Comparative chloroplast genome and species discrimination analyses in Aralia section Aralia (Araliaceae)

Abstract

Aralia section Aralia is a subset of Araliaceae; it constitutes a small lineage that has been utilized in East Asian traditional medicines for centuries. Identifying species within this section can be challenging due to the complex interspecific morphological variations and the prevalence of hybridization. Accurate species identification is crucial for the application of these medicinal plants. In this study, we evaluated the effectiveness of 11 distinct barcode systems for distinguishing species of Aralia sect. Aralia. Comparative analyses of the chloroplast genomes suggested that the plastome length, gene content and order, as well as the expansion/contraction of the inverted repeat regions, are highly conserved. Species discrimination analysis revealed that complete plastomes and their partitioned data sets possessed considerably high discriminatory power (90.91%), which was equivalent to that of standard barcodes. In contrast, nuclear ribosomal DNA sequences demonstrated a marked improvement (90.91%) over nuclear ribosomal internal transcribed spacer (72.73%) in species discrimination. Evidently, nuclear markers did not perform better than plastid markers. However, a combination of barcode from both nuclear and chloroplast genomes can accurately identify all species for Aralia sect. Aralia. We therefore call for developing multilocus markers from different genomes with different inheritance for species discrimination in plant groups.