Complete Chloroplast Genomes of Saussurea katochaete, Saussurea superba, and Saussurea stella: Genome Structures and Comparative and Phylogenetic Analyses

Saussurea plants are widely distributed in Asia and Europe; however, their complex phylogenetic relationships have led to many difficulties in phylogenetic studies and interspecific identification. In this study, we assembled, annotated, and analyzed the chloroplast genomes of three Saussurea plants: Saussurea katochaete, Saussurea superba, and Saussurea stella. The results showed that the full-length sequences of the three Saussurea plants were 152,561 bp, 151,452 bp, and 152,293 bp, respectively, which represent the typical quadripartite structure, and the genomes were relatively conserved. The gene annotation results showed that the chloroplast genomes of S. katochaete, S. superba, and S. stella were annotated with 128, 124, and 127 unique genes, respectively, which included 83, 80, and 83 protein-coding genes (PCGs), respectively, 37, 36, and 36 tRNA genes, respectively, and 8 rRNA genes. Moreover, 46, 45, and 43 SSR loci, respectively, and nine highly variable regions (rpl32-trnL-UAG, rpl32, ndhF-rpl32, ycf1, trnC-GCA-petN, trnC-GCA, rpcL, psbE-petL, and rpl16-trnG-UUG) were identified and could be used as potential molecular markers for population identification and phylogenetic study of Saussurea plants. Phylogenetic analyses strongly support the sisterhood of S. katochaete with S. superba and S. stella, and are all clustered with S. depsagensis, S. inversa, S. medusa, and S. gossipihora, of which S. gossipiphora is most closely related. Additionally, the phylogenetic results indicate a high frequency of differentiation among different species of Saussurea plants, and many different species or genera are morphologically very different from each other, which may be related to certain genetic material in the chloroplasts. This study provides an important reference for the identification of Saussurea plants and studies their evolution and phylogenetics.