Comparative analysis of chloroplast genomes on Meliaceae species: insights into the evolution and species identification

Divergence time estimation indicates that most Meliaceae species have a relatively recent origin, with rapid divergence occurring during the Late Oligocene or Early Miocene epochs. Comparative analysis of cp genomes revealed that Meliaceae exhibits relative conservation in terms of cp genome size, inverted-repeat (IR) boundary, genome structure, HVRs and codon patterns. Although differences exist between the Cedreloideae and Melioideae subfamilies, the overall similarity remains notably high. Furthermore, the <i>ycf</i>1, <i>trn</i>K-<i>rps</i>16, and <i>ndh</i>F-<i>rpl</i>32 regions exhibited the highest nucleotide polymorphism within Meliaceae, while the <i>rpl</i>22 gene displayed significant genetic diversity within both subfamilies. As candidate molecular markers, these regions may effectively distinguish among species. These findings not only provide insights into the evolution and species identification but also establish a scientific foundation for future systematics within Meliaceae.