Metabolome and transcriptome analyses reveal flavonoids biosynthesis differences in Ginkgo biloba associated with environmental conditions

Ginkgo (Ginkgo biloba L.) is widely cultivated as a medicinal tree due to its leaves flavonoids pharmacological effects, which are also known to play a primary defense role against abiotic stresses such as ultraviolet radiation, low temperature, and drought. The paucity of investigations documenting flavonoids molecular regulation under environmental stress is the main driver for the present study. Here, we investigated the responses of female and male ginkgo clones to three different natural conditions at the translational and metabolic levels. We found that growing in different environments, ginkgo clones underwent remarkable reprogramming of their transcriptomes and substantial changes in their metabolomes, particularly in the flavonoid biosynthesis pathway. We performed a weighted gene co-regulatory network (WGCNA) to analyze the gene-flavonoids association and rebuilt the gene regulatory sub-networks, and identified thirteen transcription factors (TFs) from three modules highly related to flavonoid accumulation. These TFs may play important roles in transcriptional regulation of flavonoids biosynthesis by activating or repressing the expression of multiple structural genes under different environments. Additionally, our results suggested that gene expression patterns were mainly driven by environment, while female and male trees displayed similar pattern under the same environmental conditions. Our findings could provide an insight for a better understanding of the regulatory mechanism of flavonoids biosynthesis and build a scientific basis for the production quality improvement of ginkgo leaves.