Phylogenomic Analyses Based on the Plastid Genome and Concatenated NrDNA Sequence Data Reveal Cytonuclear Discordance in Genus (Asteraceae: Carduoideae)

species are widely distributed across East Asia and are cultivated as medicinal herbs in China, Japan, and Korea. Their unclear morphological characteristics and low levels of genetic divergence obscure the taxonomic relationships among these species. In this study, 24 plant samples were collected representing five species of located in China; of these, 23 belonged to members of the complex. High-throughput sequencing was used to obtain the concatenated nrDNA sequences (18S-ITS1-5.8S-ITS2-28S) and plastid genomes. The concatenated nrDNA sequence lengths for all the species were 5,849 bp, and the GC content was 55%. The lengths of the whole plastid genome sequences ranged from 152,138 bp () to 153,268 bp (), while their insertion/deletion sites were mainly distributed in the intergenic regions. Furthermore, 33, 34, 36, 31, and 32 tandem repeat sequences, as well as 30, 30, 29, 30, and 30 SSR loci, were detected in , , , , and , respectively. In addition to these findings, a considerable number of heteroplasmic variations were detected in the plastid genomes, implying a complicated phylogenetic history for . The results of the phylogenetic analysis involving concatenated nrDNA sequences showed that and formed two separate clades, with and constituting their sister clade, while , , and were found based on plastid datasets to represent a mixed clade on the phylogenetic tree. Phylogenetic network analysis suggested that may have hybridized with the common ancestor of and , while ABBA-BABA tests of SNPs in the plastid genomes showed that was more closely related to than to . This study reveals the extensive discordance and complexity of the relationships across the members of the complex (, , and ) according to cytonuclear genomic data; this may be caused by interspecific hybridization or gene introgression.