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Identification of fish eggs and larvae using a novel DNA metabarcoding approach

G. O. Costa,A. Nobile,B. Morales,B. Rossini,D. F. Souza,Érica A. Serrano Freitas,Claudio Oliveira

Published 2025 in Neotropical Ichthyology

ABSTRACT

Abstract The alarming increase in the number of threatened species underscores the urgent need for more effective conservation strategies. In this context, advancements in molecular techniques and high-throughput sequencing have been instrumental in providing faster and more precise approaches for biodiversity assessment compared to traditional methodologies. DNA metabarcoding facilitates the simultaneous identification of multiple species from pooled genomic DNA samples using universal primers. To address the limitation of short-read sequences, we developed a novel primer set that, in combination with existing primers, enables the assembly of long COI gene sequences through read overlap. This study compares the efficacy of DNA barcoding and metabarcoding in ichthyoplankton samples, focusing on their capacity for species recovery. Using similar samples, DNA barcoding identified 40 taxa, whereas DNA metabarcoding identified 47 taxa. These findings highlight the potential of DNA metabarcoding as a robust approach for ichthyoplankton community analysis, offering extensive species-level data at reduced costs and establishing it as a valuable tool for biodiversity conservation and management initiatives.

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