Abstract
The selection of specific bioinformatic pipelines to analyse Next Generation Sequencing (NGS) data is instrumental for generating accurate biological inferences; users should understand the limitations of the pipelines and incorporate existing biodiversity information to evaluate results. Pipelines that maximize the coverage and precision of taxonomic inventories and are in line with local biodiversity characteristics should be preferred. Environmental DNA (eDNA) metabarcoding based on NGS technology is projected to be widely employed for biomonitoring applications and to supplement established ways of monitoring marine biodiversity. In Indonesia, research has concentrated on assessing taxonomic composition in various geographical and environmental situations and on identifying taxa that are susceptible to environmental changes. This study aims to compare four NGS data analysis pipelines (Anacapa, QIIME2 with DADA2, QIIME2 with Deblur and Galaxy) using a 28-sample subset of published eDNA seawater samples collected from seawater across Indonesia. The outputs of the bioinformatics analyses between the pipelines differed. Anacapa, QIIME2 with DADA2, and Galaxy pipelines provide more comprehensive taxonomic coverage relevant to existing biodiversity records from the regions compared to QIIME2 with Deblur. Anacapa in particular could successfully detect taxa that have not been detected with other pipelines tested. These findings should be taken into account when doing eDNA metabarcoding analyses, especially when assessing marine biodiversity in terms of species diversity and abundance.
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Acknowledgements
This project was partly funded by IPB University (project number 15734/IT3/TU.00.01/M/B/2021) through the Post-Doctoral grant awarded to HM with the research title “Resolution and Composition of Taxa in Indonesian Marine Biodiversity: Application of Bioinformatics pipeline variety to Environmental DNA (eDNA) data”, and supported under World Class Research scheme No: 2346 /IT3.L1/PN/2021 awarded to HM for the research project entitled “Redefining hotspots of marine fishes across Indonesian coral reefs with different anthropogenic pressure using environmental DNA metabarcoding for sustainable fisheries”. We would like to thank the reviewers for taking the time and effort necessary to review the manuscript. We sincerely appreciate all valuable comments and suggestions, which helped us to improve the quality of the manuscript.
Funding
Post-Doctoral grant, 15734/IT3/TU.00.01/M/B/2021, Hawis Madduppa, World Class Research Schame, 2346 /IT3.L1/PN/2021, Hawis Madduppa.
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NKDC, AWA and HM conceived and designed the research. BS, LMI and HM contributed to sample collection and laboratory work. NKDC, AWA and MDAM analysed the data. All authors wrote the manuscript, read and approved the manuscript. HM sadly passed away before the submission of this paper; he had approved an initial draft but not the revised versions.
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Cahyani, N.K.D., Anggoro, A.W., Al Malik, M.D. et al. Inventorizing marine biodiversity using eDNA data from Indonesian coral reefs: comparative high throughput analysis using different bioinformatic pipelines. Mar. Biodivers. 54, 39 (2024). https://doi.org/10.1007/s12526-024-01432-w
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DOI: https://doi.org/10.1007/s12526-024-01432-w