Authors: Marta Muñoz-Colmenero*, Ana Sánchez, Begoña Correa, Francisco G. Figueiras, Jose L. Garrido and Carmen G. Sotelo
- Instituto de Investigaciones Marinas (CSIC), Vigo, Spain
Publication: Frontiers in Marine Science
Date: January 2021
Full paper: Evaluation of DNA Extraction Methods and Bioinformatic Pipelines for Marine Nano- and Pico-Eukaryotic Plankton Analysis
The smallest size fractions of plankton, nano- and pico-plankton, have been highlighted due to they accomplish key functions in marine ecosystems. However, the knowledge about some of them is scarce because they are difficult or impossible to be detected and identified with non-DNA-based methodologies. Here we have evaluated five DNA extraction protocols (MT1-MT5) and seven bioinformatic pipelines (P1-P7) to find the best protocol for detecting most of the eukaryotic species of nano- and pico-plankton present in an environmental sample using Ion Torrent technology. The protocol MT3 was the most reproducible methodology, showing less variation among samples, good DNA quality and sufficient quantity to amplify and sequence the eukaryote species, offering the best results after sequencing. For bioinformatic analyses, P1 and P7 resulted in the highest percentage of detection for the difficult-to-detect species in mock communities.