Gap analysis for DNA-based biomonitoring of aquatic ecosystems in China

Abstract

DNA-based taxon identification is improving the assessment and management of biodiversity in rivers. However, the lack of comprehensive DNA barcode reference libraries and globally highly unequal coverage are still hindering the application prospects of this method worldwide. Here, we analyzed the COI barcode gap in two reference libraries, Barcode of Life Data Systems (BOLD) and NCBI GenBank, with a focus on three aquatic animal groups (freshwater fish, aquatic insects and molluscs) in Chinese rivers. Our data show gaps in barcode coverage (e.g., organisms without barcodes) of ca. 40–70% of taxa in these groups in the BOLD or NCBI GenBank database, respectively. These gaps can rise even further if the barcode thresholds are set to contain at least five reference sequences per taxon. Furthermore, most barcodes are from non-local samples, and only 14.4% (BOLD) and 28.8% (NCBI GenBank) of reference sequences were from organisms sampled in China, respectively. The pairwise genetic distance of local barcodes is 3 to 5 times lower than non-local barcodes, indicating that the latter may not be a good substitute. When looking at individual catchments, ca. 60% of the potentially occurring aquatic species have one or more barcodes, yet the barcode coverage varies slightly across ten major river catchments, ranging from 54.3% (Liao River basin) to 68.2% (Huai River basin). The taxa Salmoniformes and Perciformes in freshwater fish, Odonata and Diptera in aquatic insects, and Bivalvia in molluscs have the best barcode coverage in most catchments (mean coverage >70%). This study gives the first overview and current status of barcode reference libraries of three major aquatic animal groups in Chinese rivers. Our results will help to better interpret current metabarcoding studies from China, and also provide a basis to develop a strategy of filling the gaps in the reference libraries of aquatic species in China.