Species delimitation of the liquorice tribe (Leguminosae: Glycyrrhizeae) based on phylogenomic and machine learning analyses

Abstract

The liquorice tribe Glycyrrhizeae is a leguminous herbaceous group of plants comprised of the genera Glycyrrhiza and Glycyrrhizopsis. Some Glycyrrhiza taxa contain glycyrrhizin, a pharmacologically significant sweet substance that also has applications in crafting industrial materials. Here, we utilized an expanded taxon sampling of Glycyrrhizeae to reconstruct the phylogenetic relationships in the tribe based on genome skimming data, including whole chloroplast genomes, nuclear ribosomal DNA, and low‐copy nuclear DNA. We also launched machine learning analysis (MLA) for one species pair with controversial taxonomic boundary. The integrated results indicated Glycyrrhizopsis should be split from Glycyrrhiza, while the former genus Meristotropis should be treated as part of Glycyrrhiza. Glycyrrhizopsis includes two species, Glycyrrhizopsis asymmetrica and Glycyrrhizopsis flavescens, and we recognize 13 species in Glycyrrhiza: Glycyrrhiza acanthocarpa, Glycyrrhiza astragalina, Glycyrrhiza bucharica, Glycyrrhiza echinata, Glycyrrhiza foetida, Glycyrrhiza glabra, Glycyrrhiza gontscharovii, Glycyrrhiza lepidota, Glycyrrhiza macedonica, Glycyrrhiza pallidiflora, Glycyrrhiza squamulosa, Glycyrrhiza triphylla, and Glycyrrhiza yunnanensis. We propose a broader G. glabra that includes former Glycyrrhiza aspera, G. glabra s.s., Glycyrrhiza inflata, and Glycyrrhiza uralensis, and represents the glycyrrhizin‐contained medicinal group. Our ancestral state inferences show the ancestor of Glycyrrhiza lacked glycyrrhizin, and the presence of glycyrrhizin evolved twice within Glycyrrhiza during the last one million years. Our integrative phylogenomics‐MLA study not only provides new insights into long‐standing taxonomic controversies of Glycyrrhizeae, but also represents a useful approach for future taxonomic studies on other plant taxa.

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

“…In Glycyrrhiza species, the ones without glycyrrhizic acid differentiated earlier than those with glycyrrhizic acid. This result suggested that the common ancestor of Glycyrrhiza lacked glycyrrhizic acid, consistent with previous studies ( Duan et al, 2023 ). Medicinal groups in the Eurasian continent share a common ancestor, and their descendants result from two rapid differentiation events within the last million years.…”

“…The Fabaceae family comprises 6 subfamilies and 79 tribes. Previous studies have focused on the phylogenetic relationship within the Glycyrrhiza genus ( Jo et al, 2018 ; Jia et al, 2019 ; Duan et al, 2020 ; Jiang et al, 2020 ; Duan et al, 2023 ). Research on phylogenomics of the Fabaceae family using chloroplast genome data is limited.…”

“…However, there has been ongoing controversy regarding the classification within the Glycyrrhiza genus, which has implications for the medicinal, industrial, and scientific applications of Glycyrrhiza species, as well as the collection and breeding of their germplasm resources. Non-medicinal species are sometimes sold in the market as medicinal species, and even some scientific studies on pharmacology or chemistry have used misidentified Glycyrrhiza materials ( Duan et al, 2023 ).…”

Nuclear phylogenomics of angiosperms and insights into their relationships and evolution

“…The relationships among subfamilies, tribes, and previously defined clades within subfamilies were generally well resolved (BS ≥ 90), whereas some previously defined tribes were not monophyly, such as Mimoseae, Ingeae, Acacieae, and Phaseoleae. Additionally, within the Fabaceae subfamily Papilionoideae, the relationships of the tribe Glycyrrhizeae were analyzed using nuclear genes (Duan et al, 2023). Furthermore, the relationships of the mimosoid clade (formerly Mimosoideae) (Koenen et al, 2020a) and Caesalpinioideae (Ringelberg et al, 2022) were also investigated using nuclear genes; also, nuclear phylogenetic analyses were also reported for mimosoid genera Inga and Leucaena (Nicholls et al, 2015; Abair et al, 2019).…”

Species delimitation and phylogenetic relationships of the Prionospio complex (Annelida, Spionidae) in the Northeast Atlantic

“…This method involves sequencing bulk DNA at low coverage, enabling retrieval of elements that are abundant in genomic DNA extracts, such as organelle genomes and nuclear ribosomal genes. Genome skimming significantly increases the available genetic data compared to Sanger‐based methods and has been successfully employed to delimit species in challenging groups (e.g., Duan et al., 2023; Johri et al., 2020; Maddison & Sproul, 2020). However, in studies of polychaetous annelids, the standard for molecular species delimitation and phylogenetic analyses are still based on Sanger methods (e.g., Aguado et al., 2019; Kupriyanova et al., 2023), and most existing mitogenomes are derived from single‐specimen studies (e.g., Li et al., 2016).…”