Comparative analyses of chloroplast genomes from Six Rhodiola species: variable DNA markers identification and phylogenetic relationships within the genus
Kaihui Zhao,
Lianqiang Li,
Hong Quan,
Junbo Yang,
Zhirong Zhang,
Zhihua Liao,
Xiaozhong Lan
Affiliations
Kaihui Zhao
The Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, The Center for Xizang Chinese (Tibetan) Medicine Resource, Joint Laboratory for Tibetan Materia Medica Resources Scientific Protection and Utilization Research of Tibetan Medical Research Center of Tibet, Tibet Agriculture and Animal Husbandry University
Lianqiang Li
The Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, The Center for Xizang Chinese (Tibetan) Medicine Resource, Joint Laboratory for Tibetan Materia Medica Resources Scientific Protection and Utilization Research of Tibetan Medical Research Center of Tibet, Tibet Agriculture and Animal Husbandry University
Hong Quan
The Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, The Center for Xizang Chinese (Tibetan) Medicine Resource, Joint Laboratory for Tibetan Materia Medica Resources Scientific Protection and Utilization Research of Tibetan Medical Research Center of Tibet, Tibet Agriculture and Animal Husbandry University
Junbo Yang
Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences
Zhirong Zhang
Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences
Zhihua Liao
Integrative Science Center of Germplasm Creation, The Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University
Xiaozhong Lan
The Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, The Center for Xizang Chinese (Tibetan) Medicine Resource, Joint Laboratory for Tibetan Materia Medica Resources Scientific Protection and Utilization Research of Tibetan Medical Research Center of Tibet, Tibet Agriculture and Animal Husbandry University
Abstract Background As a valuable medicinal plant, Rhodiola has a very long history of folk medicine used as an important adaptogen, tonic, and hemostatic. However, our knowledge of the chloroplast genome level of Rhodiola is limited. This drawback has limited studies on the identification, evolution, genetic diversity and other relevant studies on Rhodiola. Results Six Rhodiola complete chloroplast genomes were determined and compared to another Rhodiola cp genome at the genome scale. The results revealed a cp genome with a typical quadripartite and circular structure that ranged in size from 150,771 to 151,891 base pairs. High similarity of genome organization, gene number, gene order, and GC content were found among the chloroplast genomes of Rhodiola. 186 (R. wallichiana) to 200 (R. gelida) SSRs and 144 pairs of repeats were detected in the 6 Rhodiola cp genomes. Thirteen mutational hotspots for genome divergence were determined and could be used as candidate markers for phylogenetic analyses and Rhodiola species identification. The phylogenetic relationships inferred by members of Rhodiola cluster into two clades: dioecious and hermaphrodite. Our findings are helpful for understanding Rhodiola's taxonomic, phylogenetic, and evolutionary relationships. Conclusions Comparative analysis of chloroplast genomes of Rhodiola facilitates medicinal resource conservation, phylogenetic reconstruction and biogeographical research of Rhodiola.
