Beyond a single locus: Evolutionary constraints and genomic alternatives to plant DNA barcoding

Beyond a single locus: Evolutionary constraints and genomic alternatives to plant DNA barcoding

DNA barcoding has transformed species identification by using short, standardized genetic sequences for taxonomic assignment. While the mitochondrial COI gene is a universal barcode in animals, an equivalent marker for plants has not been established. The chloroplast genes rbcL and matK are international standards, but their limited discriminatory power has led to ongoing exploration of alternative loci and multilocus strategies. This review discusses the historical contexts, technical challenges, and biological factors, such as slow mitochondrial evolution, polyploidy, and hybridization, that have prevented the adoption of a single universal plant barcode. We examine emerging approaches that combine high-throughput sequencing, machine learning, and comprehensive reference databases, moving from a single-marker approach to a genomic toolkit. The lack of a universal barcode reflects the evolutionary complexity of plants, highlighting the need for integrative, scalable, and application-oriented frameworks in future plant barcoding research. We advocate for a practical genomic toolkit tailored to the unique challenges of plant evolution.