Genomic Phylogenetic Analysis of <i>Physaliastrum</i> and <i>Archiphysalis</i> (Solanaceae): Insights From Chloroplast Genomes Indicate Distinct Evolutionary Relationships

This research involved the sequencing and analysis of chloroplast genomes from nine species across four genera of the Solanaceae family, specifically two species of <i>Archiphysalis</i>, five species of <i>Physaliastrum</i>, and the taxa <i>Tuberowithania pengiana</i> and <i>Tubocapsicum anomalum</i>. We conducted a comprehensive series of analyses, including assessments of genome structure, gene content, codon usage, selection pressure, and other genomic features. The chloroplast genomes of <i>Archiphysalis</i> and <i>Physaliastrum</i> exhibit typical quadripartite structures, with lengths ranging from 156,345 to 156,924 bp. Notably, <i>Archiphysalis</i> contains 130 genes, while the species of <i>Physaliastrum</i> have a slightly higher gene count of 132. Phylogenetic analysis reveals that <i>A. sinensis</i> and <i>A. chamaesarachoides</i> cluster together within the subtribe Withaninae, which is consistent with their fruit morphology. Divergence time analysis indicates that <i>Physaliastrum</i> separated from <i>Archiphysalis</i> approximately 41.2 million years ago (95% HPD: 38.6-43.5 Mya), resulting in intergeneric differences in chloroplast gene features that are significantly greater than intrageneric differences, particularly in gene count, structure, and lengths of gene duplications. These findings provide genomic-level support for the classification of species within these genera and underscore the close relationship between <i>A. chamaesarachoides</i> and <i>A. sinensis</i>.