TY - JOUR
T1 - An overview of DNA barcoding of biodiversity in South Africa
AU - Kgatla, Mahlatse M.
AU - Barker, Cassandra
AU - Baxter, Janine R.
AU - Bester-Van der Merwe, Aletta E.
AU - Chaisi, Mamohale
AU - Chakona, Albert
AU - Cherry, Michael I.
AU - Daniels, Savel R.
AU - Du Preez, Louis H.
AU - Haddad, Charles R.
AU - Hawkes, Peter G.
AU - Ho, Chris
AU - Hoareau, Thierry B.
AU - Jacobs, Adriaana
AU - Jacobs, Karin
AU - Janion-Scheepers, Charlene
AU - van Vuuren, Bettine Jansen
AU - Kabongo, Ronny M.
AU - Khoza, Thembile T.
AU - Khumalo, Nozipho L.
AU - Mahlanza, Tendekai
AU - Makapela, Lindiwe
AU - Makhubo, Buyisile G.
AU - Maneveldt, Gavin W.
AU - Mashego, Kagiso
AU - Matcher, Gwynneth
AU - Matthee, Conrad A.
AU - Mavhunga, Mudzuli
AU - Midgley, John M.
AU - Mlambo, Musa
AU - Monsanto, Daniela M.
AU - Mthombeni, Rungula
AU - Murray, Shane L.
AU - Mynhardt, Samantha
AU - Nang-Mba, Brielle Jennifer
AU - Ndlovu, Mduduzi
AU - Parbhu, Shilpa P.
AU - Phetla, Veronica
AU - Phukuntsi, Metlholo
AU - Pitcher, Tristan R.
AU - Samaai, Toufiek
AU - Simon, Carol A.
AU - Sink, Kerry
AU - Sole, Catherine L.
AU - Theron, Genevieve L.
AU - van Asch, Barbara
AU - van der Bank, Michelle
AU - van Steenderen, Clarke J.M.
AU - Villet, Martin H.
AU - Visagie, Cobus M.
AU - Williams, Kirstin A.
AU - Willows-Munro, Sandi
AU - Sethusa, Mamadi T.
AU - Da Silva, Jessica M.
AU - Mwale, Monica
N1 - Publisher Copyright:
© 2026 Kgatla et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
PY - 2026/4
Y1 - 2026/4
N2 - The global decline in biodiversity, driven by habitat loss, overexploitation, climate change, biological invasions, and illegal trade, poses significant challenges for conservation management. Although many South African ecosystems and species are under threat, effective conservation efforts are hindered by incomplete foundational biodiversity data and assessments, caused by taxonomic gaps and unverified distributions. DNA barcoding has emerged as an invaluable tool for species identification and classification of biodiversity. While substantial barcoding progress has been made, for many taxa, others remain underrepresented in sequence databases. This study evaluates the status and progress of DNA barcoding in South Africa through a gap analysis, comparing verified species checklists with barcoded sequences from the Barcode of Life Database (BOLD) and GenBank to assess taxonomic and geographic representation. A literature review (2003–2023) highlights applications across terrestrial, freshwater, and marine habitats. Of the 931,476 South African species barcode records, 52% were publicly available. Although the insects dominated with the highest number of records and BINs, reptiles had the highest taxonomic representation. Plants and fungi were underrepresented (16.1% and 2.8%, respectively). Regionally, Mpumalanga and Limpopo provinces showed the highest BIN counts, while North-West and Free State provinces had the lowest. The majority of barcode records were for mtDNA genes such as cytochrome c oxidase subunit I (COI) and were contributed by both local and international institutions. Discrepancies between GenBank records and those mined by BOLD indicated that many GenBank sequences for South Africa have poor quality metadata, including geographic sampling locality information. While significant progress has been made across taxa, further efforts are needed to expand species and geographic coverage, enhance sequence quality, improve species metadata, and resolve inconsistencies in BIN assignments, particularly for underrepresented groups such as plants and fungi. These advances would strengthen biodiversity assessments and support conservation efforts in South Africa.
AB - The global decline in biodiversity, driven by habitat loss, overexploitation, climate change, biological invasions, and illegal trade, poses significant challenges for conservation management. Although many South African ecosystems and species are under threat, effective conservation efforts are hindered by incomplete foundational biodiversity data and assessments, caused by taxonomic gaps and unverified distributions. DNA barcoding has emerged as an invaluable tool for species identification and classification of biodiversity. While substantial barcoding progress has been made, for many taxa, others remain underrepresented in sequence databases. This study evaluates the status and progress of DNA barcoding in South Africa through a gap analysis, comparing verified species checklists with barcoded sequences from the Barcode of Life Database (BOLD) and GenBank to assess taxonomic and geographic representation. A literature review (2003–2023) highlights applications across terrestrial, freshwater, and marine habitats. Of the 931,476 South African species barcode records, 52% were publicly available. Although the insects dominated with the highest number of records and BINs, reptiles had the highest taxonomic representation. Plants and fungi were underrepresented (16.1% and 2.8%, respectively). Regionally, Mpumalanga and Limpopo provinces showed the highest BIN counts, while North-West and Free State provinces had the lowest. The majority of barcode records were for mtDNA genes such as cytochrome c oxidase subunit I (COI) and were contributed by both local and international institutions. Discrepancies between GenBank records and those mined by BOLD indicated that many GenBank sequences for South Africa have poor quality metadata, including geographic sampling locality information. While significant progress has been made across taxa, further efforts are needed to expand species and geographic coverage, enhance sequence quality, improve species metadata, and resolve inconsistencies in BIN assignments, particularly for underrepresented groups such as plants and fungi. These advances would strengthen biodiversity assessments and support conservation efforts in South Africa.
UR - https://www.scopus.com/pages/publications/105036456829
U2 - 10.1371/journal.pone.0345173
DO - 10.1371/journal.pone.0345173
M3 - Article
C2 - 42013141
AN - SCOPUS:105036456829
SN - 1932-6203
VL - 21
JO - PLoS ONE
JF - PLoS ONE
IS - 4 April
M1 - e0345173
ER -