Adaptation Evolution and Phylogenetic Analyses of Species in Chinese Allium Section Pallasia and Related Species Based on Complete Chloroplast Genome Sequences

The sectionPallasiais one of the components of the genusAlliumsubgenusAllium(Amaryllidaceae), and species relationship in this section is still not resolved very well, which hinders further evolutionary and adaptive studies. Here, the complete chloroplast genomes of five sect.Pallasiaspecies were reported, and a comparative analysis was performed with other three relatedAlliumspecies. The genome size of the eight species ranged from 151,672 bp to 153,339 bp in length, GC content changed from 36.7% to 36.8%, and 130 genes (exceptAllium pallasii), 37 tRNA, and 8 rRNA were identified in each genome. By analyzing the IR/LSC and IR/SSC boundary,A. pallasiiexhibited differences compared with other seven species. Phylogenetic analysis achieved high supports in each branch, seven of the eightAlliumspecies cluster into a group, andA. pallasiiexhibit a close relationship withA. obliquum. Higher pairwise Ka/Ks ratios were found inA. schoenoprasoidescompared toA. caeruleumandA. macrostemonwhile a lower value of Ka/Ks ratios was detected betweenA. caeruleumandA. macrostemon. This study will be a great contribution to the future phylogenetic and adaptive research inAllium.