Table 2_Metabolomics and transcriptomics indicate the changes in medicinal components of Amygdalus mongolica kernels during different developmental stages.xlsx

Amygdalus mongolica is a traditional Chinese and Mongolian medicine and is quite effective in relieving cough and eliminating phlegm. In this study, ultra-high performance liquid chromatography-mass spectrometry (UPLC-MS) was used to perform metabolomics analysis, combined with transcriptomic sequencing, to study the samples of A. mongolica at early, middle and late growth stages. A comprehensive analysis was conducted to systematically investigate the dynamic changes and developmental trajectories of kernel progression across distinct growth stages, utilizing differential expression analysis and pathway enrichment approaches. A total of 104 significant differential metabolites were identified across different growth stages: the early growth stage (E), the middle growth stage (M), and the late growth stage (L). Specifically, 68 and 36 differential metabolites were detected in the comparisons of E vs. M and M vs. L, respectively. Among them, 29 and 21 metabolites exhibiting up-regulation. In comparison, 39 and 15 metabolites demonstrated down-regulation. Transcriptomic analysis identified 133 differentially expressed genes associated with 62 pathways in the E vs. M. Simultaneously, 14 differentially expressed genes linked to 13 pathways in the M vs. L. The accumulation of various metabolites varied across the growth stages, with a marked increase in amino acids during the middle and late developmental phases, alongside fluctuations in the levels of flavonoid compounds. In conclusion, the study reveals significant variations in the content and types of amino acid compounds and the expression levels of key genes within relevant pathways of A. mongolica kernels throughout different growth stages. Especially, the increase in flavonoid compound expression with advancing growth stages highlights their substantial medicinal potential. These findings provide a foundation for future developing and utilizing valuable medicinal ingredients in A. mongolica kernels.

蒙古扁桃（Amygdalus mongolica）是一种传统中蒙药材，在止咳化痰方面疗效显著。本研究采用超高效液相色谱-质谱联用技术（UPLC-MS）结合转录组测序技术，对蒙古扁桃不同生长发育阶段的样本开展研究，并通过差异表达分析与通路富集分析等方法开展综合分析，系统探究其种仁在不同生长阶段的动态变化与发育轨迹。本研究共鉴定得到104个显著差异代谢物，覆盖三个生长阶段：生长早期（E）、生长中期（M）与生长晚期（L）。具体而言，在E vs. M与M vs. L的比较组中，分别检测到68个和36个差异代谢物；其中上调代谢物分别为29个与21个，下调代谢物分别为39个与15个。转录组分析结果显示，在E vs. M比较组中，共鉴定得到133个差异表达基因，涉及62条通路；而在M vs. L比较组中，共鉴定得到14个差异表达基因，涉及13条通路。不同代谢物的积累水平随生长阶段呈现显著差异：在发育中期与晚期，氨基酸类物质含量显著升高，同时黄酮类化合物的水平也存在动态波动。综上，本研究揭示了蒙古扁桃种仁在不同生长阶段中，氨基酸类化合物的含量与种类、以及相关通路关键基因的表达水平均存在显著差异。尤为值得关注的是，黄酮类化合物的表达水平随生长进程不断升高，这凸显了其可观的药用开发价值。本研究结果为后续开发利用蒙古扁桃种仁中的珍贵药用成分奠定了理论基础。