Chloroplast Genome Characterization and Phylogenetic Implications of Reyesia and Salpiglossis (Salpiglossideae, Solanaceae)

ABSTRACT Solanaceae represents one of the most economically significant families among flowering plants. Genomic research within the family has primarily concentrated on some crop genera, such as Solanum L., Nicotiana L., and Capsicum L., whereas early‐diverging clades remain comparatively understudied. This study presents the complete chloroplast (cp) genomes of two species belonging to the tribe Salpiglossideae (subfamily Cestroideae), Reyesia chilensis Clos and Salpiglossis sinuata Ruiz & Pav, and performs comprehensive comparative analyses across representative Solanaceae plastomes, focusing on genome structure, gene content, repeats, codon usage, nucleotide polymorphism (Pi), and phylogenetic relationships. The cp genomes of R. chilensis and S. sinuata have lengths of 156,969 and 156,262 bp, respectively, and both exhibit the characteristic quadripartite structure. Their genome organization and gene composition were highly conserved. The plastome of R. chilensis encoded 112 unique genes (111 in S. sinuata ), including 79 protein‐coding genes, 29 transfer RNA‐coding genes (28 in S. sinuata ), and four ribosomal RNA‐coding genes. Comparative analyses revealed only minor sequence divergence between the two plastomes, with highly similar codon usage bias and repeat sequence composition. Phylogenetic analyses supported R. chilensis and S. sinuata as a clade representing Salpiglossideae, sister to Benthamiella patagonica Speg. (Benthamielleae), together forming an early‐diverging branch within the Solanaceae. Nucleotide polymorphism analyses revealed a mean nucleotide diversity (Pi) of 0.013 within the shared genes, whereas intergenic spacers exhibited a higher sequence polymorphism (average Pi = 0.028). Several hypervariable segments were identified as promising markers for Solanaceae species delimitation and phylogenetic inference. This work contributes critical genomic datasets and further clarifies the phylogenetic comprehension across the family.