Tidying up international nucleotide sequence databases

Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS) region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD) are, however, unfiltered for quality and are often poorly annotated with metadata. 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. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/) for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/), the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi

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

Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS) region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD) are, however, unfiltered for quality and are often poorly annotated with metadata. 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. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/) for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/), the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi

Glomeromycota

SPE IPMInternational audienc

Nomenclatural clarifications in Glomeromycota

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Arbuscular mycorrhiza (AM): the first glomeromycotan sugar transporter is characterized by using the unique geosiphon symbiosis with cyanobacteria to characterize key genes in AM (like) symbioses

International audienceIn the arbuscular mycorrhizas (AM), the symbiotic interface is the site of nutrient exchange where the mycobiont receives up to 20% of the photosynthates of the photobiont as carbohydrates. We have, for the first time, functionally characterised a monosaccharide transporter type, represented by GpMST1, putatively playing a role in this process (Schüßler, A., Martin, H., Cohen, D., Fitz, M., and Wipf, D. 2006. Characterization of a carbohydrate transporter from symbiotic glomeromycotan fungi. Nature 444:933-936.). Together with the arbuscular mycorrhizal (AM) fungi, forming endomycorrhiza with the majority of land plants, Geosiphon pyriformis belongs to the Glomeromycota. Phylogenetically it is deeply embedded within the AM forming fungi. However, Geosiphon associates symbiotically with cyanobacteria instead of – or in parallel to – plants. This unique association therefore represents a symbiosis of an ‘AM fungus’ with a photoautotrophic prokaryote. Due to this unique life style, the Geosiphon-symbiosis offers fundamental advantages for basic research, when compared to the AM. Especially this holds true for investigations of the symbiotic stage: for gene expression studies, the fungal poly(A) mRNA can easily and specifically be isolated. The symbiotic stage corresponds to the intraradical phase in the AM, where fungal mRNA can hardly be separated from the plant mRNA. We use this advantage for the identification of symbiotically expressed ‘AM fungal’ genes. A fungal cDNA yeast-expression library was constructed and used for functional complementation of hexose transport null-mutants of Saccharomyces cerevisiae. The functionally characterised GpMST1 belongs to a new type of transporters, potentially involved in the immense C-transfer from about 80% of all land plants to AM fungi. Interestingly, the transporter probably also transfers cell wall derived pentoses; the uptake of cell wall derived sugars will be discussed. We suppose that the same approach can and should be used to characterise other key genes playing putative roles in the AM and AM-like symbioses

Arbuscular mycorrhiza (AM): the first glomeromycotan sugar transporter is characterized by using the unique geosiphon symbiosis with cyanobacteria to characterize key genes in AM (like) symbioses

International audienceIn the arbuscular mycorrhizas (AM), the symbiotic interface is the site of nutrient exchange where the mycobiont receives up to 20% of the photosynthates of the photobiont as carbohydrates. We have, for the first time, functionally characterised a monosaccharide transporter type, represented by GpMST1, putatively playing a role in this process (Schüßler, A., Martin, H., Cohen, D., Fitz, M., and Wipf, D. 2006. Characterization of a carbohydrate transporter from symbiotic glomeromycotan fungi. Nature 444:933-936.). Together with the arbuscular mycorrhizal (AM) fungi, forming endomycorrhiza with the majority of land plants, Geosiphon pyriformis belongs to the Glomeromycota. Phylogenetically it is deeply embedded within the AM forming fungi. However, Geosiphon associates symbiotically with cyanobacteria instead of – or in parallel to – plants. This unique association therefore represents a symbiosis of an ‘AM fungus’ with a photoautotrophic prokaryote. Due to this unique life style, the Geosiphon-symbiosis offers fundamental advantages for basic research, when compared to the AM. Especially this holds true for investigations of the symbiotic stage: for gene expression studies, the fungal poly(A) mRNA can easily and specifically be isolated. The symbiotic stage corresponds to the intraradical phase in the AM, where fungal mRNA can hardly be separated from the plant mRNA. We use this advantage for the identification of symbiotically expressed ‘AM fungal’ genes. A fungal cDNA yeast-expression library was constructed and used for functional complementation of hexose transport null-mutants of Saccharomyces cerevisiae. The functionally characterised GpMST1 belongs to a new type of transporters, potentially involved in the immense C-transfer from about 80% of all land plants to AM fungi. Interestingly, the transporter probably also transfers cell wall derived pentoses; the uptake of cell wall derived sugars will be discussed. We suppose that the same approach can and should be used to characterise other key genes playing putative roles in the AM and AM-like symbioses

Arbuscular mycorrhiza - studies on the geosiphon symbiosis lead to the characterization of the first glomeromycotan sugar transporter

Article Addendum International audienceThe intimate arbuscular mycorrhiza (AM) association between roots and obligate symbiotic Glomeromycota (‘AM fungi’) ‘feeds’ about 80% of land plants. AM forming fungi supply land plants with inorganic nutrients and have an enormous impact on terrestrial ecosystems. In return, AM fungi obtain up to 20% of the plant‑fixed CO2, putatively as monosaccharides. In a recent work we have reported the characterization of the first glomeromycotan monosaccharide transporter, GpMST1, and its gene sequence. We discuss that AM fungi might take up sugars deriving from plant cell‑wall material. The GpMST1 sequence delivers valuable data for the isolation of orthologues from other AM fungi and may eventually lead to the understanding of C‑flows in the AM

Molecular phylogeny and new taxa in the Archaeosporales (Clomeromycota) : Ambispora fennica gen. sp. nov., Ambisporaceae fam. nov., and emendation of Archaeospora and Archaeosporaceae

v2007o

Screenshot of the UNITE search page (http://unite.ut.ee/).

<p>This search tool allows queries of sequences based on taxonomic information and associated metadata.</p