Instances of erroneous DNA barcoding of metazoan invertebrates: are universal cox1 gene primers too “universal”?

Monika Mioduchowska , Michał J. Czyż , Bartłomiej Gołdyn , Jarosław Kur , Jerzy Sell

Abstract

The cytochrome c oxidase subunit I (cox1) gene is the main mitochondrial molecular marker playing a pivotal role in phylogenetic research and is a crucial barcode sequence. Folmer's ªuniversalº primers designed to amplify this gene in metazoan invertebrates allowed quick and easy barcode and phylogenetic analysis. On the other hand, the increase in the number of studies on barcoding leads to more frequent publishing of incorrect sequences, due to amplification of non-target taxa, and insufficient analysis of the obtained sequences. Consequently, some sequences deposited in genetic databases are incorrectly described as obtained from invertebrates, while being in fact bacterial sequences. In our study, in which we used Folmer's primers to amplify COI sequences of the crustacean fairy shrimp Branchipus schaefferi (Fischer 1834), we also obtained COI sequences of microbial contaminants from Aeromonas sp. However, when we searched the GenBank database for sequences closely matching these contaminations we found entries described as representatives of Gastrotricha and Mollusca. When these entries were compared with other sequences bearing the same names in the database, the genetic distance between the incorrect and correct sequences amplified from the same species was c.a. 65%. Although the responsibility for the correct molecular identification of species rests on researchers, the errors found in already published sequences data have not been re-evaluated so far. On the basis of the standard sampling technique we have estimated with 95% probability that the chances of finding incorrectly described metazoan sequences in the GenBank depend on the systematic group, and variety from less than 1% (Mollusca and Arthropoda) up to 6.9% (Gastrotricha). Consequently, the increasing popularity of DNA barcoding and metabarcoding analysis may lead to overestimation of species diversity. Finally, the study also discusses the sources of the problems with amplification of non-target sequences.
Author Monika Mioduchowska (FB / DGB)
Monika Mioduchowska,,
- Katedra Genetyki i Biosystematyki
, Michał J. Czyż
Michał J. Czyż,,
-
, Bartłomiej Gołdyn
Bartłomiej Gołdyn,,
-
, Jarosław Kur
Jarosław Kur,,
-
, Jerzy Sell (FB / DGB)
Jerzy Sell,,
- Katedra Genetyki i Biosystematyki
Journal seriesPlos One, ISSN 1932-6203, (A 35 pkt)
Issue year2018
Vol13
No6
Pages1-16
Publication size in sheets0.75
DOIDOI:10.1371/journal.pone.0199609
URL https://doi.org/10.1371/journal.pone.0199609
Languageen angielski
LicenseJournal (articles only); published final; Uznanie Autorstwa (CC-BY); with publication
Score (nominal)40
ScoreMinisterial score = 35.0, 03-07-2018, ArticleFromJournal
Ministerial score (2013-2016) = 40.0, 03-07-2018, ArticleFromJournal
Publication indicators WoS Impact Factor: 2016 = 2.806 (2) - 2016=3.394 (5)
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