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Basidiomycete yeasts in the cortex of ascomycete macrolichens

TLDR
Many common lichens are composed of the known ascomycete, the photosynthesizing partner, and, unexpectedly, specific basidiomycete yeasts, and their abundance correlates with previously unexplained variations in phenotype.
Abstract
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.

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Fungal Diversity Revisited: 2.2 to 3.8 Million Species

TL;DR: New evidence is examined from various sources to derive an updated estimate of global fungal diversity, concluding that the commonly cited estimate of 1.5 million species is conservative and that the actual range is properly estimated at 2.2 to 3.8 million.
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The 2016 classification of lichenized fungi in the Ascomycota and Basidiomycota – Approaching one thousand genera

TL;DR: The phylogenetic position of the 39 orders containing lichenized fungi suggests 20–30 independent lichenization events during the evolution of higher Fungi, 14–23 in the Ascomycota and 6–7 in the Basidiomycota.
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The Fungal Tree of Life: from Molecular Systematics to Genome-Scale Phylogenies.

TL;DR: This article reviews the major phyla, subphyla, and classes of the kingdom Fungi and provides brief summaries of ecologies, morphologies, and exemplar taxa and examples of how molecular phylogenetics and evolutionary genomics have advanced the understanding of fungal evolution within each of the phyla and some of the major classes.
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Fungal evolution: major ecological adaptations and evolutionary transitions.

TL;DR: A new scenario is proposed for fungal terrestralization, which considers icy environments as a transitory niche between water and emerged land and the importance of genome‐enabled inferences to envision plausible narratives and scenarios for important transitions is highlighted.
Journal ArticleDOI

Secondary metabolism in the lichen symbiosis

TL;DR: Progress in genomics, mass spectrometry and other analytical technologies are continuing to illuminate the wealth of biological and chemical diversity present within the lichen holobiome, and implementation of novel biodiscovery strategies such as metagenomic screening, coupled with synthetic biology approaches to reconstitute, re-engineer and heterologously express lichen-derived biosynthetic gene clusters in a cultivable host offer a promising means for tapping into this hitherto inaccessible wealth of natural products.
References
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Journal ArticleDOI

STAR: ultrafast universal RNA-seq aligner

TL;DR: The Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure outperforms other aligners by a factor of >50 in mapping speed.
Journal ArticleDOI

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.

TL;DR: EdgeR as mentioned in this paper is a Bioconductor software package for examining differential expression of replicated count data, which uses an overdispersed Poisson model to account for both biological and technical variability and empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference.
Journal ArticleDOI

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

TL;DR: This version of MAFFT has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update.
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