43 research outputs found
Genome sequencing provides insight into the reproductive biology, nutritional mode and ploidy of the fern pathogen M ixia osmundae
Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/106716/1/nph12653.pd
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Genome sequencing provides insight into the reproductive biology, nutritional mode and ploidy of the fern pathogen Mixia osmundae
Mixia osmundae (Basidiomycota, Pucciniomycotina) represents a monotypic class containing
an unusual fern pathogen with incompletely understood biology. We sequenced and analyzed
the genome of M. osmundae, focusing on genes that may provide some insight into its
mode of pathogenicity and reproductive biology.
Mixia osmundae has the smallest plant pathogenic basidiomycete genome sequenced to
date, at 13.6 Mb, with very few repeats, high gene density, and relatively few significant gene
family gains.
The genome shows that the yeast state of M. osmundae is haploid and the lack of segregation
of mating genes suggests that the spores produced on Osmunda spp. fronds are probably
asexual. However, our finding of a complete complement of mating and meiosis genes suggests
the capacity to undergo sexual reproduction. Analyses of carbohydrate active enzymes
suggest that this fungus is a biotroph with the ability to break down several plant cell wall
components.
Analyses of publicly available sequence data show that other Mixia members may exist on
other plant hosts and with a broader distribution than previously known.Keywords: Fungal genomics, Myxomycetes, CAZy, Osmunda spp., Biotrophic fungi, Sporogenesi
FungalTraits:A user-friendly traits database of fungi and fungus-like stramenopiles
The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies. Over the past decades, rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats. Yet, in spite of the progress of molecular methods, knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging. In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels. Combining the information from previous efforts such as FUNGuild and Fun(Fun) together with involvement of expert knowledge, we reannotated 10,210 and 151 fungal and Stramenopila genera, respectively. This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera, designed for rapid functional assignments of environmental studies. In order to assign the trait states to fungal species hypotheses, the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences. On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1% dissimilarity threshold
001_get_longest_transcript
Python script for identifying longest transcript
Basidiomycete yeasts in the cortex of ascomycete macrolichens
For over 140 years, lichens have been regarded as a symbiosis between a single fungus, usually an ascomycete, and a photosynthesizing partner. Other fungi have long been known to occur as occasional parasites or endophytes, but the one lichen–one fungus paradigm has seldom been questioned. Here we show that many common lichens are composed of the known ascomycete, the photosynthesizing partner, and, unexpectedly, specific basidiomycete yeasts. These yeasts are embedded in the cortex, and their abundance correlates with previously unexplained variations in phenotype. Basidiomycete lineages maintain close associations with specific lichen species over large geographical distances and have been found on six continents. The structurally important lichen cortex, long treated as a zone of differentiated ascomycete cells, appears to consistently contain two unrelated fungi
Data from: Basidiomycete yeasts in the cortex of ascomycete macrolichens
For over 140 years, lichens have been regarded as a symbiosis between a single fungus, usually an ascomycete, and a photosynthesizing partner. Other fungi have long been known to occur as occasional parasites or endophytes, but the one lichen–one fungus paradigm has seldom been questioned. Here we show that many common lichens are composed of the known ascomycete, the photosynthesizing partner, and, unexpectedly, specific basidiomycete yeasts. These yeasts are embedded in the cortex, and their abundance correlates with previously unexplained variations in phenotype. Basidiomycete lineages maintain close associations with specific lichen species over large geographical distances and have been found on six continents. The structurally important lichen cortex, long treated as a zone of differentiated ascomycete cells, appears to consistently contain two unrelated fungi
FigS14_RAxML_bipartitions.cystosSSU_120316_correct_names.test
Tree file underlying Fig. S14. See readme_align.tx
readme_scripts
File describing the scripts included in this Dryad accessio