Genome-wide dissection of the chalcone synthase gene family in Oryza sativa

Enzymes of the chalcone synthase (CHS) family catalyze the generation of multiple secondary metabolites in fungi, plants, and bacteria. These metabolites have played key roles in antimicrobial activity, UV protection, flower pigmentation, and pollen fertility during the evolutionary process of land plants. We performed a genome-wide investigation about CHS genes in rice (Oryza sativa). The phylogenetic relationships, gene structures, chromosomal locations, and functional predictions of the family members were examined. Twenty-seven CHS family genes (OsCHS01-27) were identified in the rice genome and were found to cluster into six classes according to their phylogenetic relationships. The 27 OsCHS genes were unevenly distributed on six chromosomes, and 17 genes were found in the genome duplication zones with two segmental duplication and five tandem duplication events that may have played key roles in the expansion of the rice CHS gene family. In addition, the OsCHS genes exhibited diverse expression patterns under salicylic acid treatment. Our results revealed that the OsCHS genes exhibit both diversity and conservation in many aspects, which will contribute to further studies of the function of the rice CHS gene family and provide a reference for investigating this family in other plants.