Comparative transcriptomic analyses of chlorogenic acid and luteolosides biosynthesis pathways at different flowering stages of diploid and tetraploid Lonicera japonica

The Flos Lonicerae Japonicae (FLJ), Lonicera japonica Thunb, belonging to the Caprifoliaceae family, is an economically important plant that is highly utilized in traditional Chinese medicine as well as in Japanese medicine. The flowers of these plants are rich in chlorogenic acid (CGA) and luteoloside. Our previous study revealed that tetraploid L. japonica has higher fresh/dry weight, phenolic acids and flavonoids contents than those of diploid plants. However, why tetraploid L. japonica can yield higher CGA and luteolosides than that in diploid and what is the difference in the molecular regulatory mechanism of these pathways between diploid and tetraploids remained unclear. Therefore, in the present study, we performed comprehensive transcriptome analyses of different flowering stages of diploid and tetraploid L. japonica. The CGA content of tetraploid was found higher than that of diploid at all the growth stages. While the luteoloside content of diploid was higher than that of tetraploid at S4 and S6 growth stages. We obtained a high-quality transcriptome assembly (N50 = 2,055 bp; Average length = 1,331 bp) compared to earlier studies. Differential expression analysis revealed that several important genes involving in plant hormone signal transduction, carbon metabolism, starch/sucrose metabolism and plant-pathogen interaction were upregulated in tetraploid compared with the diploid L. japonica, reflecting the higher adaptability and resistance of tetraploid species. Furthermore, by associating the phenotypic data and gene expression profiles, we were able to characterize the potential molecular regulatory mechanism of important biosynthetic pathways at different flowering stages. Overall, our work provides a foundation for further research on these important secondary metabolite pathways and their implications in traditional Chinese/Japanese medicine.