Test species discrimination in Codonopsis (Campanulaceae) using genome skimming data

To overcome the limitations of conventional barcoding loci, plastid genome (plastome) and nuclear ribosomal DNA (nrDNA) sequences recovered from genome skimming, proposed as "super-barcodes," have been suggested as candidates for delimitating recently diverged species or complex plant groups. DNA super-barcodes must be further assessed for their effectiveness in other diverse plant groups. This research focused on the genus <i>Codonopsis</i>, a medicinally significant yet taxonomically complex group characterized by morphology similarity and high phenotypic plasticity in response to environmental conditions. We analyzed standard DNA barcodes and super-barcodes across 81 individuals from 36 of the 42 species of <i>Codonopsis</i> from Asia. Our work provides a comprehensive DNA barcode library for <i>Codonopsis</i> species identification. Our findings demonstrated that super-barcodes significantly improved the phylogenetic resolution and the discriminatory power compared to standard DNA barcodes. Since mitochondrial sequence variation is generally low in plant species, few studies have assessed its effectiveness as super-barcodes. We screened the mitochondrial protein-coding sequences (CDS) using genome skimming and evaluated the identification capacity of their combination. Unexpectedly, the discriminatory power of mitochondrial DNA with high nucleotide variation was comparable to that of the concatenated plastid CDS. However, the organelle genome cannot wholly determine the species boundaries of <i>Codonopsis</i>, which might be related to their rapid evolutionary radiation, ILS, hybridization, and strong natural selection. Future multi-locus nuclear markers will likely be developed in plants for additional discriminatory power. Our study provides new knowledge and insights into species discrimination of recently evolved <i>Codonopsis</i> taxa in a biodiversity hotspot.