Plastome architecture and maternal relationships of cultivated almond (Prunus dulcis) and its wild relatives.

Plastome structure and gene content are invariant across almond and its wild relatives; the spacers rpl33-rps18, rps2-rpoC2 and psbB-psbT are the most variable regions and strongest candidate markers for Amygdalus. Almond (Prunus dulcis) is a major tree nut crop whose domestication narrowed its genetic base, whilst its wild relatives retain adaptive diversity. Complete plastomes remain scarce for almond. We sequenced three new plastomes (P. arabica, P. argentea and P. dulcis) from Türkiye and compared them with ten further Prunus plastomes from public reads, giving 13 uniformly annotated genomes rooted on P. persica and P. avium. All had the conserved quadripartite structure (157,756-158,070 bp), GC content near 36.7%, fixed junctions and an identical set of 113 genes: 79 protein-coding, 30 tRNA and 4 rRNA genes, 18 intron-containing. Codon use was A/U-biassed and the plastome repeat-poor, dominated by A/T mononucleotide microsatellites, ycf1 carrying the most cpSSR loci. Across 128 kb of alignment the thirteen plastomes differed at 956 positions (π = 0.0014); six of the nine cultivated accessions, from China to Spain, shared one haplotype, two more lay within six substitutions of it, and only the Iranian accession diverged (180-185 substitutions). The most variable regions, rpl33-rps18, rps2-rpoC2 and psbB-psbT, are nominated as candidate plastid markers. Maximum-likelihood and Bayesian phylogenies, and haplotype network were congruent: P. arabica was the wild plastome, closest to the cultivated cluster, P. argentea, the Iranian accession and P. webbii diverged successively outside it, and a relaxed clock calibrated on the almond-peach split placed these separations within roughly the last five million years. Amongst the sampled accessions, the cultivated plastomes form one tight maternal lineage, consistent with a narrow founder base, though clonal propagation and limited sampling may contribute.