Structural divergence and phylogenetic relationships of Ajania (Asteraceae) from plastomes and ETS

BACKGROUND: Ajania Poljakov, an Asteraceae family member, grows mostly in Asia’s arid and semi-desert areas and is a significant commercial and decorative plant. Nevertheless, the genus’ classification has been disputed, and the evolutionary connections within the genus have not been thoroughly defined. Hence, we sequenced and analyzed Ajania’s plastid genomes and combined them with ETS data to assess their phylogenetic relationships. RESULTS: We obtained a total of six new Ajania plastid genomes and nine ETS sequences. The whole plastome lengths of the six species sampled ranged from 151,002 bp to 151,115 bp, showing conserved structures. Combined with publicly available data from GenBank, we constructed six datasets to reconstruct the phylogenetic relationships, detecting nucleoplasmic clashes. Our results reveal the affinities of Artemisia, Chrysanthemum and Stilpnolepis to Ajania and validate the early taxonomy reclassification. Some of the plastid genes with low phylogenetic information and gene trees with topological differences may have contributed to the ambiguous phylogenetic results of Ajania. There is extensive evolutionary rate heterogeneity in plastid genes. The psbH and ycf2 genes, which are involved in photosynthesis and ATP transport, are under selective pressure. Plastomes from Ajania species diverged, and structural aspects of plastomes may indicate some of the real evolutionary connections. We suggest the ycf1 gene as a viable plastid DNA barcode because it has significant nucleotide diversity and better reflects evolutionary connections. CONCLUSION: Our findings validate the early Ajania taxonomy reclassification and show evolutionary rate heterogeneity, genetic variety, and phylogenetic heterogeneity of plastid genes. This research might provide new insights into the taxonomy and evolution of Ajania, as well as provide useful information for germplasm innovation and genetic enhancement in horticultural species. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-023-09716-4.