Corresponding author: André O. Ferreira (
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DNA metabarcoding is particularly helpful for monitoring taxonomically complex communities and hard to identify morphologically, such as several zoo and ichthyoplankton, which contain eggs and larval stages of unknown species. However, the efficiency of metabarcoding in diversity recovery is dependent on the targeted genetic markers and primers employed. In this work, we compared the performance of three different primer pairs from cytochrome oxidase subunit I (COI) genetic marker in species detection from marine mesozooplankton samples and its potential to be implemented in biomonitoring programs. We employed the mlCOIintF/LoboR1 primer combination targeting marine metazoans, and two newly designed fish-specific primer cocktails for targeting the ichthyoplankton. Mesozooplankton samples were collected at 4 locations on the Portuguese coast – 1 in the northwest (Viana do Castelo) and 3 in the south (coastal lagoons of Ria de Alvor and Ria Formosa, and in the river Guadiana estuary). Bulk community DNA was extracted using a non-destructive protocol and amplicon libraries produced for the 3 primers combinations. After quality-filtering bioinformatic steps, we obtained 3.04 x 105 usable sequences, of which 76.26% were clustered into OTUs (operational taxonomic units) and 46.30% were identified at species level - corresponding to 103 taxa from 8 different metazoan Phyla. The most diverse classes were
André O. Ferreira
International Conference on DNA Barcoding and Biodiversity (ICDBB), May 25-27, Sofia, Bulgaria
This work was supported by National Funds (through the Portuguese Science Foundation, FCT, I.P.) by means of the research project A-Fish-DNA-Scan (CIRCNA/BRB/0156/2019); André O. Ferreira was supported by grant DFA/BD/6653/2020.
This work was supported by National Funds (through the Portuguese Science Foundation, FCT, I.P.) by means of the research project A-Fish-DNA-Scan (CIRCNA/BRB/0156/2019); André O. Ferreira was supported by grant DFA/BD/6653/2020.