Comparative Genomic Analysis of Two Phyllanthus emblica Genomes with Endemic and Widespread Cultivar Backgrounds

Phyllanthus emblica is valued for its nutritional and medicinal properties, yet the genomic divergence between localized and widespread cultivars remains poorly understood. We investigated the genomes of two individuals from the endemic cultivar ‘Hongguang’ (HG), propagated via regional grafting, and the commercially widespread ‘Dongkeng’ (DK), known for its superior protein content. Using whole-genome sequencing, we reconstructed phylogenies from two nuclear markers, profiled genome-wide variations, assembled chloroplast genomes, and verified relative plastid copy numbers via real-time quantitative PCRs (qPCRs). Nuclear internal transcribed spacer (ITS) and phytochrome C (PHYC) phylogenies confirmed both samples belonged to the P. emblica lineage, while revealing a distinct genetic identity for the HG individual. Genome-wide variant profiling of the two individuals identified KEGG enrichment in plant hormone signaling pathways; DK variants mapped to the canonical auxin axis, while HG variants were annotated to reversible protein phosphorylation. Comparative chloroplast genomics demonstrated shared maternal inheritance and shared mutations in key photosynthetic genes (psaB, petA, and the ndh cluster) between the two genomes, though qPCR validation revealed a higher relative chloroplast DNA copy number in the DK sample. Despite the two-individual limitation, these findings revealed preliminary genomic variations, offering candidate molecular markers for future population studies and marker-assisted breeding.