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.

青钱兰是胡桃科青钱兰属的一种濒危药用植物，其叶子具有多种药理活性成分，被广泛用于开发保健茶和药物。这是组件杂四倍体的~634.90 MB染色体水平单倍体基因组的第一次报告青钱柳（2N = 4倍= 64条染色体）与46292蛋白质编码基因。系统发育树表明，C. paliurus与J. sigillata、J. regia和C. illinoinensis的亲缘关系密切并且在大约 2400 万年前（Mya）在系统发育上与共同祖先（Juglandales）分离。比较基因组分析表明，在C. paliurus的同源多倍体化之前，只有一个最近的 WGD 事件与胡桃类 WGD 事件不同，并且发生在 3.22 至 4.86 Mya。共鉴定出 626 个差异积累代谢物 (DAM) 和 6,138 个差异表达基因 (DEG)，主要参与C. paliurus叶片不同阶段的类固醇、黄酮类和多糖生物合成。代谢组学和转录组学数据显示，10M-YL和10M-ML组与降糖代谢物生物合成相关的大部分基因均显着高于10M-OL组，包括CpHMGS，CpMVK，CpMVD，CpCMK，CpDXS，CpC4Hs，CpCHIs，CpF3Hs，CPF 3'5' ħ，CpDFRs，CpANS，CpFK，CpmanA，CpmanB，CpRHM，和CpUXE。结果表明，这些DEGs与DAMs在降糖代谢物生物合成中具有很强的相关性，包括d - glyceraldehyde -3-phosphate、1- deoxy - d-xylulose-5'-磷酸、肉桂酸、果糖、甘露糖-6-磷酸和UDP-葡萄糖。这些发现可以帮助改善代谢降糖叶中与不同期限的分子机制的了解青钱柳，并为开发和利用提供理论依据和技术支持青钱柳。