Simple Summary
Blue Sky VineThunbergia grandiflora (Acanthaceae) holds medicinal and economic value, yet its genomic background remains poorly understood. Habitat loss and overexploitation further threaten Acanthaceae species, underscoring the need for genomics-based conservation. Its chloroplast was sequenced and comparatively analyzed with those of 27 representative species spanning 24 genera across all five subfamilies of Acanthaceae, and a robust phylogenetic tree encompassing 68 Acanthaceae species was constructed. Key findings revealed distinct genetic variation within the family, including a notable contraction in the inverted repeat region of Strobilanthes species, which phylogenetically supports their unique clade formation. The identification of simple sequence repeats, hypervariable regions, and adaptive evolution patterns provides molecular insights into species differentiation and environmental adaptation. By integrating published chloroplast genomes and coding sequences from seven additional genera, this work enhances phylogenetic resolution and establishes a genomic foundation for classification, evolutionary studies, and conservation planning in Acanthaceae. Further integration of nuclear and morphological data will help clarify the diversification mechanisms within this family.
Abstract
The medicinally and ornamentally valuable genus Thunbergia faces taxonomic uncertainty, while certain Acanthaceae species are threatened by habitat loss, underscoring the need for chloroplast genome studies to support conservation efforts. The chloroplast genome of Thunbergia grandiflora was sequenced and assembled. Additionally, 28 Acanthaceae species with significant medicinal value were selected for comparative genomic analysis. Based on the chloroplast genome data of Acanthaceae species, this study conducted phylogenetic and comparative evolutionary analyses. The results preliminarily support a systematic framework that divides Acanthaceae into eight tribes within five subfamilies. Concurrently, the study revealed significant inverted repeat (IR) region structural variations. A clear correspondence was observed between the contraction of IR length and the topological structure of the phylogenetic tree. In particular, species within the genus Strobilanthes exhibited significant contraction in their IR regions, which corresponded consistently with their tendency to cluster into an independent clade in the phylogenetic tree. This suggests that structural variation in the IR regions may be closely associated with the evolutionary divergence of this group. SSR analysis revealed a prevalent mononucleotide A/T repeat dominant pattern across Acanthaceae species. Furthermore, selection pressure analysis detected positive selection acting on multiple key genes, including rbcL, rps3, rps12, cemA, and ycf4, suggesting that these genes may play important roles in the adaptive evolution of Acanthaceae. This study reveals that the chloroplast genomes of Acanthaceae exhibit distinctive characteristics in phylogenetic architecture, dynamic variations in IR regions, and adaptive evolution of key genes, providing important molecular insights for understanding the mechanisms underlying species diversity and for the conservation of medicinal resources within this family.