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

DOI: 10.1186/1471-2148-8-50

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Most species of Inocybe were found to have less than 3% intraspecific variability in the ITS2 region of the nuclear ribosomal DNA. This cut-off value was used jointly with phylogenetic analysis to delimit and identify unidentified Inocybe sequences to species level. A total of 177 unidentified Inocybe ITS sequences corresponding to 98 species were recovered, 32% of which were successfully identified to species level in this study. These sequences account for an unexpectedly large proportion of the publicly available unidentified fungal ITS sequences when compared with other mycorrhizal genera. Eight Inocybe species were reported from multiple hosts and some even from hosts forming arbutoid or orchid mycorrhizae. Furthermore, Inocybe sequences have been reported from four continents and in climate zones ranging from cold temperate to equatorial climate. Out of the 19 species found in more than one study, six were found in both Europe and North America and one was found in both Europe and Japan, indicating that at least many north temperate species have a wide distribution.Although DNA-based species identification and circumscription are associated with practical and conceptual difficulties, they also offer new possibilities and avenues for research. Metadata assembly holds great potential to synthesize valuable information from community studies for use in a species and taxonomy-oriented framework.The taxonomy of fungi is largely based on ephemeral and irregularly occurring propagation structures, notably sexual fruiting-bodies. The main part of the fungal life cycle is, however, a somatic – typically mycelial – phase that offers few discriminatory morphological characters and that may be difficult to assign even to family or ordinal level. This means that alternatives to morphological characters are essential to get a complete picture of the fungal diversity and ecology at any given locality and time. Indeed, DNA-based methods have been in long use for identificatio


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