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Background   Physalis  L. is a genus of herbaceous plants of the family Solanaceae, which has important medicinal, edible, and ornamental values. The morphological characteristics of  Physalis  species are similar, and it is difficult to rapidly and accurately distinguish them based only on morphological characteristics. At present, the species classification and phylogeny of  Physalis  are still controversial. In this study, the complete chloroplast (cp) genomes of four  Physalis  species ( Physalis angulata ,  P. alkekengi  var.  franchetii ,  P. minima  and  P. pubescens ) were sequenced, and the first comprehensive cp genome analysis of  Physalis  was performed, which included the previously published cp genome sequence of  Physalis peruviana .    Results  The  Physalis  cp genomes exhibited typical quadripartite and circular structures, and were relatively conserved in their structure and gene synteny. However, the  Physalis  cp genomes showed obvious variations at four regional boundaries, especially those of the inverted repeat and the large single-copy regions. The cp genomes’ lengths ranged from 156,578 bp to 157,007 bp. A total of 114 different genes, 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes, were observed in four new sequenced  Physalis  cp genomes. Differences in repeat sequences and simple sequence repeats were detected among the  Physalis  cp genomes. Phylogenetic relationships among 36 species of 11 genera of Solanaceae based on their cp genomes placed  Physalis  in the middle and upper part of the phylogenetic tree, with a monophyletic evolution having a 100% bootstrap value.    Conclusion  Our results enrich the data on the cp genomes of the genus  Physalis . The availability of these cp genomes will provide abundant information for further species identification, increase the taxonomic and phylogenetic resolution of  Physalis , and assist in the investigation and utilization of  Physalis  plants.

Complete chloroplast genomes of four Physalis species (Solanaceae): lights into genome structure, comparative analysis, and phylogenetic relationships