Addressing nontarget amplification in DNA metabarcoding studies of arthropod-feeding rodents.
Metabarcoding
PCR
degenerate primers
nontarget amplification
rodents
Journal
Mammal research
ISSN: 2199-2401
Titre abrégé: Mamm Res
Pays: Germany
ID NLM: 101665631
Informations de publication
Date de publication:
Oct 2022
Oct 2022
Historique:
entrez:
27
3
2023
pubmed:
28
3
2023
medline:
28
3
2023
Statut:
ppublish
Résumé
High-throughput sequencing approaches have revolutionized how we study animal diets by enabling the detection of dietary components from the metabarcoding of DNA in excrement. Mitochondrial cytochrome oxidase C subunit I (mtCOI) DNA metabarcoding is commonly used to study the diets of arthropod-feeding animals; however, this approach is susceptible to nontarget amplification of the consumer species mtCOI locus. Nontarget amplification is often an unforeseen complication that can drastically reduce the quality and utility of the results generated by high-throughput amplicon sequencing. By interrogating the diets of new world rodents in the genus
Identifiants
pubmed: 36968646
doi: 10.1007/s13364-022-00646-2
pmc: PMC10035264
mid: NIHMS1881569
doi:
Types de publication
Journal Article
Langues
eng
Pagination
499-509Subventions
Organisme : NIGMS NIH HHS
ID : T32 GM141848
Pays : United States
Déclaration de conflit d'intérêts
Conflicts of interest: The authors of this study have no conflicts of interest to disclose.
Références
J Mammal. 2016 Jun 9;97(3):663-688
pubmed: 29692469
Ecol Evol. 2018 Oct 12;8(22):10914-10937
pubmed: 30519417
Mol Ecol Resour. 2014 Nov;14(6):1160-70
pubmed: 24751203
Ecol Evol. 2020 Jul 23;10(18):9721-9739
pubmed: 33005342
PCR Methods Appl. 1993 Dec;3(3):S30-7
pubmed: 8118394
Lancet Microbe. 2022 Apr;3(4):e294-e302
pubmed: 35544066
Mol Ecol Resour. 2011 Mar;11(2):236-44
pubmed: 21429129
Mol Ecol. 2019 Jan;28(2):391-406
pubmed: 29858539
Sci Rep. 2019 Mar 26;9(1):5190
pubmed: 30914730
Genome Res. 2002 Apr;12(4):656-64
pubmed: 11932250
Mol Ecol Resour. 2019 May;19(3):711-727
pubmed: 30779309
Appl Microbiol Biotechnol. 2006 Aug;71(5):575-86
pubmed: 16683135
Front Zool. 2008 Jul 20;5:12
pubmed: 18638418
Mol Ecol Resour. 2022 Oct;22(7):2713-2731
pubmed: 35599377
Methods Mol Biol. 2018;1783:149-169
pubmed: 29767361
Mol Ecol Resour. 2015 Jul;15(4):819-30
pubmed: 25454249
Bioinformatics. 2009 Jun 1;25(11):1422-3
pubmed: 19304878
Ecol Evol. 2017 Nov 26;8(1):185-196
pubmed: 29321862
Proc Biol Sci. 2003 Aug 7;270 Suppl 1:S96-9
pubmed: 12952648
Ecol Evol. 2020 May 21;10(13):6310-6332
pubmed: 32724515
Nat Methods. 2016 Jul;13(7):581-3
pubmed: 27214047
Environ Microbiol. 2014 Sep;16(9):2869-78
pubmed: 24373154
PLoS One. 2013 Apr 22;8(4):e61217
pubmed: 23630581
ISME J. 2017 Dec;11(12):2639-2643
pubmed: 28731476
Microb Ecol. 2022 May;83(4):916-928
pubmed: 34269858
Appl Environ Microbiol. 2007 Aug;73(16):5261-7
pubmed: 17586664
Appl Environ Microbiol. 2008 Mar;74(5):1660-3
pubmed: 18192413
PeerJ. 2019 Oct 7;7:e7745
pubmed: 31608170
Mol Ecol Resour. 2019 Jan;19(1):176-190
pubmed: 30281913