The Complete Chloroplast Genomes of Two Physalis Species, Physalis macrophysa and P. ixocarpa: Comparative Genomics, Evolutionary Dynamics and Phylogenetic Relationships

Physalis macrophysa (PMA) and Physalis ixocarpa (PIX) have significant economic, medicinal, and ornamental value and are often used in the fields of edible fruits, medicinal herbs, and ornamental plants. In the present study, we obtained the complete chloroplast (cp) genome sequences of PMA and PIX, compared to the cp genome sequences of 10 Physalis species, and constructed the phylogenetic tree among the tribe Physaleae. The results showed that the cp genomes of PMA and PIX consisted of a large single copy (LSC) region (87,115 bp and 87,103 bp, respectively), a small single copy (SSC) region (18,412 bp and 18,420 bp, respectively), and a pair of same-length inverted-repeat (IRa and IRb) regions (25,604 bp and 25,674 bp, respectively). The two species contained 132 genes, including 87 encoding proteins, eight encoding ribosomal RNAs (rRNAs), and 37 encoding transfer RNAs (tRNAs), which indicated that the two species have strong similarities with respect to genome structure and gene content. PMA and PIX contained repeat sequences (35 and 40, respectively) and simple-sequence repeats (SSRs) (61 and 60, respectively). Nine regions with considerable nucleotide divergence were found, most of which were located in the LSC and SSC regions. The gene selective pressure analysis indicated that eight genes were affected by positive selection, the Ka/Ks values of which were greater than one. Our phylogenetic results indicated that PMA and PIX had the closest genetic relationship and are closely adjacent to Physalis philadelphica (PPH) in the subtribe Physalinae. Our analysis of the cp genomes in both Physalis species will be beneficial for further research into species identification, phylogeny, evolution, and the potential for germplasm resource exploitation in Physalis.