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 stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite. ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|

The mechanisms of carbon starvation: how, when, or does it even occur at all?Recent observations of increasing vegetation mortality events appear to be a result of changing climate, in particular, an increase in the frequency, length and intensity of droughts (e.g. Allen et al., 2010). The threat of widespread increases in future mortality has rekindled interest in the mechanisms of plant mortality and survival because we do not yet understand them well enough to confidently model future vegetation dynamics (Sitch et al., 2008). In this issue of New Phytologist, provide a viewpoint on the 'carbon (C) starvation hypothesis ' (McDowell et al., 2008). Their viewpoint is invaluable for stimulating our field to explicitly refine our definitions and identify the key experiments needed to understand mechanisms of vegetation survival and mortality. Two important conclusions of their paper were that mortality can occur at nonzero carbohydrate levels and that careful experiments focused on the explicit mechanisms of C starvation, as well as on partitioning the roles of hydraulic failure and C starvation, are needed to understand the physiological underpinnings of how plants die. We applaud these conclusions, and agree that hasty acceptance of any hypothesis before adequate testing is foolish. In this commentary, we highlight some of the valuable ideas from Sala et al. and provide additional comments that we hope will prompt careful future tests on the mechanisms of plant mortality.When the C-starvation hypothesis was proposed (McDowell et al., 2008), it represented an attempt to summarize and interpret the existing literature on vegetation mortality, of which there was a wealth of indirect studies, but a paucity of true, mechanistic tests. The original formulation of the hypothesis suggested that stomatal closure minimizes hydraulic failure during drought, causing photosynthetic C uptake to decline to low levels, thereby promoting carbon starvation as carbohydrate demand continues for maintenance of metabolism and defense. The plant either starves outright, or succumbs to attack by insects or pathogens, whichever occurs first. By contrast, failure to maintain xylem water tension lower than its cavitation threshold results in embolisms, which, if unrepaired, can eventually lead to widespread hydraulic failure, desiccation and mortality. We hoped that the C-starvation and hydraulic failure hypotheses would generate discussion and new ideas; and 'The paucity of studies that quantified mortality forces scientists to use data from nonmortality studies to develop hypotheses … we do this at the risk of confusing stress responses with mortality mechanisms.' , as summarized by Sala et al., active discussion is taking place. A primary conclusion from the discussion is that we need clarification of the various mechanisms by which C starvation can occur, if it occurs at all.Plants maintain metabolism through respiratory processes that consume carbohydrates, and in doing so their C budgets must obey the law of conservation of energ...

The aim of the present study was to investigate the phylogeny and evolution of sequestrate fungi (with gastroid or partially exposed basidiomes) in relation to their gilled relatives from the Cortinariaceae (Basidiomycetes). Phylogenetic analyses of 151 ITS sequences from 77 gilled species and 37 sequestrate taxa were performed using maximum parsimony and maximum likelihood methods. Results show that sequestrate basidiome forms occur in all three major ectomycorrhizal lineages of Cortinariaceae: the clades Cortinarius, Hebeloma/Hymenogaster/Naucoria, and Descolea. However, these forms do not appear within the saprobic outgroup Gymnopilus, indicating multiple origins of sequestrate forms from ectomycorrhizal ancestors. Additionally, within the Cortinarius clade sequestrate forms have multiple origins: emergent Cortinarius spp., Thaxterogaster, Quadrispora, Protoglossum, and two Hymenogaster spp. (H. remyi, H. sublilacinus) share common ancestors with Cortinarius spp., but these sequestrate genera are not closely related to each other (with exception of Thaxterogaster and Quadrispora). Hymenogaster sensu stricto, Setchelliogaster, and Descomyces were placed in the two other major clades. Thus, sequestrate taxa evolved independently many times within brown-spored Agaricales. Furthermore, emergent, secotioid, and gastroid forms have evolved independently from each other, and so are not necessarily intermediate forms. After their establishment, these apparently morphologically stable taxa show a tendency to radiate.

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Different distance-based threshold selection approaches were used to assess and compare use of the internal transcribed spacer (ITS) region to distinguish among 901 Cortinarius species represented by >3000 collections. Sources of error associated with genetic markers and selection approaches were explored and evaluated using MOTUs from genus and lineage based-alignments. Our study indicates that 1%-2% more species can be distinguished by using the full-length ITS barcode as compared to either the ITS1 or ITS2 regions alone. Optimal threshold values for different picking approaches and genetic marker lengths inferred from a subset of species containing major lineages ranged from 97.0% to 99.5% sequence similarity using clustering optimization and UNITE SH, and from 1% to 2% sequence dissimilarity with CROP. Errors for the optimal cutoff ranged from 0% to 70%, and these can be reduced to a maximum of 22% when excluding species lacking a barcode gap. A threshold value of 99% is suitable for distinguishing species in the majority of lineages in the genus using the entire ITS region but only 90% of the species could be identified using just the ITS1 or ITS2 region. Prior identification of species, lacking barcode gaps and their subsequent separate analyses, maximized the accuracy of threshold approaches.