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

The complete plastome genome of peach represents a valuable genomic resource for elucidating the evolutionary history and phylogenetic relationships within Prunus species. This study performed plastome sequencing of two peach cultivars Clingstone (CLS) and Freestone (FRS) along with the wild relative Prunus mira, using the Illumina HiSeq 2500 platform. In this study, the plastomes of two peach cultivars-Clingstone (CLS) and Freestone (FRS)-and the wild relative Prunus mira were sequenced using the Illumina HiSeq 2500 platform. A broad comparative assessment was enabled by comparing these sequences with 22 previously sequenced Prunus plastomes. All 25 plastomes exhibited a conserved quadripartite structure, with genome sizes ranging from 157,685 to 158,955 bp and an average GC content of 37.72 %. Structural variations were observed, including gene rearrangements and boundary shifts between the IR, LSC,and Small Single-Copy (SSC) regions. These boundary shifts, together with the identified sequence rearrangements, highlighted potential mutational hotspot regions. Considerable diversity was detected in Simple Sequence Repeats (SSRs), including polymorphic loci with total counts ranging from 559 to 1064 per plastome, comprising mono-, di-, penta-, and hexa-nucleotide motifs.Variable Simple Sequence Repeats (SSRs) and codon usage patterns were identified as evolutionary hotspots. Out of 40 genes, 28 single-copy and 12 multi-copy were consistently found across all plastomes. Such variation patterns underscore regions with high phylogenetic informativeness. Phylogenomic analysis revealed well-supported monophyletic clades, clarifying evolutionary relationships among peach, cherry, and almond groups. Divergence time estimates place the split between cultivated peach (Prunus persica, including CLS and FRS) and P. mira in the Eocene. This comprehensive plastome-based study enriches our understanding of the evolutionary dynamics of peach cultivars, particularly Clingstone and Freestone, in relation to wild Prunus relatives. The identified SSR loci, codon usage features, and structural variations offer potential molecular markers for peach genetic evolution and precise taxonomic resolution at the subspecies level.