Deciphering growth stage-specific transcriptomic changes in KIOM-patented in vitro propagated Asparagus cochinchinensis

Asparagus cochinchinensis is an endangered medicinal plant widely used in Korea, China, and Japan. Although in vitro micropropagation techniques have enabled successful regeneration of A. cochinchinensis, the molecular mechanisms underlying developmental transitions during propagation and acclimatization remain poorly understood. Herein, we performed de novo transcriptomic profiling across three key developmental stages (callus, in vitro plantlets, and acclimatized plants) to understand gene expression changes related to growth regulation and secondary metabolite biosynthesis. We obtained approximately 21 million clean reads through paired-end sequencing. De novo assembly generated 42,193 unigenes, and 12,850 differentially expressed genes were identified. Annotation against the Kyoto Encyclopedia of Genes and Genomes pathway database revealed distinct pathways for auxin biosynthesis at each stage. According to the transcript expression levels, the callus stage utilized the indole acetamide pathway and then shifted to the indole pyruvate pathway during growth in in vitro chambers. These results indicated an adaptive transition of plant cells during development based on environmental conditions. Furthermore, one-month acclimatized plants activated environmental adaptation genes related to pathogen infection, such as plant-pathogen interactions and the mitogenactivated protein kinase signaling pathway, highlighting that plants require prolonged periods to reach a stable physiology. In addition, upregulation of genes involved in steroid and flavonoid biosynthesis was observed during the callus stage, highlighting early activation of secondary metabolite production pathways. The current findings provide fundamental insights relevant to the future development of A. cochinchinensis studies, especially for regeneration systems and mass production of pharmacologically active metabolites from A. cochinchinensis.