1. Identifying Fishes through DNA Barcodes and Microarrays
- Author
-
Manfred Nölte, Gudmundur O. Hreggvidsson, Monica Landi, Eva Garcia Vazquez, Dietmar Blohm, Marc Kochzius, Christian Seidel, Sigridur Hjorleifsdottir, Fausto Tinti, Antonios Magoulas, Janet Hauschild, Caroline Hervet, Moleyur M.N. Venugopal, Serge Planes, Aglaia Antoniou, Hannes Weber, Cemal Turan, Daniel Campo, Alessia Cariani, Kristina Kappel, Viggo Marteinsson, Sandeep Kumar Botla, Kochzius M., Seidel C., Antoniou A., Kumar Botla S., Campo D., Cariani A., Garcia Vazquez E., Hauschild J., Hervet C., Hjörleifsdottir S., Hreggvidsson G., Kappel K., Landi M., Magoulas A., Marteinsson V., Nölte M., Planes S., Tinti F., Turan C., Venugopa M.N., Weber H., Blohm D., Ecology and Systematics, and Universidade do Minho
- Subjects
0106 biological sciences ,Fish Proteins ,Mitochondrial DNA ,Marine and Aquatic Sciences/Genetics, Genomics, and Barcoding ,Molecular Sequence Data ,Psychologie appliquée ,lcsh:Medicine ,Biology ,010603 evolutionary biology ,01 natural sciences ,DNA barcoding ,DNA, Ribosomal ,Electron Transport Complex IV ,03 medical and health sciences ,media_common.cataloged_instance ,Animals ,DNA Barcoding, Taxonomic ,14. Life underwater ,European union ,lcsh:Science ,Phylogeny ,030304 developmental biology ,media_common ,Oligonucleotide Array Sequence Analysis ,Genetics ,0303 health sciences ,Multidisciplinary ,Cytochrome b ,Hybridization probe ,lcsh:R ,Fishes ,DNA ,Sciences bio-médicales et agricoles ,Consumer protection ,Cytochromes b ,Marine and Aquatic Sciences/Fisheries ,Marine and Aquatic Sciences/Conservation Science ,lcsh:Q ,DNA microarray ,Biologie ,Research Article - Abstract
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. Methodology/Principal Findings: 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 hybridization experiments (, SCOPUS: ar.j, info:eu-repo/semantics/published
- Published
- 2010