Towards a unified paradigm for sequence‐based identification of fungi

@article{Kljalg2013TowardsAU,
  title={Towards a unified paradigm for sequence‐based identification of fungi},
  author={Urmas K{\~o}ljalg and Rolf Henrik Nilsson and Kessy Abarenkov and Leho Tedersoo and Andy F. S. Taylor and Mohammad Bahram and Scott T. Bates and Thomas D. Bruns and Johan Bengtsson-Palme and Tony Martin Callaghan and Brian Douglas and Tiia Drenkhan and Ursula Eberhardt and Margarita Due{\~n}as and Tine Grebenc and Gareth W. Griffith and Martin Hartmann and Paul M. Kirk and Petr Kohout and Ellen Larsson and Bj{\"o}rn D. Lindahl and Robert L{\"u}cking and Mar{\'i}a Paz Mart{\'i}n and P. Brandon Matheny and Nhu H. Nguyen and Tuula Niskanen and Jane Oja and Kabir Gabriel Peay and Ursula Peintner and Marko Peterson and Kadri P{\~o}ldmaa and Lauri Saag and Irja Saar and Arthur Sch{\"u}{\ss}ler and James A Scott and Carolina Sen{\'e}s and Matthew E. Smith and Ave Suija and D. Lee Taylor and M. Teresa Telleria and Michael Wei{\ss} and Karl-Henrik Larsson},
  journal={Molecular Ecology},
  year={2013},
  volume={22}
}
The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized… 

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References

SHOWING 1-10 OF 35 REFERENCES

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

The present study uses a large set of fungal DNA sequences from the inclusive International Nucleotide Sequence Database to show that the taxon sampling of fungi is far from complete, that about 20% of the entries may be incorrectly identified to species level, and that the majority of entries lack descriptive and up-to-date annotations.

UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi.

The UNITE database, an open-access database dedicated to the reliable identification of ECM fungi, comprises well annotated fungal ITS sequences from well defined herbarium specimens that include full her barium reference identification data, collector/source and ecological data.

Tidying Up International Nucleotide Sequence Databases: Ecological, Geographical and Sequence Quality Annotation of ITS Sequences of Mycorrhizal Fungi

To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches.

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation.

Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences.

A set of guidelines to assist in manual quality management of newly generated, near-full-length (Sanger-derived) fungal ITS sequences and to some extent also sequences of shorter read lengths, other genes or markers, and groups of organisms are provided.

PlutoF—a Web Based Workbench for Ecological and Taxonomic Research, with an Online Implementation for Fungal ITS Sequences

The web-based workbench PlutoF is described, which is designed to bridge the gap between the needs of contemporary research in biology and the existing software resources and databases.

Defining operational taxonomic units using DNA barcode data

Using the DNA barcode data from meiofaunal surveys, the benefits of treating the taxa defined by barcodes without reference to their correspondence to ‘species’ are discussed and it is suggested that using this non-idealist approach facilitates access to taxon groups that are not accessible to other methods of enumeration and classification.

Mining metadata from unidentified ITS sequences in GenBank: A case study in Inocybe (Basidiomycota)

Undiscovered Inocybe ITS sequences account for an unexpectedly large proportion of the publicly available unidentified fungal ITS sequences when compared with other mycorrhizal genera.

Fungal community analysis by high-throughput sequencing of amplified markers – a user's guide

Taking advantage of the collective experience of six research groups, the different stages involved in fungal community analysis are reviewed, from field sampling via laboratory procedures to bioinformatics and data interpretation, and potential pitfalls, alternatives, and solutions are discussed.