Comparative genomics and phylogenomics of the genus Glycyrrhiza (Fabaceae) based on chloroplast genomes

Liwei Wu; Panhui Fan; Jiaying Cai; Chenxi Zang; Yulin Lin; Zhichao Xu; Zhengjun Wu; Wei Gao; Jingyuan Song; Hui Yao

doi:10.3389/fphar.2024.1371390

Comparative genomics and phylogenomics of the genus Glycyrrhiza (Fabaceae) based on chloroplast genomes

Front Pharmacol. 2024 Mar 7:15:1371390. doi: 10.3389/fphar.2024.1371390. eCollection 2024.

Authors

Liwei Wu¹, Panhui Fan¹, Jiaying Cai¹, Chenxi Zang¹, Yulin Lin¹, Zhichao Xu², Zhengjun Wu³, Wei Gao³, Jingyuan Song^{1

4}, Hui Yao^{1

4}

Affiliations

¹ State Key Laboratory of Basis and New Drug Development of Natural and Nuclear Drugs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
² College of Life Science, Northeast Forestry University, Harbin, China.
³ China Resources Sanjiu Medical & Pharmaceutical Co., Ltd., Shenzhen, China.
⁴ Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, China.

Abstract

Glycyrrhiza (Fabaceae) species are rich in metabolites and widely used in medicine. Research on the chloroplast genome of Glycyrrhiza is important for understanding its phylogenetics, biogeography, genetic diversity, species identification, and medicinal properties. In this study, comparative genomics and phylogenomics of Glycyrrhiza were analyzed based on the chloroplast genome. The chloroplast genomes of six Glycyrrhiza species were obtained using various assembly and annotation tools. The final assembled chloroplast genome sizes for the six Glycyrrhiza species ranged from 126,380 bp to 129,115 bp, with a total of 109-110 genes annotated. Comparative genomics results showed that the chloroplast genomes of Glycyrrhiza showed typically lacking inverted repeat regions, and the genome length, structure, GC content, codon usage, and gene distribution were highly similar. Bioinformatics analysis revealed the presence of 69-96 simple sequence repeats and 61-138 long repeats in the chloroplast genomes. Combining the results of mVISTA and nucleotide diversity, four highly variable regions were screened for species identification and relationship studies. Selection pressure analysis indicated overall purifying selection in the chloroplast genomes of Glycyrrhiza, with a few positively selected genes potentially linked to environmental adaptation. Phylogenetic analyses involving all tribes of Fabaceae with published chloroplast genomes elucidated the evolutionary relationships, and divergence time estimation estimated the chronological order of species differentiations within the Fabaceae family. The results of phylogenetic analysis indicated that species from the six subfamilies formed distinct clusters, consistent with the classification scheme of the six subfamilies. In addition, the inverted repeat-lacking clade in the subfamily Papilionoideae clustered together, and it was the last to differentiate. Co-linear analysis confirmed the conserved nature of Glycyrrhiza chloroplast genomes, and instances of gene rearrangements and inversions were observed in the subfamily Papilionoideae.

Keywords: Fabaceae; Glycyrrhiza; chloroplast genome; comparative genomics; phylogenomics.

Grants and funding

The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. This work was supported by the National Natural Science Foundation of China (No. 32070368) and the Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Sciences (CIFMS) (No. 2021-I2M-1-071).