Solanum aculeatissimum is a medicinally and economically significant crop characterized by its aerial organs, which are densely covered with trichomes and spines. Trichomes serve as crucial sites for the synthesis of secondary metabolites in medicinal plants and represent important structural adaptations for resisting biotic and abiotic stresses. Elucidating the molecular mechanisms underlying trichome formation in S. aculeatissimum holds significant implications for enhancing both its medicinal value and stress resistance. The R2R3-MYB subfamily, the largest within the MYB transcription factor family, plays a pivotal role in regulating trichome development. Here, we present the first genome-wide identification of the R2R3-MYB gene family in S. aculeatissimum, characterizing 99 members. Phylogenetic analysis classified these SaMYBs into 10 groups. Cis-element predictions in their promoter regions revealed an abundance of light-responsive, phytohormone-responsive, and abiotic stress-responsive elements, suggesting roles in environmental adaptation. Furthermore, synteny analysis identified 25 segmentally duplicated gene pairs, and the purifying selection has been the dominant evolutionary force. Through comparative transcriptomic analysis of leaves from wild-type and sparse-trichome plants, we identified 16 differentially expressed SaMYB genes, comprising 3 upregulated and 13 downregulated genes. Subsequent qRT-PCR analysis showed that SaMYB1, SaMYB59, and SaMYB36 were highly expressed during early leaf development. Virus-induced gene silencing (VIGS) targeting these candidates demonstrated that silencing SaMYB59 significantly reduced trichome density, whereas silencing SaMYB1 or SaMYB36 produced no observable phenotypic change, confirming SaMYB59 as a key positive regulator of trichome formation. Our findings provide crucial molecular targets for elucidating the mechanisms of trichome development in S. aculeatissimum and establish a theoretical foundation for genetic improvement of this medicinal plant through regulation of the SaMYB59 gene.

Centella asiatica (L.) Urb., a perennial herb of the Apiaceae family, is an important medicinal plant with diverse therapeutic applications. In this study, we integrated phenotypic evaluation, SSR markers, and HPLC fingerprinting to assess the diversity of 24 C. asiatica accessions collected from Yunnan Province, China. Considerable phenotypic, genetic, and biochemical diversity was observed. The Shannon–Wiener index ranged from 2.20 to 3.14 for qualitative traits. Principal component analysis identified five components accounting for 82.54% of the total phenotypic variance, with leaf morphology as the primary determinant. Q-type cluster analysis grouped the accessions into five phenotypic clusters. Transcriptome analysis revealed 16,799 SSR loci, with dinucleotide repeats as the most frequent motif (44.31%). UPGMA clustering based on SSR markers delineated five genetic groups that correlated with geographic origin, with accessions from the two northernmost sites forming a distinct cluster. HPLC fingerprints identified 16 common peaks, among which five major bioactive constituents—madecassoside, asiaticoside, kaempferol, madecassic acid, and asiatic acid—were quantified. The total content of these five compounds varied markedly among accessions (4.09–20.18 mg·g⁻¹), with the highest found in Zhaoyang (S5). Most accessions exhibited high chemical similarity (>0.9), except for Yiliang (S12), which displayed a distinct profile. The partial correlation between SSR-based classifications and geographic origin, together with the inconsistency between phenotypic and chemical groupings, indicates that morphological variation is shaped by both environmental factors and complex genetic regulatory mechanisms. These findings provide a scientific basis for germplasm conservation, selective breeding, and the sustainable utilization of C. asiatica.