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.完整质体基因组（plastome）可为解析李属（Prunus）物种间的演化关系提供关键信息。本研究以两个桃栽培品种——粘核桃（Clingstone, CLS）与离核桃（Freestone, FRS）、野生近缘种光核桃（Prunus mira Koehne），以及22个已发表的李属质体基因组作为研究材料，对质体基因组变异进行比较分析。结果显示，这25个质体基因组均具有典型的四分体结构，基因组大小介于157,685 bp至158,955 bp之间，平均GC含量为37.72%。研究中观察到显著的结构变异，包括独特的基因重排以及反向重复区（Inverted Repeat, IR）、大单拷贝区（Large Single-Copy, LSC）与小单拷贝区（Small Single-Copy, SSC）边界处的序列变化。这些变异提示了潜在的进化热点区域，包括变异的简单序列重复（Simple Sequence Repeats, SSRs）与密码子使用模式，可为后续演化研究提供参考价值。本研究在25个质体基因组中鉴定出多态性SSR位点，其长度介于559 bp至1064 bp之间，涵盖单核苷酸、二核苷酸、五核苷酸以及六核苷酸重复序列。我们对长度范围为559 bp至1064 bp的SSR位点以及密码子使用模式展开分析，结果显示所有组装的质体基因组中共包含40个基因，其中28个为单拷贝基因，12个为多拷贝基因。系统基因组学分析构建了支持度较高的单系群，明确了桃、樱桃与扁桃进化枝间清晰的演化关系。分化时间估算结果表明，粘核桃、离核桃两个栽培品种及其野生近缘种光核桃的分化时间约为35.15百万年前（Mya）。本研究为粘核桃与离核桃栽培品种的质体基因组演化提供了重要见解，并揭示了其在桃果实质地遗传改良以及育种项目中亚种水平物种鉴定方面的潜在应用价值。