PUBLICATION
Metabarcoding by capture using a single COI probe (MCSP) to identify and quantify fish species in ichthyoplankton swarms
- Authors
- Mariac, C., Vigouroux, Y., Duponchelle, F., García-Dávila, C., Nunez, J., Desmarais, E., Renno, J.F.
- ID
- ZDB-PUB-180913-29
- Date
- 2018
- Source
- PLoS One 13: e0202976 (Journal)
- Registered Authors
- Keywords
- none
- MeSH Terms
-
- High-Throughput Nucleotide Sequencing
- Animals
- Larva/genetics*
- Databases, Genetic
- Biodiversity
- DNA Barcoding, Taxonomic/methods*
- Fishes/classification*
- Fishes/genetics
- PubMed
- 30208069 Full text @ PLoS One
Citation
Mariac, C., Vigouroux, Y., Duponchelle, F., García-Dávila, C., Nunez, J., Desmarais, E., Renno, J.F. (2018) Metabarcoding by capture using a single COI probe (MCSP) to identify and quantify fish species in ichthyoplankton swarms. PLoS One. 13:e0202976.
Abstract
The ability to determine the composition and relative frequencies of fish species in large ichthyoplankton swarms could have extremely important ecological applications However, this task is currently hampered by methodological limitations. We proposed a new method for Amazonian species based on hybridization capture of the COI gene DNA from a distant species (Danio rerio), absent from our study area (the Amazon basin). The COI sequence of this species is approximately equidistant from all COI of Amazonian species available. By using this sequence as probe we successfully facilitated the simultaneous identification of fish larvae belonging to the order Siluriformes and to the Characiformes represented in our ichthyoplankton samples. Species relative frequencies, estimated by the number of reads, showed almost perfect correlations with true frequencies estimated by a Sanger approach, allowing the development of a quantitative approach. We also proposed a further improvement to a previous protocol, which enables lowering the sequencing effort by 40 times. This new Metabarcoding by Capture using a Single Probe (MCSP) methodology could have important implications for ecology, fisheries management and conservation in fish biodiversity hotspots worldwide. Our approach could easily be extended to other plant and animal taxa.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping