Pragmatic Applications and Universality of DNA Barcoding for Substantial Organisms at Species Level: A Review to Explore a Way Forward

Abstract

DNA barcodes are regarded as hereditary succession codes that serve as a recognition marker to address several queries relating to the identification, classification, community ecology, and evolution of certain functional traits in organisms. The mitochondrial cytochrome c oxidase 1 (CO1) gene as a DNA barcode is highly efficient for discriminating vertebrate and invertebrate animal species. Similarly, different specific markers are used for other organisms, including ribulose bisphosphate carboxylase (rbcL), maturase kinase (matK), transfer RNA-H and photosystem II D1-ApbsArabidopsis thaliana (trnH-psbA), and internal transcribed spacer (ITS) for plant species; 16S ribosomal RNA (16S rRNA), elongation factor Tu gene (Tuf gene), and chaperonin for bacterial strains; and nuclear ITS for fungal strains. Nevertheless, the taxon coverage of reference sequences is far from complete for genus or species-level identification. Applying the next-generation sequencing approach to the parallel acquisition of DNA barcode sequences could greatly expand the potential for library preparation or accurate identification in biodiversity research. Overall, this review articulates on the DNA barcoding technology as applied to different organisms, its universality, applicability, and innovative approach to handling DNA-based species identification.

The status of COI and 12S rRNA DNA barcode reference libraries for freshwater fish in South Africa: Implications for future eDNA projects

“…For future eDNA studies in South Africa to be comparable to those conducted in other parts of the globe, this review suggests that a multi-marker approach (using both COI and 12S rRNA) be used. Moreover, using other genes, such as 12S rRNA and 16S rRNA, in addition to COI will allow for more accurate species assignment and the elucidation of phylogenetic relationships at higher taxonomic levels (Duarte et al 2020; Ahmed et al 2022). To this end, it is also essential that the present 12S rRNA reference library for freshwater fish in South Africa be improved, particularly for native species.…”

The continuing evolution of barcode applications: Functional toxicology to cell lineage

“…DNA sequences are then compared using GenBank data sets or barcode of life data set (BOLD). 6,7 While CO1 barcoding has provided species-level specificity for mammals, fish, and birds, retrieving full-length barcodes may be difficult. 8 First, DNA may be degraded from stored samples or processed food.…”

BarKeeper—a versatile web framework to assemble, analyse and manage DNA barcoding data and metadata

“…In a zoological context, researchers commonly employ a part of the mitochondrial Cytochrome Oxidase 1 ( CO1 ) gene as a marker region for this purpose (Hebert, Cywinska, et al, 2003). In many animal taxa, very high identification success rates can be achieved using CO1 , often down to the species level (Ahmed et al, 2022; Hebert, Ratnasingham, et al, 2003; Meyer & Paulay, 2005). In plants, mitochondrial genes evolve slower and barely show substitutions between closely related species.…”

“…down to the species level (Ahmed et al, 2022;Hebert, Ratnasingham, et al, 2003;Meyer & Paulay, 2005). In plants, mitochondrial genes evolve slower and barely show substitutions between closely related species.…”