DNA barcoding in diet assessment

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DNA barcoding in diet assessment is the use of DNA barcoding to analyse the diet of organisms.[1][2] and further detect and describe their trophic interactions.[3][4] This approach is based on the identification of consumed species by characterization of DNA present in dietary samples,[5] 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[6]).

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.[5]

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.[7] 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.[7] For animal prey, the most broadly used DNA barcode markers to identify diets are the mitochondrial cytochrome C oxydase (COI) and cytochrome b (cytb).[8] When the diet is broad and diverse, DNA metabarcoding is used to identify most of the consumed items.[9]

  1. ^ King RA, Read DS, Traugott M, Symondson WO (February 2008). "Molecular analysis of predation: a review of best practice for DNA-based approaches". Molecular Ecology. 17 (4): 947–63. doi:10.1111/j.1365-294X.2007.03613.x. PMID 18208490. S2CID 44796921.
  2. ^ Pompanon F, Deagle BE, Symondson WO, Brown DS, Jarman SN, Taberlet P (April 2012). "Who is eating what: diet assessment using next generation sequencing". Molecular Ecology. 21 (8): 1931–50. doi:10.1111/j.1365-294X.2011.05403.x. PMID 22171763. S2CID 10013333.
  3. ^ Sheppard SK, Harwood JD (October 2005). "Advances in molecular ecology: tracking trophic links through predator-prey food-webs". Functional Ecology. 19 (5): 751–762. doi:10.1111/j.1365-2435.2005.01041.x.
  4. ^ Kress WJ, García-Robledo C, Uriarte M, Erickson DL (January 2015). "DNA barcodes for ecology, evolution, and conservation". Trends in Ecology & Evolution. 30 (1): 25–35. doi:10.1016/j.tree.2014.10.008. PMID 25468359.
  5. ^ a b Pompanon F, Deagle BE, Symondson WO, Brown DS, Jarman SN, Taberlet P (April 2012). "Who is eating what: diet assessment using next generation sequencing". Molecular Ecology. 21 (8): 1931–50. doi:10.1111/j.1365-294x.2011.05403.x. PMID 22171763. S2CID 10013333.
  6. ^ Harwood JD, Desneux N, Yoo HJ, Rowley DL, Greenstone MH, Obrycki JJ, O'Neil RJ (October 2007). "Tracking the role of alternative prey in soybean aphid predation by Orius insidiosus: a molecular approach". Molecular Ecology. 16 (20): 4390–400. doi:10.1111/j.1365-294x.2007.03482.x. PMID 17784913. S2CID 21211301.
  7. ^ a b Kress WJ, García-Robledo C, Uriarte M, Erickson DL (January 2015). "DNA barcodes for ecology, evolution, and conservation". Trends in Ecology & Evolution. 30 (1): 25–35. doi:10.1016/j.tree.2014.10.008. PMID 25468359.
  8. ^ Tobe SS, Kitchener A, Linacre A (December 2009). "Cytochrome b or cytochrome c oxidase subunit I for mammalian species identification—An answer to the debate". Forensic Science International: Genetics Supplement Series. 2 (1): 306–307. doi:10.1016/j.fsigss.2009.08.053. ISSN 1875-1768.
  9. ^ Jakubavičiūtė E, Bergström U, Eklöf JS, Haenel Q, Bourlat SJ (October 2017). "DNA metabarcoding reveals diverse diet of the three-spined stickleback in a coastal ecosystem". PLOS ONE. 12 (10): e0186929. Bibcode:2017PLoSO..1286929J. doi:10.1371/journal.pone.0186929. PMC 5653352. PMID 29059215.