Molecular Discrimination and Phylogenetic Relationships of Physalis Species Based on ITS2 and rbcL DNA Barcode Sequence

Abstract

Plants of the genus Physalis are of economic interest because of their fleshy edible fruits with high nutritional value. Some species have high medicinal value with a long history of ethno-medicinal use to treat diverse diseases. There is therefore a need to correctly discriminate the different species of Physalis for proper utilization. Although most Physalis species have unique morphologies, their vegetative stages are identical, making it difficult to accurately identify them based on morphological characteristics. DNA barcoding has the potential to discriminate species accurately. In this study, ribulose bisphosphate carboxylase large (rbcL) and internal transcribed spacer 2 (ITS2) regions were used to discriminate Physalis species and to reveal their phylogenetic relationships and genetic diversity. Physalis plant samples were collected from seven counties in Kenya based on the availability of the germplasm. The voucher specimens were identified using the botanical taxonomy method and were deposited in the University of Nairobi herbarium. Genomic DNA was isolated from leaf samples of 64 Physalis accessions and used for PCR amplification and the sequencing of rbcL and ITS2 barcode regions. The discriminatory ability of the barcodes was based on BLASTn comparison, phylogenetic reconstruction and cluster analysis, and the determination of inter- and intra-specific distances. The nucleotide polymorphism, genetic diversity and distance of the identified Physalis species were determined using DnaSP and MEGA 11.0 software. Species discrimination was more robust using ITS2 sequences. The species identified and discriminated by ITS2 sequences were Physalis purpurea, Physalis peruviana and Physalis cordata. The rbcL sequences were only able to identify Physalis to the genus level. There was high interspecific and low intraspecific divergence within the identified Physalis species based on ITS2 sequences. The ITS2 barcode is an ideal DNA barcode for use in the discrimination of species, as well as in genetic diversity studies of Physalis accessions in Kenya.

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

“…The taxonomy of Physalis is considered to be a highly complex issue within the Solanaceae due to the significant intraspecific morphological variation and substantial interspecific similarity ( Axelius, 1996 ; Sullivan, 2004 ; Whitson and Manos, 2005 ; Olmstead et al., 2008 ; Pretz and Deanna, 2020 ). In recent years, molecular analyses have yielded new insights into this problem ( Whitson and Manos, 2005 ; Olmstead et al., 2008 ; Feng et al., 2016 ; Zamora-Tavares et al., 2016 ; Feng et al., 2020 ; Pere et al., 2023 ). ITS regions of nrDNA are widely used for studying phylogenic relationships among angiosperms, including the genus Physalis , at the interspecific and infrageneric level.…”

“…ITS regions of nrDNA are widely used for studying phylogenic relationships among angiosperms, including the genus Physalis , at the interspecific and infrageneric level. This is due to their biparental inheritance, simplicity, universality, intra-genome consistency, inter-genome variability, and high copy number ( Whitson and Manos, 2005 ; Xiang et al., 2013 ; Feng et al., 2016 ; Zamora-Tavares et al., 2016 ; Pere et al., 2023 ; Jalab and Al-Rufaye, 2024 ). Whitson and Manos (2005) conducted a study on the phylogenetic relationships among 35 species of Physalis and the relationships among the genera of the subtribe Physalinae utilizing the sequence analysis of the nrDNA ITS region and the nuclear gene waxy .…”