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Research Article

Taxonomic Reliability of DNA Sequences in Public Sequence Databases: A Fungal Perspective

  • R. Henrik Nilsson mail,

    To whom correspondence should be addressed. E-mail: henrik.nilsson@botany.gu.se

    Affiliation: Department of Plant and Environmental Sciences, Göteborg University, Göteborg, Sweden

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  • Martin Ryberg,

    Affiliation: Department of Plant and Environmental Sciences, Göteborg University, Göteborg, Sweden

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  • Erik Kristiansson,

    Affiliation: Department of Mathematical Statistics, Chalmers University of Technology, Göteborg, Sweden

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  • Kessy Abarenkov,

    Affiliation: Institute of Botany and Ecology, University of Tartu, Tartu, Estonia

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  • Karl-Henrik Larsson,

    Affiliation: Department of Plant and Environmental Sciences, Göteborg University, Göteborg, Sweden

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  • Urmas Kõljalg

    Affiliation: Institute of Botany and Ecology, University of Tartu, Tartu, Estonia

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  • Published: December 20, 2006
  • DOI: 10.1371/journal.pone.0000059

Reader Comments (7)

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Article discussed at the Barcode of Life Blog

Posted by RHNi on 18 Jun 2007 at 09:46 GMT

It was brought to my attention that this article is discussed over at the Barcode of Life blog:

http://phe.rockefeller.ed...

RHN


RE: Article discussed at the Barcode of Life Blog

RHNi replied to RHNi on 18 Jun 2007 at 10:27 GMT

I noticed that the paper has been cited by the following PLoS ONE paper:

Kress & Erickson, A Two-Locus Global DNA Barcode for Land Plants: The Coding rbcL Gene Complements the Non-Coding trnH-psbA Spacer Region

(http://www.plosone.org/ar...)

It would be very interesting to see some statistics on citations to, and from, PLoS ONE. It is for example common with PLoS ONE - PLoS ONE citations? How many times, in total, has PLoS ONE papers been cited, and from what journals?

I should probably do my homework as to what databases that PLoS ONE is indexed in / tracked by. Has anyone done that?

RHN


Plos citations

ncorradi replied to RHNi on 28 Nov 2007 at 18:29 GMT

I recently ran a quick search using PubMed and Google scholar and, altought I cannot provide any RAW-statistical data here, I was positively surprised about the amount of citations PLOS one paper are getting overall.

I was suprised since:

1) Plos One is a faily new journal.

2) I found that many papers are cited within a few months after appearance.

Anyways I am going a bit off topic here and I take this opportunity to congratulate the authors of this article, which showed once again that, especially for Fungi, much more carefullness is required to assign DNA sequences to a given species (and even higher taxonomical rankings).

I've been working on arbuscular mycorrhizal fungi for some time, and I still remember finding that (around 50%) of the sequences present in the databases at that time, were wrongly assigned to different genera or even diferent fungal phyla! (yes different Phyla, not species!). This is apparently not the case anymore but it still happens.

E.g. Redecker et al. 1999, Schüssler 1999, Corradi et al. 2004.

Best

Nicolas