ycf1-ndhF genes, the most promising plastid genomic barcode, sheds light on phylogeny at low taxonomic levels inPrunus persica

Background Chloroplast 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 geneycf1 andndhF, to estimate the rate of molecular evolution in thePrunusgenus at low taxonomic levels. Results Here, 25 chloroplast genomes ofPrunusgenus 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 geneycf1 andndhF were the most variable regions within the coding genes inPrunuswith 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). Theycf1-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 inPrunusspecies, offering unambiguous identification without overlapping groups between peach, almond, and cherry. Conclusion To this end, we put forward the domain of the two-locusycf1-ndhF genes as the most promising coding plastid DNA barcode inP. persicaat 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 inP. persicafor further phylogeny study and species identification.