Comparative plastome analysis of the Vandenboschia radicans complex in Korea: insights into its evolutionary history

Vandenboschia radicans and its close relatives are difficult to distinguish based on morphological characteristics because of reticulate evolution within the complex. Therefore, cytological and molecular approaches have been proposed for accurate identification of taxa within this complex. However, conventional plastid markers lack sufficient discriminatory power at the species level. In Korea, the V. radicans complex comprises nine genotypes associated with varying ploidy levels and hybrid origins. The maternal genotypes are classified into three groups: α, β, and γ. In this study, nine complete plastomes from the V. radicans complex were sequenced to investigate the evolution of different genotypes and find candidate plastome marker regions to facilitate the accurate identification of maternal lineage.

The nine plastome sequences ranged from 146,846 to 147,247 bp, with identical gene content. The junctions between single copy and inverted repeat regions of Vandenboschia plastomes were categorized into three types. The phylogenetic tree inferred from 84 concatenated genes robustly supported the monophyly of each genotype within the V. radicans complex with high bootstrap values. However, the α genotype clade and its internal nodes showed only moderate gene concordance factors calculated from 84 individual gene trees. To identify candidate plastid markers for distinguishing maternal lineages, 1,719 phylogenetic trees were generated using sliding window analysis. Of these, 1,363 trees supported the monophyly of all genera within Hymenophyllaceae and all maternal genotypes within the V. radicans complex. Across the entire plastome, phylogenetic trees inferred from ycf2, rpoC2, ycf1, and rpoB showed almost identical topologies to the concatenated plastome tree based on the 84 concatenated genes. Among the 420 branch-model analyses (84 genes × 5 foreground branches), 20 yielded p-values below the significance threshold, and the estimated ω values for the foreground branches were less than 1, indicating purifying selection, rather than positive selection.

Short branch lengths in the phylogeny, purifying selection of plastome genes, minimal sequence length variations, and negligible genome rearrangements among plastomes of the V. radicans complex collectively indicate low genetic variation within the complex. Independent gametophyte stage, which allows populations to persist through clonal propagation, together with recent speciation was likely a major factor contributing to the low level of genetic variation within V. radicans complex.