Comparing chloroplast genomes of Tulipa species: genome evolution and phylogenomic implications

Tulips are economically important ornamental plants that are distributed in Europe, North Africa, and Asia. The Tianshan Mountains are a center of tulip diversity, but there have been few molecular studies of endemic Tulipa species. In this study, we assembled chloroplast genomes of four Tulipa species from the Tianshan Mountains: Tulipa iliensis, Tulipa patens, Tulipa buhseana, and Tulipa thianschanica. The chloroplast genome sequences, including those of Tulipa altaica and Tulipa sylvestris, were collectively analyzed and compared with those of other Liliaceae species. We found that T. iliensis, T. patens, T. buhseana, and T. thianschanica were highly conserved in structure, gene order, and content and ranged in size from 151,744 to 152,122 bp. Through comparative analysis, we identified the genes ycf1, ycf2, ndhF, and rpoC1 as having evolved under positive selection pressure among Tulipa species. Significant variation was observed in the large single-copy (LSC) region at rps11–rps8 and the small single-copy (SSC) region at rps15–trnN− GUU. These two informative sites demonstrate considerable potential as candidate molecular markers for both species identification and phylogenetic studies within the Tulipa genus. Phylogenetic reconstruction from 30 chloroplast genomes provided strong evidence that tulips are monophyletic and that the genera Tulipa, Amana, and Erythronium form a clade as sister groups. The species T. buhseana, T. patens, and T. sylvestris clustered into one branch, and T. altaica, T. iliensis, and T. thianschanica clustered into another branch, thus revealing a clear genetic relationship among these six species. Our results provide a foundation for systematic and comparative genomics within Tulipa.