Ycf1-ndhF genes, the most promising plastid genomic barcode, sheds light on phylogeny at low taxonomic levels in Prunus persica

Mohamed Hamdy Amar

doi:10.1186/s43141-020-00057-3

Abstract

BackgroundChloroplast genome sequencing is becoming a valuable process for developing several DNA barcodes. At present, plastid DNA barcode for systematics and evolution in flowering plant rely heavily on the use of non-coding genes. The present study was performed to verify the novelty and suitability of the two hotspot barcode plastid coding gene ycf1 and ndhF, to estimate the rate of molecular evolution in the Prunus genus at low taxonomic levels. ResultsHere, 25 chloroplast genomes of Prunus genus were selected for sequences annotation to search for the highly variable coding DNA barcode regions. Among them, 5 genera were of our own data, including the ornamental, cultivated, and wild haplotype, while 20 genera have been downloaded from the GenBank database. The results indicated that the two hotspot plastid gene ycf1 and ndhF were the most variable regions within the coding genes in Prunus with an average of 3268 to 3416 bp in length, which have been predicted to have the highest nucleotide diversity, with the overall transition/transversion bias (R = 1.06). The ycf1-ndhF structural domains showed a positive trend evident in structure variation among the 25 specimens tested, due to the variant overlap’s gene annotation and insertion or deletion with a broad trend of the full form of IGS sequence. As a result, the principal component analysis (PCA) and the ML tree data drew an accurate monophyletic annotations cluster in Prunus species, offering unambiguous identification without overlapping groups between peach, almond, and cherry. ConclusionTo this end, we put forward the domain of the two-locus ycf1-ndhF genes as the most promising coding plastid DNA barcode in P. persica at low taxonomic levels. We believe that the discovering of further variable loci with high evolutionary rates is extremely useful and potential uses as a DNA barcode in P. persica for further phylogeny study and species identification.

Highlights

Chloroplast genome sequencing is becoming a valuable process for developing several DNA barcodes
Performance of ycf1 and ndhF genes identifications At first, to empirically test the regions identified as most appropriate for barcoding in the plastid coding genes of P. persica, automatic genome annotations were performed among the 25 Chloroplast DNA (cpDNA) genomes of Rosaceae (Fig. 1)
To circumvent the challenges related to a single-locus approach, this study undertook a two-locus analysis with its overlapping or intergenic spacer (IGS) and insertion/deletion as a useful option in delineating closely related peach sequence variations based on the combination of complete two proteincoding genes ycf1-ndhF of the chloroplast genome

Summary

Introduction

Chloroplast genome sequencing is becoming a valuable process for developing several DNA barcodes. The present study was performed to verify the novelty and suitability of the two hotspot barcode plastid coding gene ycf and ndhF, to estimate the rate of molecular evolution in the Prunus genus at low taxonomic levels. Peach [Prunus persica (L.) Batsch], a member of the Rosaceae family, is one of the most genetically important fruit trees in temperate regions [1]. Lovell [4], provided a new era for the development of comparative cpDNA genome studies and the discovery of DNA barcode genes in peach. The non-coding and coding regions of the chloroplast genome had a diverse signature at both high and low taxonomic levels, making them appropriate for systematic and evolution studies [10]. The noncoding region has less functional constraint than the coding region, it offers superior levels of evolutionary rate for phylogenetic and barcoding studies at the subspecies level, while the coding region is highly conserved and suitable only for higher taxonomic levels [11]

Methods

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Discussion

Conclusion