# Genomic Phylogenetic Analysis of Physaliastrum and Archiphysalis (Solanaceae): Insights From Chloroplast Genomes Indicate Distinct Evolutionary Relationships

## TL;DR

This study uses chloroplast genome data to clarify the evolutionary relationships and classification of species in the Physaliastrum and Archiphysalis genera within the Solanaceae family.

## Contribution

The study provides genomic evidence for the distinct evolutionary status of Physaliastrum and Archiphysalis and supports the classification of species within these genera.

## Key findings

- Phylogenetic analysis shows Archiphysalis species cluster within the Withaninae subtribe, matching their fruit morphology.
- Physaliastrum and Archiphysalis diverged around 41.2 million years ago, with significant genomic differences between the genera.
- Genomic features like gene count and duplication lengths show greater intergeneric than intrageneric variation.

## Abstract

This research involved the sequencing and analysis of chloroplast genomes from nine species across four genera of the Solanaceae family, specifically two species of Archiphysalis, five species of Physaliastrum, and the taxa Tuberowithania pengiana and Tubocapsicum anomalum. 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 Archiphysalis and Physaliastrum exhibit typical quadripartite structures, with lengths ranging from 156,345 to 156,924 bp. Notably, Archiphysalis contains 130 genes, while the species of Physaliastrum have a slightly higher gene count of 132. Phylogenetic analysis reveals that
A. sinensis
and A. chamaesarachoides cluster together within the subtribe Withaninae, which is consistent with their fruit morphology. Divergence time analysis indicates that Physaliastrum separated from Archiphysalis 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 A. chamaesarachoides and
A. sinensis
.

This research involved the sequencing and analysis of chloroplast genomes from nine species across four genera of the Solanaceae family, specifically two species of Archiphysalis, five species of Physaliastrum, and the taxa Tuberowithania pengiana and Tubocapsicum anomalum. We conducted a phylogenetic analysis that clarifies the relationships among these genera and confirms their distinct generic statuses. Additionally, this study provides genomic evidence supporting their classification and highlights the close relationship between
A. sinensis
and A. chamaesarachoides.