Data from: A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents

Introduction: The PCR-based analysis of homologous genes has become one of
the most powerful approaches for species detection and identification,
particularly with the recent availability of Next Generation Sequencing
platforms (NGS) making it possible to identify species composition from a
broad range of environmental samples. Identifying species from these
samples relies on the ability to match sequences with reference barcodes
for taxonomic identification. Unfortunately, most studies of environmental
samples have targeted ribosomal markers, despite the fact that the
mitochondrial Cytochrome c Oxidase subunit I gene (COI) is by far the most
widely available sequence region in public reference libraries. This is
largely because the available versatile (“universal”) COI primers target
the 658 barcoding region, whose size is considered too large for many NGS
applications. Moreover, traditional barcoding primers are known to be
poorly conserved across some taxonomic groups. Results: We first design a
new PCR primer within the highly variable mitochondrial COI region, the
“mlCOIintF” primer. We then show that this newly designed forward primer
combined with the “jgHCO2198” reverse primer to target a 313 bp fragment
performs well across metazoan diversity, with higher success rates than
versatile primer sets traditionally used for DNA barcoding (i.e.
LCO1490/HCO2198). Finally, we demonstrate how the shorter COI fragment
coupled with an efficient bioinformatics pipeline can be used to
characterize species diversity from environmental samples by
pyrosequencing. We examine the gut contents of three species of
planktivorous and benthivorous coral reef fish (family: Apogonidae and
Holocentridae). After the removal of dubious COI sequences, we obtained a
total of 334 prey Operational Taxonomic Units (OTUs) belonging to 14 phyla
from 16 fish guts. Of these, 52.5% matched a reference barcode
(>98% sequence similarity) and an additional 32% could be assigned
to a higher taxonomic level using Bayesian assignment. Conclusions: The
molecular analysis of gut contents targeting the 313 COI fragment using
the newly designed mlCOIintF primer in combination with the jgHCO2198
primer offers enormous promise for metazoan metabarcoding studies. We
believe that this primer set will be a valuable asset for a range of
applications from large-scale biodiversity assessments to food web
studies.