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Metabarcoding using multiplexed markers increases species detection in complex zooplankton communities.

Guang K Zhang1, Frédéric J J Chain1,2, Cathryn L Abbott3

  • 1Department of Biology McGill University Montreal Quebec Canada.

Evolutionary Applications
|November 22, 2018
PubMed
Summary
This summary is machine-generated.

This study introduces a versatile metabarcoding protocol using two DNA barcode markers (COI and 18S) and multiple primer pairs. This enhanced approach significantly improves species detection rates for biomonitoring zooplankton communities.

Keywords:
18Scytochrome c oxidase subunit Imetabarcodingmultigenemultiple primer pairszooplankton

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Area of Science:

  • Environmental DNA (eDNA) analysis
  • Molecular ecology
  • Biodiversity assessment

Background:

  • Metabarcoding relies on DNA barcoding and high-throughput sequencing for analyzing diverse samples.
  • Species identification accuracy is constrained by marker choice and primer pairs, creating a trade-off between amplification success and taxonomic resolution.

Purpose of the Study:

  • To develop and validate a versatile metabarcoding protocol for biomonitoring using two markers (COI and 18S) and multiple primer pairs.
  • To assess the impact of combining markers and primers on species detection rates in mock zooplankton communities.

Main Methods:

  • A metabarcoding protocol was developed using two barcode markers (COI and 18S) with four primer pairs in a single high-throughput sequencing run via sample multiplexing.
  • The protocol was validated on 24 mock zooplanktonic communities with varying genetic diversity.

Main Results:

  • Using a single marker/primer pair yielded a maximum species recovery of 77%.
  • Combining both COI and 18S markers improved species detection from 89%-93%, a 14%-35% increase over single marker approaches.
  • Multiplexing did not negatively affect read assignment proportions or the total number of species detected.

Conclusions:

  • Combining evolutionarily independent markers, such as COI and 18S, with multiple primer pairs per marker significantly enhances species detection in metabarcoding studies.
  • This optimized metabarcoding approach offers a cost-effective and robust method for biomonitoring zooplankton communities, reducing false negatives.