Comparative chloroplast genomics of Ajania sericea and sympatric Asteraceae species identifies shared candidate molecular features associated with alpine adaptation

Ajania sericea is endemic to the Dali region of Yunnan and is currently the southernmost known member of the genus Ajania worldwide. It co-occurs with Aster brachytrichus , Anaphalis pannosa , and Leontopodium dedekensii in alpine habitats of northwestern Yunnan, where plants are exposed to strong ultraviolet radiation, low temperatures, strong winds, and drought. To explore whether sympatric Asteraceae species from different lineages share chloroplast genomic features associated with alpine response, we sequenced, assembled, and compared the chloroplast genomes of these four species. All four chloroplast genomes exhibited the typical quadripartite structure, with the highest GC content in the IR regions (42.99%-43.07%). A total of 142–145 gene copies were annotated. Ana. pannosa and L. dedekensii lacked ycf15 , and Ana. pannosa further lacked trnT-GGU . Codon usage bias was generally weak, with preferred codons mainly ending in A/T, while neutrality and ENC-plot analyses suggested that factors other than mutational pressure, potentially including natural selection, may also contribute. Five hypervariable regions ( petN , trnY-GUA , pafI-trnS-GGA , ndhC-trnV-UAC , and rpl32 ) were identified as potential candidate DNA barcode regions for Asteraceae. Phylogenetic analyses based on maximum likelihood and Bayesian inference yielded consistent topologies, and Aj. sericea was most closely related to Aj. nematoloba . Ka/Ks analysis indicated that most chloroplast protein-coding genes were under purifying selection, whereas only a few genes, including rpl14 , rpl33 , and rps2 , showed relatively elevated Ka/Ks values or candidate selection signals. Integrated analyses of sequence variation, selection signals, and functional annotation suggested that rpl14 , rpl33 , petN , ndhC , and ndhF were mainly associated with chloroplast translation, photosynthetic electron transport, and redox regulation. In addition, the chloroplast genomes of three Aj. sericea samples collected at different elevations were highly similar, with no clear elevation-associated plastome differentiation detected. This study showed that the chloroplast genomes of four sympatric Asteraceae species were highly conserved in overall structure, but still exhibited certain differences in gene loss, IR boundary variation, repeat sequence composition, and local hypervariable regions. These features provide useful references for interspecific differentiation studies and the development of potential molecular markers in Asteraceae. No clear elevation-associated plastome differentiation was detected among the three Aj. sericea samples within the elevational range examined in this study. Overall, the candidate genes identified in this study, including rpl14 , rpl33 , petN , ndhC , and ndhF , suggest potentially shared molecular response features among sympatric Asteraceae species in alpine environments and provide new chloroplast genomic evidence for understanding their environmental responses and evolutionary divergence.