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How does marker choice affect your diet analysis: comparing genetic markers and digestion levels for diet metabarcoding of tropical-reef piscivores

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dc.contributor James Cook University
dc.contributor Australian Institute Of Marine Science
dc.contributor Lab Biodivers & Evolutionary Genom
dc.contributor Univ Virgin Isl
dc.contributor Ku Leuven
dc.contributor Katholieke Univ Leuven
dc.contributor Oceans & Atmosphere
dc.contributor Sch Biol Sci Quantitat Marine Sci
dc.contributor James Cook Univ
dc.contributor Csiro
dc.contributor Commonwealth Scientific & Industrial Research Organisation (csiro)
dc.contributor Uz Leuven
dc.contributor University Hospital Leuven
dc.contributor Ctr Marine & Environm Studies
dc.contributor Ctr Human Genet
dc.contributor University Of Tasmania
dc.contributor Australian Inst Marine Sci
dc.contributor Ctr Sustainable Trop Fisheries & Aquaculture
dc.contributor Univ Tasmania
dc.contributor Coll Sci & Engn
dc.contributor Comparat Genom Ctr HEUPEL, MICHELLE R. DEVLOO-DELVA, FLORIAAN HUERLIMANN, ROGER MATLEY, JORDAN K. SIMPFENDORFER, COLIN A. MAES, GREGORY E. CHUA, GLADYS 2019-01-06T18:53:40Z 2019-01-06T18:53:40Z 2019-07-08T02:18:37Z 2019-01-06T18:53:40Z 2019-01-06T18:53:40Z 2019-07-08T02:18:37Z 2019-01-01
dc.identifier.citation Devloo-Delva F, Huerlimann R, Chua G, Matley JK, Heupel MR, Simpfendorfer CA, Maes GE (2019) How does marker choice affect your diet analysis: comparing genetic markers and digestion levels for diet metabarcoding of tropical-reef piscivores. Marine and Freshwater Research 70: 8-18
dc.identifier.issn 1323-1650
dc.description.abstract Tropical reefs are highly diverse ecosystems, and reliable biomonitoring, through diet metabarcoding, is needed to understand present and future trophic relationships in this changing habitat. Several studies have assessed the reliability and effectiveness of single molecular markers; however, a cross-marker validation has rarely been performed. This study identified crucial properties for 12S rDNA, 16S rDNA and COI metabarcoding in tropical-reef piscivores (Plectropomus spp.). In addition, three new versatile primer sets for 16S were designed in silico for metabarcoding of reef fish. Results showed that COI was overall better at recovering true diversity because of a well-supported database. Second, optimal 16S amplicon sizes ranged between 160 and 440 base pairs for full diversity recovery, with increased species detection for the 270-base pairs region. Finally, blocking of predator-specific COI sequences was not equally effective in all host species, potentially introducing bias when diet compositions are directly compared. In conclusion, this novel study showed that marker success for prey identification is highly dependent on the reference database, taxonomic scope, DNA quality, amplicon length and sequencing platform. Results suggest that COI, complemented with 16S, yields the best outcome for diet metabarcoding in reef piscivores. Findings in this paper are relevant to other piscivores and other metabarcoding applications.
dc.description.sponsorship The authors thank the following for field assistance: S. Moore, J. Eurich, J. Smart, P. Tenzing, V. Messmer, E. Ledee, F. de Faria, P. Yates, M. Espinoza and A. Tobin. This research pertained to permits issued by the Great Barrier Reef Marine Park Authority (G12/35236.1 and G14/36624.1) and Queensland Department of Primary Industries and Fisheries (144482). All research was conducted under JCU Animal Ethics Permit A1933. This project was funded by the Australian Government's National Environmental Research Program (Tropical Ecosystems Hub Project 6.1) and supported by an Australian Research Council Future Fellowship (#FT100101004). The authors sincerely appreciate the valuable comments of two anonymous reviewers to improve this manuscript.
dc.language English
dc.subject Primers
dc.subject Fisheries
dc.subject Diversity
dc.subject Amplicon Length
dc.subject Identification
dc.subject Metabarcoding Performance
dc.subject 16s Metabarcoding Primers
dc.subject Gut Contents
dc.subject Limnology
dc.subject Marine & Freshwater Biology
dc.subject Coral Trout
dc.subject Marine Predators
dc.subject Oceanography
dc.subject Library
dc.subject Dna
dc.subject Size
dc.title How does marker choice affect your diet analysis: comparing genetic markers and digestion levels for diet metabarcoding of tropical-reef piscivores
dc.type journal article
dc.identifier.doi 10.1071/MF17209
dc.identifier.wos WOS:000453226400002

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