Identifying Fishes through DNA Barcodes and Microarrays.
BACKGROUND
International fish trade reached an import value of 62.8 billion Euro in 2006, of which 44.6% are covered by the European Union. Species identification is a key problem throughout the life cycle of fishes: from eggs and larvae to adults in fisheries research and control, as well as processed fish products in consumer protection.


RESULTS
This study aims to evaluate the applicability of the three mitochondrial genes 16S rRNA (16S), cytochrome b (cyt b), and cytochrome oxidase subunit I (COI) for the identification of 50 European marine fish species by combining techniques of "DNA barcoding" and microarrays. In a DNA barcoding approach, neighbour Joining (NJ) phylogenetic trees of 369 16S, 212 cyt b, and 447 COI sequences indicated that cyt b and COI are suitable for unambiguous identification, whereas 16S failed to discriminate closely related flatfish and gurnard species. In course of probe design for DNA microarray development, each of the markers yielded a high number of potentially species-specific probes in silico, although many of them were rejected based on microarray hybridisation experiments. None of the markers provided probes to discriminate the sibling flatfish and gurnard species. However, since 16S-probes were less negatively influenced by the "position of label" effect and showed the lowest rejection rate and the highest mean signal intensity, 16S is more suitable for DNA microarray probe design than cty b and COI. The large portion of rejected COI-probes after hybridisation experiments (>90%) renders the DNA barcoding marker as rather unsuitable for this high-throughput technology.


CONCLUSIONS
Based on these data, a DNA microarray containing 64 functional oligonucleotide probes for the identification of 30 out of the 50 fish species investigated was developed. It represents the next step towards an automated and easy-to-handle method to identify fish, ichthyoplankton, and fish products.
Kochzius
Marc
M
Centre for Applied Gene Sensor Technology, FB2-UFT, University of Bremen, Bremen, Germany. marc.kochzius@vub.ac.be
Seidel
Christian
C
Antoniou
Aglaia
A
Botla
Sandeep Kumar
SK
Campo
Daniel
D
Cariani
Alessia
A
Vazquez
Eva Garcia
EG
Hauschild
Janet
J
Hervet
Caroline
C
Hjörleifsdottir
Sigridur
S
Hreggvidsson
Gudmundur
G
Kappel
Kristina
K
Landi
Monica
M
Magoulas
Antonios
A
Marteinsson
Viggo
V
Nölte
Manfred
M
Planes
Serge
S
Tinti
Fausto
F
Turan
Cemal
C
Venugopal
Moleyur N
MN
Weber
Hannes
H
Blohm
Dietmar
D
D000818:Animals; D045303:Cytochromes b / Q000235:genetics; D004247:DNA / Q000235:genetics; D058893:DNA Barcoding, Taxonomic; D004275:DNA, Ribosomal / Q000235:genetics; D003576:Electron Transport Complex IV / Q000235:genetics; D029941:Fish Proteins / Q000235:genetics; D005399:Fishes / Q000145:classification* / Q000235:genetics*; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D010802:Phylogeny
D004275:DNA, Ribosomal; D029941:Fish Proteins; D004247:DNA; D045303:Cytochromes b; D003576:Electron Transport Complex IV