Comprehensive analysis of the complete chloroplast genome of white pomegranate and phylogenetic relationships within Myrtales

Pomegranate is nutrient-rich, offers significant health benefits and high ornamental value. The chloroplast genomes of wild pomegranate and several cultivars have been successfully annotated. However, despite the rich germplasm resources and high genetic diversity of pomegranate, the phylogenetic and evolutionary history of white pomegranate remains unclear to this day. We sequenced and annotated the complete chloroplast genome of white pomegranate and compared it with related species of Myrtales order based on the chloroplast genome in this study. The complete chloroplast genome of white pomegranate cultivar ‘Sanbaitian’ was 158,651 bp long and includes typical quadripartite structure with a large single copy (LSC) region, a small single copy (SSC) region, and a pair of inverted repeat (IR) regions. The genome size was larger than that of the wild pomegranate. There were 130 genes in the genome, including 85 protein coding genes, 37 tRNA genes and 8 rRNA genes. The clpP and ycf3 genes had two introns, and the trnK-UUU gene had the longest intron in the LSC region. An assessment of codon usage, repetitive sequences, and simple sequence repeats (SSRs) had been carried out. Leucine was the most prevalent amino acid, and UUA codon had the highest RSCU value of 1.9296. Mononucleotide SSRs were the most abundant in pomegranate. The white pomegranate exhibited highly conserved chloroplast sequences and gene arrangements, demonstrating significant structural and organizational similarities to other species within the Myrtales order.The nucleotide polymorphism in the IR region was higher than that in the SSC and LSC regions. The Pi values of the trnS-GCU, trnT-GGU, trnR-ACG, and trnV-GAC genes were relatively high and can be used as potential molecular markers for species identification. Positive selection was observed for the psbI, psbK, rps18, ycf2, and ycf4 genes. Phylogenetic tree analysis indicated that white pomegranate was most closely related to different pomegranate cultivars, and Woodfordia fruticosa and Pemphis acidula in the Lythaceae family. The complete chloroplast genomes of white pomegranate were sequenced and annotated, which expanded new insight into phylogeny and taxonomy of genus Punica. The results provide important foundation for species identification, molecular breeding, genetic diversity, and evolutionary exploration of Myrtales order.