Application of the Ribosomal DNA ITS2 Region of Physalis (Solanaceae): DNA Barcoding and Phylogenetic Study

Abstract

Recently, commercial interest in Physalis species has grown worldwide due to their high nutritional value, edible fruit, and potential medicinal properties. However, many Physalis species have similar shapes and are easily confused, and consequently the phylogenetic relationships between Physalis species are poorly understood. This hinders their safe utilization and genetic resource conservation. In this study, the nuclear ribosomal ITS2 region was used to identify species and phylogenetically examine Physalis. Eighty-six ITS2 regions from 45 Physalis species were analyzed. The ITS2 sequences were aligned using Clustal W and genetic distances were calculated using MEGA V6.0. The results showed that ITS2 regions have significant intra- and inter-specific divergences, obvious barcoding gaps, and higher species discrimination rates (82.2% for both the BLASTA1 and nearest distance methods). In addition, the secondary structure of ITS2 provided another way to differentiate species. Cluster analysis based on ITS2 regions largely concurred with the relationships among Physalis species established by many previous molecular analyses, and showed that most sections of Physalis appear to be polyphyletic. Our results demonstrated that ITS2 can be used as an efficient and powerful marker in the identification and phylogenetic study of Physalis species. The technique provides a scientific basis for the conservation of Physalis plants and for utilization of resources.

Molecular identification of species of Physalis (Solanaceae) using a candidate DNA barcode: the chloroplast psbA–trnH intergenic region

“…Physalis is one of the important genera of the plant family Solanaceae, comprising ranged from 75 to 120 species (Maggie 2005;Martinez 1998;Chinese Academy of Sciences 1978;Wei et al 2012). Most Physalis species are distributed in tropical and temperate regions of the Americas, and a few species are native to Eurasia and Southeast Asia (Feng et al 2016;Maggie 2005;Martinez 1998;Chinese Academy of Sciences 1978;Wei et al 2012). In China, there are five Physalis species (Physalis alkekengi, P. angulate, P. peruviana, P. pubescens, and P. minima) and two varieties (P. alkekengi var.…”

Internal transcribed spacer 2 (ITS2) barcodes: A useful tool for identifying Chinese Zanthoxylum

“…In the nuclear genome, the ITS gene, especially ITS2, is a potential DNA barcode, and it has been used in multi‐loci barcode combinations (Chase et al., ; Feng et al., ). Schultz et al.…”

“…() tested the discriminatory ability of ITS2 in more than 6600 plant samples belonging to 4800 species from 753 distinct genera, and proposed that it can be used as a standard DNA barcode to identify medicinal plants. ITS2 has since been shown to be a promising and effective region for identifying medicinal samples (Feng et al., ; Han et al., ).…”

“…Because identifications based on molecular markers are independent of environmental variation, molecular markers have been popular tools for modern taxonomists due to their stability and universality (Feng et al., ). Some molecular markers, including simple sequence repeat (SSR) and sequence‐related amplified polymorphism (SRAP) markers, have been used for analysis of Zanthoxylum species.…”

Phylogenetic Analysis of Astigmatid Mites Sarcoptes scabiei and Dermatophagoides farinae using ITS-2 as a Genetic Marker

“…In acarological research, the internal transcribed spacer ITS-2 gene has been used to study organization and kinship of a population, and to 16 identify taxonomically challenging species. Previous literature showed that the ITS-2 region has been used as a genetic marker for scrutinizing the diversity and exploring phylogenetic relationships 17 among astigmatid mites. ITS-2 marker has been used to successfully verify the taxonomy of closely related species and to differentiate and identify 18,19 different species of astigmatid mites.…”