10.5061/DRYAD.8P425
Gleason, Lani U
University of California, San Diego
Burton, Ronald S
University of California, San Diego
Data from: High-throughput molecular identification of fish eggs using
multiplex suspension bead arrays
Dryad
dataset
2011
suspension bead arrays
fish egg identification
2011-06-20T18:52:14Z
2011-06-20T18:52:14Z
en
https://doi.org/10.1111/j.1755-0998.2011.03059.x
414430 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
The location and abundance of fish eggs provide information concerning the
timing and location of spawning activities and can provide
fishery-independent estimates of spawning biomass. However, the full value
of egg and larval surveys is severely restricted because many species’
eggs and larvae are morphologically similar, making species-level
identification difficult. Recent efforts have shown that nearly all
species of fish may be identified by mitochondrial DNA (mtDNA) sequences
(e.g., via “DNA barcoding”). By taking advantage of a DNA barcode
database, we have developed oligonucleotide probes for 23 marine fish
species that produce pelagic eggs commonly found in California waters.
Probes were coupled to fluorescent microspheres to create a suspension
bead array. Biotin-labeled primers were used to amplify the mitochondrial
cytochrome oxidase subunit I (COI) and 16S ribosomal rRNA genes from
individual fish eggs. The amplicons were then hybridized to the bead array
and after addition of a reporter fluorophore, samples were analyzed by
flow cytometry with Luminex 100 instrumentation. Probes specifically
targeted eggs that are abundant and/or from morphologically
indistinguishable species pairs. Results showed the 33 different probes
designed for this study accurately identified all samples when PCR was
successful. Suspension bead arrays have a number of benefits over other
methods of molecular identification; these arrays permit high
multiplexing, simple addition of new probes, high throughput, and lower
cost than DNA sequencing. The increasing availability of DNA barcode data
for numerous fish faunas worldwide suggests bead arrays could be developed
and widely used for fish egg, larval and tissue identifications.
Failed probe sequences for DryadThese are the oligonucleotide probe
sequences (designed using Primer BLAST available through the NCBI website)
for the 33 fish species included in this study. Using nucleotide BLAST in
NCBI, these probe sequences were found to match non-target species in the
GenBank database and were thus discarded and not utilized further in the
study.
Southern California