Martin Ryberg

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The internal transcribed spacer (ITS) region of the nuclear ribosomal repeat unit is the most popular locus for species identification and subgeneric phylogenetic inference in sequence-based mycological research. The region is known to show certain variability even within species, although its intraspecific variability is often held to be limited and(More)
BACKGROUND DNA sequences are increasingly seen as one of the primary information sources for species identification in many organism groups. Such approaches, popularly known as barcoding, are underpinned by the assumption that the reference databases used for comparison are sufficiently complete and feature correctly and informatively annotated entries. (More)
The advent of new high-throughput DNA-sequencing technologies promises to redefine the way in which fungi and fungal communities--as well as other groups of organisms--are studied in their natural environment. With read lengths of some few hundred base pairs, massively parallel sequencing (pyrosequencing) stands out among the new technologies as the most(More)
We introduce an open source software utility to extract the highly variable ITS1 and ITS2 subregions from fungal nuclear ITS sequences, the region of choice for environmental sampling and molecular identification of fungi. Inclusion of parts of the neighbouring, very conserved, ribosomal genes in the sequence identification process regularly leads to(More)
Fungi from environmental samples are typically identified to species level through DNA sequencing of the nuclear ribosomal internal transcribed spacer (ITS) region for use in BLAST-based similarity searches in the International Nucleotide Sequence Databases. These searches are time-consuming and regularly require a significant amount of manual intervention(More)
Global species richness patterns of soil micro-organisms remain poorly understood compared to macro-organisms. We use a global analysis to disentangle the global determinants of diversity and community composition for ectomycorrhizal (EcM) fungi-microbial symbionts that play key roles in plant nutrition in most temperate and many tropical forest ecosystems.(More)
The environmental and distributional data associated with fungal internal transcribed spacer (ITS) sequences in GenBank are investigated and a new web-based tool with which these sequences can be explored is introduced. All fungal ITS sequences in GenBank were classified as either identified to species level or insufficiently identified and compared using(More)
Mohammad Bahram*, Urmas K~ oljalg, Pierre-Emmanuel Courty, Abdala G. Di edhiou, Rasmus Kjøller, Sergei P~ olme, Martin Ryberg†, Vilmar Veldre and Leho Tedersoo Institute of Ecology and Earth Sciences, Tartu University, 14A Ravila, 50411 Tartu, Estonia; Natural History Museum of Tartu University, 46 Vanemuise St. 51054 Tartu, Estonia; Zurich-Basel Plant(More)
The nuclear ribosomal internal transcribed spacer (ITS) region is the most commonly chosen genetic marker for the molecular identification of fungi in environmental sequencing and molecular ecology studies. Several analytical issues complicate such efforts, one of which is the formation of chimeric-artificially joined-DNA sequences during PCR amplification(More)
The ectomycorrhizal (ECM) symbiosis is the most widespread biotrophic nutritional mode in mushroom-forming fungi. ECM fungi include, though are not limited to, about 5000 described species of Agaricales from numerous, independently evolved lineages. Two central hypotheses suggest different explanations for the origin of ECM fungal diversity: (i) dual(More)