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Chloroplast Phylogenomics Reveals the Intercontinental Biogeographic History of the Liquorice Genus (Leguminosae: Glycyrrhiza).

ABSTRACT: The liquorice genus, Glycyrrhiza L. (Leguminosae), is a medicinal herb with great economic importance and an intriguing intercontinental disjunct distribution in Eurasia, North Africa, the Americas, and Australia. Glycyrrhiza, along with Glycyrrhizopsis Boiss. and Meristotropis Fisch. & C.A.Mey., comprise Glycyrrhiza s.l. Here we reconstructed the phylogenetic relationships and biogeographic history in Glycyrrhiza s.l. using sequence data of whole chloroplast genomes. We found that Glycyrrhiza s.l. is sister to the tribe Wisterieae and is divided into four main clades. Clade I, corresponds to Glycyrrhizopsis and is sister to Glycyrrhiza sensu Meng. Meristotropis is embedded within Glycyrrhiza sensu Meng, and these two genera together form Clades II-IV. Based on biogeographic analyses and divergence time dating, Glycyrrhiza s.l. originated during the late Eocene and its most recent common ancestor (MRCA) was distributed in the interior of Eurasia and the circum-Mediterranean region. A vicariance event, which was possibly a response to the uplifting of the Turkish-Iranian Plateau, may have driven the divergence between Glycyrrhiza sensu Meng and Glycyrrhizopsis in the Middle Miocene. The third and fourth main uplift events of the Qinghai-Tibetan Plateau may have led to rapid evolutionary diversification within Glycyrrhiza sensu Meng. Subsequently, the MRCA of Clade II might have migrated to North America (G. lepidota) via the Bering land bridge during the early Pliocene, and reached temperate South America (G. astragalina) by long-distance dispersal (LDD). Within Clade III, the ancestor of G. acanthocarpa arrived at southern Australia through LDD after the late Pliocene, whereas all other species (the SPEY clade) migrated to the interior of Eurasia and the Mediterranean region in the early Pleistocene. The MRCA of Clade IV was restricted in the interior of Eurasia, but its descendants have become widespread in temperate regions of the Old World Northern Hemisphere during the last million years.

SUBMITTER: Duan L

PROVIDER: S-EPMC7318913 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Chloroplast Phylogenomics Reveals the Intercontinental Biogeographic History of the Liquorice Genus (Leguminosae: Glycyrrhiza).

Duan Lei L Harris A J AJ Su Chun C Zhang Zhi-Rong ZR Arslan Emine E Ertuğrul Kuddisi K Loc Phan Ke PK Hayashi Hiroaki H Wen Jun J Chen Hong-Feng HF

Frontiers in plant science 20200617

The liquorice genus, Glycyrrhiza L. (Leguminosae), is a medicinal herb with great economic importance and an intriguing intercontinental disjunct distribution in Eurasia, North Africa, the Americas, and Australia. Glycyrrhiza, along with Glycyrrhizopsis Boiss. and Meristotropis Fisch. & C.A.Mey., comprise Glycyrrhiza s.l. Here we reconstructed the phylogenetic relationships and biogeographic history in Glycyrrhiza s.l. using sequence data of whole chloro ...[more]

PMID: 32636856

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Project description: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.

Dataset Information

Chloroplast Phylogenomics Reveals the Intercontinental Biogeographic History of the Liquorice Genus (Leguminosae: Glycyrrhiza).

Publications

Chloroplast Phylogenomics Reveals the Intercontinental Biogeographic History of the Liquorice Genus (Leguminosae: <i>Glycyrrhiza</i>).

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