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- DNA barcoding in diet assessment is the use of DNA barcoding to analyse the diet of organisms. and further detect and describe their trophic interactions. This approach is based on the identification of consumed species by characterization of DNA present in dietary samples, e.g. individual food remains, regurgitates, gut and fecal samples, homogenized body of the host organism, target of the diet study (for example with whole body of insects). The DNA sequencing approach to be adopted depends on the diet breadth of the target consumer. For organisms feeding on one or only few species, traditional Sanger sequencing techniques can be used. For polyphagous species with diet items more difficult to identify, it is conceivable to determine all consumed species using NGS methodology. The barcode markers utilized for amplification will differ depending on the diet of the target organism. For herbivore diets, the standard DNA barcode loci will differ significantly depending on the plant taxonomic level. Therefore, for identifying plant tissue at the taxonomic family or genus level, the markers rbcL and trn-L-intron are used, which differ from the loci ITS2, matK, trnH-psbA (noncoding intergenic spacer) used to identify diet items to genus and species level. For animal prey, the most broadly used DNA barcode markers to identify diets are the mitochondrial cytocrome C oxydase (COI) and cytochrome b (cytb). When the diet is broad and diverse, DNA metabarcoding is used to identify most of the consumed items. (en)
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