Complete Plastome of Physalis angulata var. villosa, Gene Organization, Comparative Genomics and Phylogenetic Relationships among Solanaceae

Abstract

Physalis angulata var. villosa, rich in withanolides, has been used as a traditional Chinese medicine for many years. To date, few extensive molecular studies of this plant have been conducted. In the present study, the plastome of P. angulata var. villosa was sequenced, characterized and compared with that of other Physalis species, and a phylogenetic analysis was conducted in the family Solanaceae. The plastome of P. angulata var. villosa was 156,898 bp in length with a GC content of 37.52%, and exhibited a quadripartite structure typical of land plants, consisting of a large single-copy (LSC, 87,108 bp) region, a small single-copy (SSC, 18,462 bp) region and a pair of inverted repeats (IR: IRA and IRB, 25,664 bp each). The plastome contained 131 genes, of which 114 were unique and 17 were duplicated in IR regions. The genome consisted of 85 protein-coding genes, eight rRNA genes and 38 tRNA genes. A total of 38 long, repeat sequences of three types were identified in the plastome, of which forward repeats had the highest frequency. Simple sequence repeats (SSRs) analysis revealed a total of 57 SSRs, of which the T mononucleotide constituted the majority, with most of SSRs being located in the intergenic spacer regions. Comparative genomic analysis among nine Physalis species revealed that the single-copy regions were less conserved than the pair of inverted repeats, with most of the variation being found in the intergenic spacer regions rather than in the coding regions. Phylogenetic analysis indicated a close relationship between Physalis and Withania. In addition, Iochroma, Dunalia, Saracha and Eriolarynx were paraphyletic, and clustered together in the phylogenetic tree. Our study published the first sequence and assembly of the plastome of P. angulata var. villosa, reported its basic resources for evolutionary studies and provided an important tool for evaluating the phylogenetic relationship within the family Solanaceae.

Plastomes of Garcinia mangostana L. and Comparative Analysis with Other Garcinia Species

“…Genetic variations in G. mangostana cultivars have been shown by randomly amplified DNA fingerprinting (RAF) and inter simple sequence repeat (ISSR) molecular markers [ 58 , 59 , 60 ]. Plastomes also contain SSR and long repeats [ 61 , 62 , 63 , 64 ]. SSR, which is a stretch of 1–6 bp small repeats, is found extensively in different regions of the plastome, such as the intergenic regions, intron regions, and protein-coding regions [ 24 ].…”

Advances in Physalis molecular research: applications in authentication, genetic diversity, phylogenetics, functional genes, and omics

“…villosa Bonati, P. alkekengi , P. minima , P. pubescens , P. peruviana , P. pruinosa , Physalis cordata Houst. ex Mill., P. philadelphica , Physalis macrophysa Rydb., and P. ixocarpa were available ( Sandoval-Padilla et al., 2019 ; Zamora-Tavares et al., 2019 ; Feng et al., 2020 ; Zhan et al., 2022 ; Sandoval-Padilla et al., 2022a , b ; Zhang et al., 2023 ) ( Table 3 ). The complete chloroplast genomes mentioned above ranged in size from 156,578 to 157,007 bp, with the number of protein coding genes ranging from 79 to 80 and the number of tRNA genes ranging from 30 to 31 ( Sandoval-Padilla et al., 2019 ; Zamora-Tavares et al., 2019 ; Feng et al., 2020 ; Sandoval-Padilla et al., 2022a , b ).…”

Development of Chloroplast Microsatellite Markers and Evaluation of Genetic Diversity and Population Structure of Cutleaf Groundcherry (Physalis angulata L.) in China

“…P. angulata has high potential medicinal value and a very long history of being used in traditional medicines around the world. Recent phytochemical and pharmacological studies have confirmed that P. angulata is rich in vitamins, minerals, antioxidants, and many important pharmacologically active constituents, including antibacterial, anti-inflammatory, and anticancer ingredients [3][4][5][6]. In many countries, such as China, Indonesia, Peru, Mexico, and Brazil, P. angulata is often used to treat a variety of illnesses, including dermatitis, tracheitis, impaludism, rheumatism, hepatitis, and analogous conditions [7][8][9][10].…”

“…In many countries, such as China, Indonesia, Peru, Mexico, and Brazil, P. angulata is often used to treat a variety of illnesses, including dermatitis, tracheitis, impaludism, rheumatism, hepatitis, and analogous conditions [7][8][9][10]. Recently, increasing attention has been paid to the phytochemical and pharmacological aspects of P. angulata, and a variety of bioactive steroids with antitumor activities, including physagulins (A−Q), physangulidines (A−C), withangulatins (A−I), physalins (B, D, F−H), and withaminimin, have been isolated from the species [4,5,11]. Due to their important medicinal value, P. angulata plants have been widely cultivated in some regions of China for decades.…”