Insights into the evolution and hypoglycemic metabolite biosynthesis of autotetraploid Cyclocarya paliurus by combining genomic, transcriptomic and metabolomic analyses

Cyclocarya paliurus is an endangered medicinal plant of the genus Cyclocarya within the family Juglandaceae, and its leaves have been widely used for the development of healthy tea and medicine with a variety of pharmacologically bioactive components. This is the first report of an ∼634.90 Mb chromosome-level haploid genome assembly of heterozygous autotetraploid C. paliurus (2n = 4x = 64 chromosomes) with 46,292 protein-coding genes. The phylogenetic tree showed that C. paliurus had a close relationship to J. sigillata, J. regia and C. illinoinensis and phylogenetically diverged from the common ancestor (Juglandales) approximately 24 million years ago (Mya). Comparative genome analysis indicated that only one recent WGD event before the autopolyploidization in C. paliurus was distinct from the juglandoid WGD event and occurred from 3.22 to 4.86 Mya. A total of 626 differentially accumulated metabolites (DAMs) and 6,138 differentially expressed genes (DEGs) were identified and mainly involved in steroid, flavonoid and polysaccharide biosynthesis in C. paliurus leaves at different stages. Metabolomics and transcriptomics data showed that most of the genes related to hypoglycemic metabolite biosynthesis in the 10M-YL and 10M-ML groups were significantly higher than those in the 10M-OL group, including CpHMGS, CpMVK, CpMVD, CpCMK, CpDXS, CpC4Hs, CpCHIs, CpF3Hs, CpF3′5′H, CpDFRs, CpANS, CpFK, CpmanA, CpmanB, CpRHM, and CpUXE. The results showed that these DEGs have a strong correlation with DAMs in hypoglycemic metabolite biosynthesis, including d-glyceraldehyde-3-phosphate, 1-deoxy-d-xylulose-5′-phosphate, cinnamic acid, fructose, mannose-6-phosphate and UDP-glucose. These findings can help improve the understanding of the molecular mechanism of hypoglycemic metabolites in leaves with different maturities in C. paliurus and provide a theoretical basis and technical support for the development and utilization of C. paliurus.