Structural analysis of clingstone and freestone peach (Prunus persica L.) plastome genome: provides insight into phylogeny and time diversification

The complete plastome genome (plastome) provides vital information for determining evolutionary relationships among Prunus species. We compared plastome variations using two peach cultivars, Clingstone (CLS) and Freestone (FRS), the wild relative P. mira (Koehne), and 22 previously published Prunus plastomes. The results indicate that the 25 plastomes possess a typical quadripartite structure, with sizes ranging from 157,685 bp to 158,955 bp and an average GC content of 37.72%. Significant structural variations, including distinctive gene rearrangements and changes at the boundaries between the Inverted Repeat (IR), Large Single-Copy (LSC), and Small Single-Copy (SSC) regions, were observed. These variations highlight potential hotspot regions, including variable Simple Sequence Repeats (SSRs) and codon usage patterns, which could be valuable for future evolutionary studies. Polymorphic SSR loci were identified in the 25 plastome genomes, with sizes ranging from 559 to 1064 bp, including mono-, di-, penta-, and hexanucleotide sequences. We investigated SSR loci, which ranged from 559 to 1064 bp and the codon usage patterns revealing a total of 40 genes 28 single-copy and 12 multi-copy genes across all constructed plastome genomes. Phylogenomic analysis inferred strongly supported monophyletic groups, revealing clear evolutionary relationships among peach, cherry, and almond clades. The divergence time estimates showed that the CLS and FRS peach cultivars, and a wild relative (P. mira Koehne) diverged approximately 35.15 Mya. This study offers significant insights of the plastome evolution of CLS and FRS cultivars, highlighting potential uses for genetic improvement of peach fruit texture and species identification at subspecies level in breeding programs.