Integrative chloroplast genomics unravels phylogenetic discordance in Glehnia (Apiaceae)

The Glehnia F. Schmidt ex Miq. is a monotypic genus exhibiting a trans-Pacific disjunction pattern across East Asia and western North America. It comprises G. littoralis F. Schmidt ex Miq., located in East Asia, and its western North American subspecies, G. littoralis ssp. leiocarpa Hultén. Glehnia is a traditional medicinal herb and a promising crop, with notable medicinal value and significant agronomic potential. However, the phylogenetic relationships within Glehnia remain unresolved. In this study, chloroplast genomes of 24 Glehnia individuals from diverse geographical locations were reconstructed using Illumina sequencing coupled with reference-guided de novo assembly. All samples displayed the typical quadripartite structure characteristic of chloroplast genomes. Genome annotation resolved 114 non-redundant functional modules, comprising four ribosomal RNA genes, 30 transfer RNA genes, and 80 protein-coding genes. The chloroplast genomes of Glehnia exhibited high similarity with respect to genomic architecture, gene content and arrangement, and codon usage bias. However, variations were observed in genome size, single-copy and inverted repeat boundaries, repeat sequence loci, and nucleotide variation. Chloroplast genome-based phylogenetic analysis revealed that Glehnia is not monophyletic. The genus can be classified into three lineages: the East Asian group, the North American cluster comprising individuals from Humboldt and Lincoln, and the second North American cluster encompassing Clatsop and Mendocino individuals. Collectively, the integration of chloroplast genome with phylogenetic analysis offers key evolutionary insights into the phylogenetic framework of Glehnia, as well as Angelica and Selineae.