Identification and Expression Profile of the Chalcone Synthase (CHS) Gene Family in Litchi

The chalcone synthase (CHS) genes play an important role in the biosynthesis of flavonoids and anthocyanins. However, research into the genomic characteristics and evolutionary patterns of the CHS gene family in lychee remains limited. In this study, six LcCHS genes were identified from the litchi genome. Most members of the LcCHS family consist of two exons and possess eight conserved motifs; furthermore, all members exhibit highly similar three-dimensional protein structures. LcCHS genes were closely related to homologs of Sapindaceae species and experienced gene duplication events during dicotevolution. Comparative colinearity analysis revealed conserved colinearity relationships among most LcCHS genes, and all members of the LcCHS family exhibited distinct colinearity with homologues in longan. LcCHS genes exhibited significant tissue-specific expression preferentially in reproductive tissues rather than vegetative tissues. Transcription analysis of ‘Jinggang Hongnuo’ litchi fruit development divided LcCHS genes into two negatively correlated expression modules and LcCHS members interacted with numerous transcription factors (e.g., flavonoid biosynthesis, hormone signaling and developmental regulation). Spatiotemporal expression profiling of LcCHS genes in ‘Guiwei’, ‘Feizixiao’ and ‘Ziniangxi’ litchi cultivars revealed obvious tissue specificity and developmental stage preference of these genes. Gene expression of LcCHS genes in ‘Guiwei’ high correlated with the flavonoid content. Furthermore, promoter cis-element analysis identified 34 types of cis elements in LcCHS promoters that participate in plant growth and development, hormone response and stress adaptation, implying that LcCHS genes may participate in litchi growth, hormone signal transduction, and stress-response processes. Comprehensive characterization of the chalcone synthase gene family could provide insights into the genetic improvement of litchi.