Physiological, transcriptome and metabolome analyses provide molecular insights to seasonal development in Ginkgo biloba xylem

Ginkgo biloba’s wood has high economic value; however, little is known about the molecular response of its xylem seasonal development. Based on physiological change in secondary cell wall (SCW) components, non-structural carbohydrates (NC), and endogenous phytohormones (EP) concentrations during development seasons, we performed transcriptome and metabolome sequencing on current- and second-year xylem to explore the molecular physiological responses of Ginkgo developing xylem induced by seasonal effects. Results revealed that SCW component, NC, and EP showed distinct seasonal patterns in concentration change. The expression profiles of corresponding differentially expressed genes (DEGs) and differentially abundant metabolites (DAMs) in phenylpropanoid (monolignol) biosynthesis (14 DEGs), plant hormone biosynthesis (10 DAMs), signaling (37 DEGs) and carbohydrate metabolism (37 DEGs and 8 DAMs) were revealed. Most of these DEGs were up-regulated in spring (May) to summer (July), while down-regulated in winter (December). Trend cluster showed that 15 DEGs in brassinolide (BR) biosynthesis and signaling, jasmonic acid (JA), and auxin (IAA) signaling were clustered into top 2 profiles with most DEGs in lignin biosynthesis. Correlation analysis indicated that BR concentration was negatively related with lignin content, while positively associated with 8 DEGs in lignin biosynthesis, suggesting that BR had a potential to coordinate lignin deposition. Additionally, the expression levels of DEGs in (abscisic acid) ABA signaling had positive association with those of DEGs related starch and sucrose biosynthesis, while had inverse correlation with DEGs related glucose and galactose biosynthesis. Also, ABA concentration was positively correlated with NC content, implying the dominant role of ABA in seasonal carbohydrate metabolism, conjoint analysis of DEGs and DAMs also supported this finding. Our study provided a new foundation for endogenous hormone-mediated seasonal development of xylem. [Display omitted] •Physiological changes in Ginkgo’s xylem during different seasons were clarified.•Expression profiles of DEGs and DAMs related to seasonal biosynthesis of monolignol, plant hormone signaling and carbohydrate metabolism were revealed.•Brassinolide (BR) may coordinate seasonal lignin biosynthesis in Ginkgo’s xylem.•Abscisic acid (ABA) may direct carbohydrate metabolism in seasonal Ginkgo’s xylem development.