Advertisement
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

    X
  • Martin Ryberg,

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

    X
  • Erik Kristiansson,

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

    X
  • Kessy Abarenkov,

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

    X
  • Karl-Henrik Larsson,

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

    X
  • Urmas Kõljalg

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

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

Reader Comments (7)

Post a new comment on this article

This paper is cited by the below peer-reviewed papers

Posted by RHNi on 01 Apr 2008 at 12:58 GMT

The paper has been cited by the below, peer-reviewed publications

Bidartondo et al. 2008. Preserving Accuracy in GenBank. Science 319: 1616.

Bruns TD et al. 2008. Fungal networks made of humans: UNITE, FESIN, and frontiers in fungal ecology. New Phytologist 177: 586–588.

Ryberg M et al. 2008. Mining metadata from unidentified ITS sequences in GenBank: A case study in Inocybe (Basidiomycota). BMC Evolutionary Biology 2008, 8:50.

Balajee et al. 2007. DNA and the classical way: identification of medically important molds for the 21st century. Medical Mycology 45: 475-490.

Costa et al. 2007. The barcode of life initiaitve: synopsis and prospective societal impacts of DNA barcoding of Fish. Genomics, Society and Policy 3: 29-40.

Johnson et al. 2007. DNA barcoding as a means to identify organisms associated with amphibian eggs. Herpetological Conservation and Biology 3: 116-127.

Kress WJ et al. 2007. A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region. PLoS ONE 2: e508.

Nilsson RH et al. 2006. Fruiting body-guided molecular identification of root-tip mantle mycelia provides strong indications of ectomycorrhizal associations in two species of Sistotrema (Basidiomycota). Mycological Research 110: 1426-1432.


RE: This paper is cited by the below peer-reviewed papers

RHNi replied to RHNi on 27 Jun 2008 at 08:54 GMT

Nilsson et al. 2008. Intraspecific ITS variability in the kingdom fungi as expressed in the international sequence databases and its implications for molecular species identification. Evolutionary Bioinformatics 4: 193-201.

Pleijel et al. 2008. Phylogenies without roots? A plea for the use of vouchers in molecular phylogenetic studies. Molecular Phylogenetics and Evolution 48: 369-371.


RE: This paper is cited by the below peer-reviewed papers

RHNi replied to RHNi on 16 Jul 2008 at 12:46 GMT

Larsson KH. 2007. Re-thinking the classification of corticioid fungi. Mycological Research 111: 1040-1063.


RE: This paper is cited by the below peer-reviewed papers

RHNi replied to RHNi on 22 Aug 2008 at 10:15 GMT

Hildén et al. 2008. Molecular characterization of the basidiomycete isolate Nematoloma frowardii b19 and its manganese peroxidase places the fungus in the corticioid genus Phlebia. Microbiology 154: 2371-2379.


RE: This paper is cited by the below peer-reviewed papers

RHNi replied to RHNi on 29 Aug 2008 at 12:39 GMT

Mitchell. 2008. DNA barcoding demystified. Australian Journal of Entomology 47: 169-173.


RE: This paper is cited by the below peer-reviewed papers

RHNi replied to RHNi on 08 Sep 2008 at 11:34 GMT

Wong E, Hanner R. 2008. DNA barcoding detects market substitution in North American seafood. Food Research International 41: 828-837.


RE: This paper is cited by the below peer-reviewed papers

RHNi replied to RHNi on 14 Sep 2008 at 00:02 GMT

Aveskamp MM et al. 2008. Biology and recent developments in the systematics of Phoma, a complex genus of major quarantine significance. Fungal Diversity 31: 1-18.


RE: This paper is cited by the below peer-reviewed papers

RHNi replied to RHNi on 26 Sep 2008 at 12:37 GMT

Rossman et al. 2008. Systematics of plant pathogenic fungi: why it matters. Plant Disease 92: 1376-1386.


RE: This paper is cited by the below peer-reviewed papers

RHNi replied to RHNi on 28 Sep 2008 at 13:12 GMT

Desnos-Ollivier M et al. 2008. Debaryomyces hansenii (Candida famata): a rare human fungal pathogen often misidentified as Pichia guilliermondii (Candida guilliermondii). Journal of Clinical Microbiology doi:10.1128/JCM.01451-08.


RE: This paper is cited by the below peer-reviewed papers

RHNi replied to RHNi on 29 Sep 2008 at 19:59 GMT

Hyde KD et al. 2008. Epitypification: should we epitypify? J Zhejiang Univ Sci B 9:842-846.


RE: This paper is cited by the below peer-reviewed papers

RHNi replied to RHNi on 30 Oct 2008 at 15:17 GMT

Peay et al. 2008. Fungal community ecology: a hybrid beast with a molecular master. BioScience 58: 799-810.


RE: This paper is cited by the below peer-reviewed papers

RHNi replied to RHNi on 14 Nov 2008 at 09:30 GMT

Taylor AFS. 2008. Recent advances in our understanding of fungal ecology. Coolia 51: 197-212.


RE: This paper is cited by the below peer-reviewed papers

RHNi replied to RHNi on 15 Nov 2008 at 10:09 GMT

Seifert KA. 2008. Integrating DNA barcoding into the mycological sciences. Inoculum 59: 2-6.


RE: This paper is cited by the below peer-reviewed papers

RHNi replied to RHNi on 18 Dec 2008 at 12:44 GMT

Ryberg M et al. 2009. An outlook on the fungal internal transcribed spacer sequences in GenBank and the introduction of a web-based tool for the exploration of fungal diversity. New Phytologist 181: 471 - 477.


RE: This paper is cited by the below peer-reviewed papers

RHNi replied to RHNi on 19 Dec 2008 at 09:18 GMT

Seifert KA. 2008. Integrating DNA Barcoding into the Mycological Sciences. Persoonia 162-166.


RE: This paper is cited by the below peer-reviewed papers

RHNi replied to RHNi on 22 Dec 2008 at 12:48 GMT

Rajala T. Responses of soil microbial communities to clonal variation of Norway spruce. Dissertationes Forestales 58: 1-50.


RE: This paper is cited by the below peer-reviewed papers

RHNi replied to RHNi on 23 Dec 2008 at 19:02 GMT

Rinaldi et al. 2008. Ectomycorrhizal diversity: separating the wheat from the chaff. Fungal Diversity 33: 1-45.


RE: This paper is cited by the below peer-reviewed papers

RHNi replied to RHNi on 03 Jan 2009 at 22:49 GMT

Keller et al. 2009. 5.8S-28S rRNA interaction and HMM-based ITS2 annotation. Gene 430: 50-57 .


RE: This paper is cited by the below peer-reviewed papers

RHNi replied to RHNi on 07 Jan 2009 at 21:21 GMT

Hyde et al. 2007. Understanding microfungal diversity - a critique. Cryptogamie Mycologie 28: 281-289.


RE: This paper is cited by the below peer-reviewed papers

RHNi replied to RHNi on 15 Jan 2009 at 11:24 GMT

Nilsson et al. 2009. A software pipeline for processing and identification of fungal ITS sequences. Source Code for Biology and Medicine 2009, 4:1.


RE: This paper is cited by the below peer-reviewed papers

RHNi replied to RHNi on 16 Jan 2009 at 15:13 GMT

Brock et al. 2009. How to know unknown fungi: the role of a herbarium. New Phytologist 181: 719-724.


RE: This paper is cited by the below peer-reviewed papers

RHNi replied to RHNi on 31 Jan 2009 at 07:06 GMT

Christen R. 2008. Global sequencing: a review of current molecular data and new methods available to assess microbial diversity. Microbes and Environments 23: 253-268.


RE: This paper is cited by the below peer-reviewed papers

RHNi replied to RHNi on 19 Feb 2009 at 11:05 GMT

Shenoy BD. 2007. Multigene phylogeny of selected anamorphic ascomycetes. Ph D Thesis, University of Hong Kong.


RE: This paper is cited by the below peer-reviewed papers

RHNi replied to RHNi on 19 Feb 2009 at 11:08 GMT

Hultman J. 2009. Microbial diversity in the municipal composting process and development of detection methods. Ph D Thesis, University of Helsinki.


RE: This paper is cited by the below peer-reviewed papers

RHNi replied to RHNi on 12 Mar 2009 at 09:39 GMT

Slapeta J. 2009. Centenary of the genus Cryptosporidium: from morphological to molecular species identification. In: M. G. Ortega-Pierres, S. Caccio, R. Fayer, T. Mank, H. Smith, R. C. A. Thompson (Eds). Giardia and Crytosporidium, CABI Publishing


RE: This paper is cited by the below peer-reviewed papers

RHNi replied to RHNi on 24 Mar 2009 at 16:42 GMT

Berner et al. 2009. Mixed model analysis combining disease ratings and DNA sequences to determine host range of Uromyces salsolae for biological control of Russian thistle. Biological Control 49: 68-76 .

No competing interests declared.

RE: This paper is cited by the below peer-reviewed papers

RHNi replied to RHNi on 08 Apr 2009 at 06:21 GMT

Berner DK et al. 2009. Mixed model analysis combining disease ratings and DNA sequences to determine host range of Uromyces salsolae for biological control of Russian thistle. Biological Control 49: 68-76.

No competing interests declared.

RE: This paper is cited by the below peer-reviewed papers

RHNi replied to RHNi on 08 Apr 2009 at 06:25 GMT

Balajee SA et al. 2009. Sequence-based identification of Aspergillus, Fusarium, and Mucorales species in the clinical mycology laboratory: where are we and where should we go from here? Journal of Clinical Microbiology 47: 877-884.

No competing interests declared.

RE: This paper is cited by the below peer-reviewed papers

RHNi replied to RHNi on 05 May 2009 at 14:00 GMT

Landlinger et al. 2009. Species-specific identification of a wide range of clinically relevant fungal pathogens by use of Luminex xMAP technology. Journal of Clinical Microbiology 47: 1063-1073.

No competing interests declared.