Identifying Fishes through DNA Barcodes and Microarrays

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dc.authoridAntoniou, Aglaia (Cilia)/0000-0003-1119-9820
dc.authoridLandi, Monica/0000-0003-2180-5062
dc.authoridTINTI, FAUSTO/0000-0002-8649-5387
dc.authoridNolte, Manfred/0000-0002-8029-4162
dc.authoridKochzius, Marc/0000-0001-8953-4719
dc.authoridBotla, Sandeep/0000-0001-9937-0455
dc.authoridHreggvidsson, Gudmundur Oli/0000-0002-4958-1673
dc.contributor.authorKochzius, Marc
dc.contributor.authorSeidel, Christian
dc.contributor.authorAntoniou, Aglaia
dc.contributor.authorBotla, Sandeep Kumar
dc.contributor.authorCampo, Daniel
dc.contributor.authorCariani, Alessia
dc.contributor.authorGarcia Vazquez, Eva
dc.date.accessioned2024-09-18T21:06:33Z
dc.date.available2024-09-18T21:06:33Z
dc.date.issued2010
dc.departmentHatay Mustafa Kemal Üniversitesien_US
dc.description.abstractBackground: 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 hybridisation experiments (>90%) renders the DNA barcoding marker as rather unsuitable for this high-throughput technology. Conclusions/Significance: 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.en_US
dc.description.sponsorshipEuropean Commission [505491]en_US
dc.description.sponsorshipThe research project Fish & Chips (Towards DNA chip technology as a standard analytical tool for the identification of marine organisms in biodiversity and ecosystem research)'' (www.fish-and-chips.uni-bremen.de) was funded by the European Commission in the Framework of the 6th Framework Programme (http://ec.europa.eu/research/fp6/index_en.cfm) under the contract no. 505491. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.en_US
dc.identifier.doi10.1371/journal.pone.0012620
dc.identifier.issn1932-6203
dc.identifier.issue9en_US
dc.identifier.pmid20838643en_US
dc.identifier.scopus2-s2.0-77958588566en_US
dc.identifier.scopusqualityQ1en_US
dc.identifier.urihttps://doi.org/10.1371/journal.pone.0012620
dc.identifier.urihttps://hdl.handle.net/20.500.12483/13692
dc.identifier.volume5en_US
dc.identifier.wosWOS:000281631300040en_US
dc.identifier.wosqualityQ1en_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakScopusen_US
dc.indekslendigikaynakPubMeden_US
dc.language.isoenen_US
dc.publisherPublic Library Scienceen_US
dc.relation.ispartofPlos Oneen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectSpecies Identificationen_US
dc.subjectMolecular-Identificationen_US
dc.subjectGenetic Identificationen_US
dc.subjectCytochrome-Ben_US
dc.subjectHybridizationen_US
dc.subjectPositionen_US
dc.subjectRevealsen_US
dc.subjectPcren_US
dc.subjectDifferentiationen_US
dc.subjectDiscriminationen_US
dc.titleIdentifying Fishes through DNA Barcodes and Microarraysen_US
dc.typeArticleen_US

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