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

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

JOURNAL=Frontiers in Pharmacology

VOLUME=15

YEAR=2024

URL=https://www.frontiersin.org/journals/pharmacology/articles/10.3389/fphar.2024.1371390

DOI=10.3389/fphar.2024.1371390

ISSN=1663-9812

ABSTRACT=<p><italic>Glycyrrhiza</italic> (Fabaceae) species are rich in metabolites and widely used in medicine. Research on the chloroplast genome of <italic>Glycyrrhiza</italic> is important for understanding its phylogenetics, biogeography, genetic diversity, species identification, and medicinal properties. In this study, comparative genomics and phylogenomics of <italic>Glycyrrhiza</italic> were analyzed based on the chloroplast genome. The chloroplast genomes of six <italic>Glycyrrhiza</italic> species were obtained using various assembly and annotation tools. The final assembled chloroplast genome sizes for the six <italic>Glycyrrhiza</italic> 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 <italic>Glycyrrhiza</italic> 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 <italic>Glycyrrhiza</italic>, 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 <italic>Glycyrrhiza</italic> chloroplast genomes, and instances of gene rearrangements and inversions were observed in the subfamily Papilionoideae.</p>