IMR Press / FBL / Volume 27 / Issue 8 / DOI: 10.31083/j.fbl2708236
Open Access Original Research
Comparative Genomic and Phylogenetic Analysis of Forty Gentiana Chloroplast Genomes
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1 School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, 430070 Wuhan, Hubei, China
2 Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700 Beijing, China
3 National Engineering Technology Research Center for Miao Medicine, College of Pharmaceutical Sciences, Guizhou University of Traditional Chinese Medicine, 550025 Guiyang, Guizhou, China
*Correspondence: (Xia Liu); (Li Xiang)
Academic Editor: Changsoo Kim
Front. Biosci. (Landmark Ed) 2022, 27(8), 236;
Submitted: 15 June 2022 | Revised: 12 July 2022 | Accepted: 12 July 2022 | Published: 9 August 2022
Copyright: © 2022 The Author(s). Published by IMR Press.
This is an open access article under the CC BY 4.0 license.

Background: Gentiana plants, which have great medicinal and ornamental value, are widely distributed in diverse habitats and have complex taxonomy. Here 40 Gentiana chloroplast genomes were used for comparative genomic analysis and divergence time estimation. Methods: The complete chloroplast genome of G. rhodantha was sequenced, assembled, and annotated. Comparative genomic and phylogenetic analysis were provided for variation analysis of Gentiana. Results: Gentiana species satisfy the characteristics of intra-Sect conservation and inter-Sect variation in chloroplast genome structure and IR boundaries. All Gentiana Sects can be clustered into a single one and separated from each other; however, Ser. Apteroideae and Ser. Confertifoliae in Sect. Monopodiae are more closely related to Sect. Frigida and Sect. Cruciata, respectively. Gentiana has experienced two large gene loss events; the first, the collective loss of the rps16 gene at genus formation and the second, the collective loss of the ndh gene when Ser. Ornatae and Ser. Verticillatae completed their differentiation. Comparative genomic analysis support that Sect. Stenogyne and Sect. Otophora became the independent genera Metagentiana and Kuepferia. Seven divergence hotspot regions were screened based on Pi values, and could serve as DNA-specific barcodes for Gentiana. Conclusions: This study provides a further theoretical basis for taxonomic analysis, genetic diversity, evolutionary mechanism and molecular identification in Gentiana.

chloroplast genome
comparative genomics
sequence divergence
gene loss
U1812403-1/National Natural Science Foundation of China
81891010/National Natural Science Foundation of China
81891013/National Natural Science Foundation of China
2019YFC1711100/National key research and development program
ZZ13-YQ-102/Fundamental Research Funds
CI2021A05103/CACMS Innovation Fund
Fig. 1.
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