DNA Microarrays for Identifying Fishes

Abstract

In many cases marine organisms and especially their diverse developmental stages are difficult to identify by morphological characters. DNA-based identification methods offer an analytically powerful addition or even an alternative. In this study, a DNA microarray has been developed to be able to investigate its potential as a tool for the identification of fish species from European seas based on mitochondrial 16S rDNA sequences. Eleven commercially important fish species were selected for a first prototype. Oligonucleotide probes were designed based on the 16S rDNA sequences obtained from 230 individuals of 27 fish species. In addition, more than 1200 sequences of 380 species served as sequence background against which the specificity of the probes was tested in silico. Single target hybridisations with Cy5-labelled, PCR-amplified 16S rDNA fragments from each of the 11 species on microarrays containing the complete set of probes confirmed their suitability. True-positive, fluorescence signals obtained were at least one order of magnitude stronger than false-positive cross-hybridisations. Single nontarget hybridisations resulted in cross-hybridisation signals at approximately 27% of the cases tested, but all of them were at least one order of magnitude lower than true-positive signals. This study demonstrates that the 16S rDNA gene is suitable for designing oligonucleotide probes, which can be used to differentiate 11 fish species. These data are a solid basis for the second step to create a "Fish Chip" for approximately 50 fish species relevant in marine environmental and fisheries research, as well as control of fisheries products.

Wildlife DNA forensics—bridging the gap between conservation genetics and law enforcement

“…The development of multiplex assays that can simultaneously detect any species from a target set is increasing the utility of these approaches (Tobe & Linacre 2008). The recent transfer of array-based genotyping methods from human to non-human research has led to the development of SNP assays for the simultaneous detection of large numbers of target species (Kochzius et al 2008) and it is anticipated that this technology will soon become available to the wildlife forensic community.…”

“…The development of multiplex assays that can simultaneously detect any species from a target set is increasing the utility of these approaches (Tobe & Linacre 2008). The recent transfer of array-based genotyping methods from human to non-human research has led to the development of SNP assays for the simultaneous detection of large numbers of target species (Kochzius et al 2008) and it is anticipated that this technology will soon become available to the wildlife forensic community.The power to identify species offered by DNA sequencing and the ability to analyze mixed DNA through SNP approaches can be combined. By using species-specific PCR-primers it is possible to generate a single DNA sequence for the target species from a sample containing multiple species DNA.…”

Assessing DNA Barcodes for Identification of Pufferfish Species (Tetraodontidae) in Turkish Marine Waters

“…The DNA barcoding approach is concentrated on a single part of the mitochondrial genome, because it presents portions conserved across taxa that are appropriate for primer design, while including polymorphism between and within species (Hebert et al, 2003;Kress & Erickson, 2008). The cytochrome oxidase subunit I (COI) region of the mitochondrial genome is sufficiently diverse so as to let the specific identification of a great majority of fish species (Kochzius et al, 2008;Kochzius et al, 2010).…”

Non-Native Species and Biodiversity Assessment

“…Advances in sampling technology permit to survey previously unexplored areas and improve assessment of biodiversity, a fundamental step in defining the state of exploited specie and the environmental changes [6]. Several different approaches may be applied to discriminate among species, including analysis of geographic variations in morphometric and meristic characters [7], electrophoresis and isoelectric focusing [8], immunological methods [9] and, more recently, proteomic analysis [10] and DNA microarrays [11]. Generally, these techniques, especially isoelectric focusing, have been widely used and proved to be reliable and discriminative.…”