Background: Genomic analysis is crucial for better understanding the evolutionary history of species and for their conservation. Shizhenia pinguicula is a rare medicinal plant endemic to China. However, the complete chloroplast genome of this species has not been reported to date. Insufficient genomic research on S. pinguicula has hindered effective conservation efforts for this valuable plant. Methods: In this study, we sequenced and assembled the first complete chloroplast genome of S. pinguicula using Illumina sequencing technology. We conducted a comparative analysis of its chloroplast genome with related species and reconstructed phylogenetic relationships. Results: The chloroplast genome of S. pinguicula exhibited a typical quadripartite structure with a length of 158,658 bp. A total of 123 genes, 118 simple sequence repeats, and 51 dispersed repetitive sequences were identified. The inverted repeat boundaries were significantly expanded, along with the pseudogenization and loss of multiple NDH genes. Codon usage bias is primarily influenced by natural selection and other factors, with the ycf3 gene under positive selection. Additionally, 10 hypervariable regions were detected for species identification and evolutionary studies. Phylogenetic analysis indicated that Ponerorchis gracilis and Hemipilia yajiangensis form a clade, with S. pinguicula as their sister species, located at the basal position of the Ponerorchis-Hemipilia alliance. Conclusions: The chloroplast genome structure and gene content of S. pinguicula exhibit certain degrees of variation compared to other species within the Orchidinae subtribe. This genome should be useful for further investigations into the biology of Shizhenia and the development of biodiversity conservation strategies.

Background: Phanera Lour., a genus in the subfamily Cercidoideae of the family Leguminosae, is characterized by woody liana habit, tendrils, and distinctive bilobate or bifoliolate leaves. The genus holds important medicinal value and constitutes a complex group characterized by morphological diversity and unstable taxonomic boundaries. However, limited information on the chloroplast genomes of this genus currently available constrains our understanding of its species diversity. Hence, it is necessary to obtain more chloroplast genome information to uncover the genetic characteristics of this genus. Methods: We collected and assembled the complete chloroplast genomes of nine representative Phanera plants, including Phanera erythropoda, Phanera vahlii, Phanera aureifolia, Phanera bidentata, Phanera japonica, Phanera saigonensis, Phanera championii, Phanera yunnanensis, and Phanera apertilobata. We then conducted a comparative analysis of these genomes and constructed phylogenetic trees. Results: These species are each characterized by a typical quadripartite structure. A total of 130–135 genes were annotated, and the GC content ranged from 39.25–42.58%. Codon usage analysis indicated that codons encoding alanine were dominant. We found 82–126 simple sequence repeats, along with 5448 dispersed repeats, mostly in the form of forward repeats. Phylogenetic analysis revealed that 16 Phanera species form a well-supported monophyletic group, suggesting a possible monophyletic genus. Furthermore, 10 hypervariable regions were detected for identification and evolutionary studies. Conclusions: We focused on comparing chloroplast genome characteristics among nine Phanera species and conducted phylogenetic analyses, laying the foundation for further phylogenetic research and species identification of Phanera.

Bauhinia s.s. belongs to the Cercidoideae subfamily, located at the base of the Leguminosae family. It displays a variety of growth habits and morphologies, and is widely utilized as both ornamental and medicinal plants globally. The objective of this research is to uncover chloroplast genomes of species from Eastern Asia and Southern Africa, thereby advancing our understanding of the diversity within this genus. This study sequenced Bauhinia purpurea, Bauhinia brachycarpa var. microphylla, Bauhinia variegata var. candida, Bauhinia galpinii, and Bauhinia monandra using the Illumina platform and conducted the construction of phylogenetic trees as well as the estimation of divergence times. Compared to Asian species, the IR regions of African species underwent a contraction of approximately 100–400 bp. The phylogenetic analysis indicated that Asian and African species clustered into two distinct clades, with high support. The divergence of Bauhinia s.s. species occurred in the late Paleocene, and the rps18 and cemA genes were under positive selection. Six hypervariable regions were screened for evolutionary studies and the super-barcode data were used for species delimitation. The results revealed certain differences between African and Asian species in their chloroplast genomes of Bauhinia species.

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.