Vis enkel innførsel

dc.contributor.authorChua, Physilia Y. S.
dc.contributor.authorCrampton-Platt, Alex
dc.contributor.authorLammers, Youri
dc.contributor.authorAlsos, Inger G.
dc.contributor.authorBoessenkool, Sanne
dc.contributor.authorBohmann, Kristine
dc.date.accessioned2021-08-10T10:39:08Z
dc.date.available2021-08-10T10:39:08Z
dc.date.issued2021-05-10
dc.description.abstractMetagenomics can generate data on the diet of herbivores, without the need for primer selection and PCR enrichment steps as is necessary in metabarcoding. Metagenomic approaches to diet analysis have remained relatively unexplored, requiring validation of bioinformatic steps. Currently, no metagenomic herbivore diet studies have utilized both chloroplast and nuclear markers as reference sequences for plant identification, which would increase the number of reads that could be taxonomically informative. Here, we explore how in silico simulation of metagenomic data sets resembling sequences obtained from faecal samples can be used to validate taxonomic assignment. Using a known list of sequences to create simulated data sets, we derived reliable identification parameters for taxonomic assignments of sequences. We applied these parameters to characterize the diet of western capercaillies (Tetrao urogallus) located in Norway, and compared the results with metabarcoding trnL P6 loop data generated from the same samples. Both methods performed similarly in the number of plant taxa identified (metagenomics 42 taxa, metabarcoding 43 taxa), with no significant difference in species resolution (metagenomics 24%, metabarcoding 23%). We further observed that while metagenomics was strongly affected by the age of faecal samples, with fresh samples outperforming old samples, metabarcoding was not affected by sample age. On the other hand, metagenomics allowed us to simultaneously obtain the mitochondrial genome of the western capercaillies, thereby providing additional ecological information. Our study demonstrates the potential of utilizing metagenomics for diet reconstruction but also highlights key considerations as compared to metabarcoding for future utilization of this technique.en_US
dc.identifier.citationChua, Crampton-Platt, Lammers, Alsos, Boessenkool, Bohmann. Metagenomics: A viable tool for reconstructing herbivore diet. Molecular Ecology Resources. 2021:1-15en_US
dc.identifier.cristinIDFRIDAID 1913911
dc.identifier.doi10.1111/1755-0998.13425
dc.identifier.issn1755-098X
dc.identifier.issn1755-0998
dc.identifier.urihttps://hdl.handle.net/10037/21971
dc.language.isoengen_US
dc.publisherWileyen_US
dc.relation.journalMolecular Ecology Resources
dc.relation.projectIDinfo:eu-repo/grantAgreement/EC/Plant.ID/765000/Norway/Molecular Identification of Plants//en_US
dc.rights.accessRightsopenAccessen_US
dc.rights.holderCopyright 2021 The Author(s)en_US
dc.subjectVDP::Mathematics and natural science: 400::Zoology and botany: 480en_US
dc.subjectVDP::Matematikk og Naturvitenskap: 400::Zoologiske og botaniske fag: 480en_US
dc.titleMetagenomics: A viable tool for reconstructing herbivore dieten_US
dc.type.versionpublishedVersionen_US
dc.typeJournal articleen_US
dc.typeTidsskriftartikkelen_US
dc.typePeer revieweden_US


Tilhørende fil(er)

Thumbnail

Denne innførselen finnes i følgende samling(er)

Vis enkel innførsel