluminum chloride colorimetry.This work indicates that flavonoids may play important roles in bacterial wilt resistance for mulberry plants and provides valuable gene targets for breeding disease-resistant mulberry cultivars.