| Summary: | Cassava is susceptible to mites, especially <i>Tetranychus cinnabarinus</i>. Secondary metabolism products such as flavonoids play an important role as antimicrobial metabolites protecting plants against biotic stressors including fungal, pathogen, bacterial, and pest defense. The chalcone synthase (CHS) is the initial step of the phenylpropanoid pathway for producing flavonoids and is the gatekeeper of the pathway. Until recently, the CHS genes family has not been systematically studied in cassava. Thirty-nine CHS genes were identified from the cassava genome database. Based on phylogenetic and sequence composition analysis, these CHSs were divided into 3 subfamilies. Within the same subfamily, the gene structure and motif compositions of these CHS genes were found to be quite conserved. Duplication events, particularly segmental duplication of the cassava CHS genes, were identified as one of the main driving force of its expansion. Various cis-elements contained in the promoter might regulate the gene expression patterns of <i>MeCHS</i>. Protein-protein interaction (PPI) network analysis showed that <i>MeCHS</i>1 and <i>MeCHS</i>10 protein are more closely related to other family members. The expression of <i>MeCHS</i> genes in young leaves was higher than that in other tissues, and their expression varies even within the same tissue. Coincidentally, these CHS genes of most LAP subclasses were highly expressed in young leaves. The verified <i>MeCHS</i> genes showed consistent with the real-time reverse transcription quantitative PCR (RT-qPCR) and proteomic expression in protected and affected leaves respectively, indicating that these <i>MeCHS</i> genes play crucial roles in the response to <i>T. cinnabarinus</i>. This study is the first to comprehensively expatiate the information on <i>MeCHS</i> family members. These data will further enhance our understanding both the molecular mechanisms and the effects of CHS genes. In addition, the results will help to further clarify the effects on <i>T. cinnabarinus</i> and provide a theoretical basis for the potential functions of the specific CHS gene in resistance to mites and other biotic stress.
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