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Background  Type III polyketide synthases are important for the biosynthesis of flavonoids and various plant polyphenols. Mulberry plants have abundant polyphenols, but very little is known about the mulberry type III polyketide synthase genes. An analysis of these genes may provide new targets for genetic improvement to increase relevant secondary metabolites and enhance the plant tolerance to biotic and abiotic stresses.    Results  Eighteen genes encoding type III polyketide synthases were identified, including six chalcone synthases ( CHS ), ten stilbene synthases ( STS ), and two polyketide synthases ( PKS ). Functional characterization of four genes representing most of the  MnCHS  and  MnSTS  genes by coexpression with 4-Coumaroyl-CoA ligase in  Escherichia coli  indicated that their products were able to catalyze  p -coumaroyl-CoA and malonyl-CoA to generate naringenin and resveratrol, respectively. Microsynteny analysis within mulberry indicated that segmental and tandem duplication events contributed to the expansion of the  MnCHS  family, while tandem duplications were mainly responsible for the generation of the  MnSTS  genes. Combining the evolution and expression analysis results of the mulberry type III  PKS  genes indicated that  MnCHS  and  MnSTS  genes evolved mainly under purifying selection to maintain their original functions, but transcriptional subfunctionalization occurred during long-term species evolution. Moreover, mulberry leaves can rapidly accumulated oxyresveratrol after UV-C irradiation, suggesting that resveratrol was converted to oxyresveratrol.    Conclusions  Characterizing the functions and evolution of mulberry type III  PKS  genes is crucial for advancing our understanding of these genes and providing the basis for further studies on the biosynthesis of relevant secondary metabolites in mulberry plants.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-2843-7) contains supplementary material, which is available to authorized users.

Evolutionary and functional analysis of mulberry type III polyketide synthases