Transcriptome Analysis Elucidates the Essential Pathways and Candidate Genes Involved in Chloroplast Development Between True Leaves and Cotyledon in Trichosanthes kirilowii Maxim.

Trichosanthes kirilowii (Cucurbitaceae) is a dicotyledonous plant with morphologically and functionally distinct true leaves and cotyledons. This study integrates morphological, physiological, and transcriptomic analyses to systematically compare these two leaf types. True leaves were significantly larger, thinner, and contained higher chlorophyll a and chlorophyll b content than the smaller, thicker cotyledons. Furthermore, chloroplast thylakoid protein distribution differed between the tissues, with cotyledons enriched in low-molecular-weight chloroplast proteins. Transcriptomic profiling revealed divergent expression of genes associated with chloroplast development, including those involved in photosynthesis, pigment biosynthesis, and hormone synthesis pathways. qPCR validated key differentially expressed genes. These findings provide a comprehensive framework for understanding the molecular and functional specialization of true leaves and cotyledons in T. kirilowii, offering insights into tissue-specific chloroplast development in dicots.