Chloroplast phylogenomics reveals the maternal ancestry of cultivated chrysanthemums

Chrysanthemum (<italic>Chrysanthemum × morifolium</italic> Ramat. ex Hemsl.), a globally important ornamental plant originating from China, possesses significant economic and cultural value. However, its complex genetic background—shaped by extensive hybridization, polyploidization, and artificial selection—has obscured its parental origins. To elucidate its maternal lineage, we sequenced and assembled the complete chloroplast (cp) genomes of nine accessions <italic>de novo</italic> from four key <italic>Chrysanthemum</italic> species: <italic>C. dichrum</italic>, <italic>C. indicum</italic> (representing six distinct geographical populations), <italic>C. potentilloides</italic>, and <italic>C. rhombifolium</italic>. Comparative analysis revealed highly conserved quadripartite structures across all nine cp genomes, with sizes ranging from 150,999 to 151,252 bp and a GC content of approximately 37.46%. Crucially, phylogenetic analysis, incorporating data from 32 additional published <italic>Chrysanthemum</italic> cp genomes, revealed that all cultivated chrysanthemum accessions formed a single, monophyletic clade deeply nested within the genetic diversity of wild <italic>C. indicum</italic>. This finding strongly indicates that <italic>C. indicum</italic> is the primary maternal progenitor of the cultivated chrysanthemum. Collectively, this research clarifies the genetic diversity and complex evolutionary history of <italic>Chrysanthemum</italic>, providing a valuable genomic resource for future genetic conservation and breeding programs.