Bioinformatics and Expression Analysis of CHI Gene Family in Sweet Potato.

Abstract

Chalcone isomerase (CHI) is not only an enzyme related to flavonoid biosynthesis, but also one of the key enzymes in the flavonoid metabolic pathway. In this study, members of the CHI gene family were identified in the whole genome of sweet potato. Bioinformatics methods were used to analyze the physical and chemical properties, systematic evolution, conserved domain, chromosome location, cis-acting elements of the promoter, and so on, of CHI gene family members. In addition, the tissue site-specific expression of CHI gene family members and their expression patterns under three kinds of abiotic stress were analyzed. The results showed that five members of IbCHI gene family were identified in sweet potato, which were unevenly distributed on four chromosomes. The protein secondary structure and tertiary structure were consistent, and there was a conservative domain related to chalcone isomerase. The prediction of subcellular localization showed that it was mainly located in cytoplasm and chloroplast. Systematic evolution showed that the members of sweet potato CHI gene family could be divided into Type I-IV, and the Type I gene IbCHI1 showed CHI catalytic activity in transgenic callus. The collinearity gene pairs were identified between sweet potato and allied species. Its promoter contains light response elements, hormone response elements, and stress response elements. The results of real-time fluorescence quantitative PCR (qRT-PCR) analysis showed that the expression of the IbCHI gene was tissue-specific and that the catalytic genes IbCHI1 and IbCHI5 serve as primary responders to abiotic stress, while the non-catalytic members IbCHI3 and IbCHI4 may fine-tune metabolic flux or participate in low-temperature, salt, and drought stress signaling. This study can provide a theoretical basis for a follow-up functional genomics study of the chalcone isomerase gene family in sweet potato.