Plastome diversity and phylogenetic insights among modern Egyptian wheat cultivars: Genome-Wide and Gene-Level perspectives

This study presents a genome-wide and gene-level characterization of plastome diversity and phylogenetic relationships among ten modern Egyptian wheat cultivars, representing both hexaploid and tetraploid lineages. Raw sequencing data for all cultivars were retrieved from NCBI BioProject PRJNA1290394, and plastome assemblies were generated using the published wheat chloroplast genome (GenBank accession MW889057.1) as the seed reference under default settings. Comprehensive plastome sequencing revealed an exceptionally conserved genome structure and gene content across cultivars, yet identified distinct mutation hotspots, with the rps2 gene exhibiting the highest single-gene SNP burden (up to 21 SNPs in cultivar Sahel 1). SNP profiling demonstrated clear differentiation between genetically divergent cultivars such as Sahel 1 and GMZ9, and documented variation in overall mutational load-ranging from 7 to 74 SNPs per cultivar-mirroring phylogenetic clade structure. Chloroplast heteroplasmy analysis uncovered cultivar-specific genome stability patterns, informing breeding decisions and highlighting cytoplasmic diversity. SSR motif analysis confirmed predominant AT-rich homopolymers and subtle motif-length differences distinguishing tetraploid and hexaploid genotypes. Codon usage analysis showed a highly conserved AT-bias and effective translational optimization across ploidy levels. Phylogenetic reconstruction using complete plastome sequences resolved finer relationships than gene-based approaches, while matK emerged as a superior biomarker for distinguishing Poaceae lineages. mVISTA comparison revealed conserved plastome structure with divergence hotspots at atpH-atpI and atpA regions, underscoring their value as potential molecular markers for phylogenetic and barcoding applications. Taken together, these findings provide deep insights into plastome-driven genetic diversity, robust cultivar identification, and the evolutionary context for Egyptian wheat breeding and conservation programs. (253 words).