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

Abstract

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.

Molecular Identification and Phylogenetic Analysis of Cymbidium Species (Orchidaceae) Based on the Potential DNA Barcodes matK, rbcL, psbA-trnH, and Internal Transcribed Spacer

“…DNA barcoding is a method of molecular identification that uses brief, standardized DNA sequences to rapidly determine the species of specimens [13][14][15][16]. The mitochondrial cytochrome c oxidase 1 gene (CO1) has been widely accepted as a universal barcode for species identification in many animal groups [17][18][19].…”

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.…”

Hidden in the sand: phylogenomics unravel an unexpected evolutionary history on the desert-adapted vipers of the genusCerastes

“…Species-level phylogenies are crucial for understanding evolution and speciation (Barraclough & Nee, 2001). An accurate knowledge of phylogenetic relationships is critical to study multiple evolutionary processes such as interspecific diversification, trait evolution or adaptative responses of species to changing environments, among others (Guo et al, 2019; Schoch et al, 2009; Zhang et al, 2022). Traditionally, mitochondrial markers have been widely used in phylogenetic and/or phylogeographic approaches to infer the evolutionary history of species (Brown, 2002).…”