Metabarcoding by capture using a single COI probe (MCSP) to identify and quantify fish species in ichthyoplankton swarms.

C Mariac,C García-Dávila,Y Vigouroux,J.F Renno,J Nunez,F Duponchelle,E Desmarais,Mehrdad Hajibabaei

doi:10.1371/journal.pone.0202976

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.

Highlights

Nearly 35,000 fish species have been described, and this number is regularly increasing with ~400 new descriptions annually [1]
In fish biodiversity hotspots, such as coral reefs and the Amazon basin, the large majority of fish species have larvae that intermix in multi-specific ichthyoplankton swarms
The single probe we designed presents a mean divergence of 24.6% and a Coefficient of Variation of 10.9%, (Fig 1A and S1 Table) to the 444 Amazonian fish species in our COI database

Summary

Introduction

Nearly 35,000 fish species have been described, and this number is regularly increasing with ~400 new descriptions annually [1]. In fish biodiversity hotspots, such as coral reefs and the Amazon basin, the large majority of fish species have larvae that intermix in multi-specific ichthyoplankton swarms. Being able to determine the precise composition and relative. Metabarcoding by capture with a single probe to quantify species

Methods

Results

Discussion

Conclusion