Strengthening the DNA barcode reference library for marine copepods in South Africa

Abstract

DNA barcode reference libraries that link taxonomically verified species records to standardised barcode sequences form the basis for species identification using molecular methods. We conducted an integrated morphology and molecular study of marine copepods collected from the continental shelf of eastern South Africa, western Indian Ocean, to strengthen the regional reference library for metabarcoding applications. Regional barcode records account for endemic species and geographical variation of barcode sequences. A DNA barcode gap analysis confirmed the CO1 gene region as an effective marker for distinguishing between copepod species. Intact exoskeletons after DNA extraction were retained as voucher specimens. A total of 166 new barcode records representing 24 copepod species were added to BOLD. The new barcode records included 10 species with exact matches to existing records on BOLD, four close matches (1–4% similarity gain) for regionally collected specimens, and six distant matches (4–20% similarity gain) to genetically diverged populations of the same species. Additionally, four mismatches were identified, indicating prior misidentifications or subsequent name changes. The improved reference library increased the number of species identified in metabarcoding outputs by 29% in the ‘before’ (2019) and ‘after’ (2023) treatments that matched the same amplicon sequence variants outputs to the BOLD and NCBI GenBank barcode records.