[Genome-wide identification and expression pattern analysis of chalcone synthetase gene family in Eucommia ulmoides]

Chalcone synthetase(CHS) is a key enzyme in the flavonoid biosynthesis pathway. To investigate the functions of CHS gene in Eucommia ulmoides, this study conducted a comprehensive identification of EuCHS gene family members based on the E. ulmoides genome data by using bioinformatics methods. Systematic analyses were performed on their physicochemical properties, evolutionary relationships, conserved motifs, gene structures, chromosomal localization, promoter cis-acting elements, and expression patterns, aiming to provide a theoretical foundation for further research on the functions of EuCHS genes. In this study, a total of four EuCHS gene family members were identified, named EuCHS1 to EuCHS4. The encoded amino acids ranges from 385 to 397 aa with relative molecular weights between 42 315.75 and 43 336.97, theoretical isoelectric points ranging from 5.72 to 8.06, instability index ranging from 39.35 to 53.82, and aliphatic indices from 90.91 to 94.25. All EuCHS proteins were hydrophilic, and subcellular localization analysis showed that they were located in the cytoplasm. Evolutionary analysis indicated that the EuCHS family members were divided into two subfamilies, Group Ⅰ and Group Ⅲ, with each containing two EuCHS members. Gene structure analysis showed that all EuCHS contained two exons. Cis-acting element analysis indicated that EuCHS family members might be involved in various biological processes, including growth and development, hormone regulation, and abiotic stress responses. Transcriptome and quantitative reverse transcription-polymerase chain reaction(qRT-PCR) data analysis showed that EuCHS exhibited tissue-specific expression patterns, with most genes showing the highest expression levels in leaves, particularly during the early stages of leaf development. These genes participated in the formation of E. ulmoides gum and the leaf color of ` Ziye' E. ulmoides, as well as in floral organ development. Under drought stress, EuCHS1, EuCHS2, and EuCHS4 were upregulated, while EuCHS3 was downregulated. Gibberellic acid(GA_3) treatment suppressed EuCHS3 expression but induced EuCHS4 upregulation. Under abscisic acid(ABA) treatment, EuCHS1 and EuCHS3 were downregulated, while EuCHS2 and EuCHS4 exhibited an initial increase followed by a decrease in expression. This study identified four EuCHS gene family members with significant conservation and classified them into two subfamilies, Group I and Group Ⅲ. EuCHS genes displayed distinct expression differences across various tissues and developmental stages and were involved in abiotic stress responses in E. ulmoides. This study provides a theoretical basis for further exploring the functions of the CHS genes in E. ulmoides.