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    Author(s): Cheryl R. Kuske; Cedar N. Hesse; Jean F. Challacombe; Daniel Cullen; Joshua R. Herr; Rebecca C. Mueller; Adrian Tsang; Rytas Vilgalys
    Date: 2015
    Source: Fungal Ecology, Corrected proof. 5p.
    Publication Series: Scientific Journal (JRNL)
    Station: Forest Products Laboratory
    PDF: Download Publication  (494.24 KB)


    The ability to extract and purify messenger RNA directly from plants, decomposing organic matter and soil, followed by highthroughput sequencing of the pool of expressed genes, has spawned the emerging research area of metatranscriptomics. Each metatranscriptome provides a snapshot of the composition and relative abundance of actively transcribed genes, and thus provides an assessment of the interactions between soil microorganisms and plants, and collective microbial metabolic processes in many environments. We highlight current approaches for analysis of fungal transcriptome and metatranscriptome datasets across a gradient of community complexity, and note benefits and pitfalls associated with those approaches. We discuss knowledge gaps that limit our current ability to interpret metatranscriptome datasets and suggest future research directions that will require concerted efforts within the scientific community.

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    • This article was written and prepared by U.S. Government employees on official time, and is therefore in the public domain.


    Kuske, Cheryl R.; Hesse, Cedar N.; Challacombe, Jean F.; Cullen, Daniel; Herr, Joshua R.; Mueller, Rebecca C.; Tsang, Adrian; Vilgalys, Rytas. 2015. Prospects and challenges for fungal metatranscriptomics of complex communities. Fungal Ecology, Corrected proof. 5p.


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    Environmental RNA, Fungal metabolism, Fungal transcriptome, K-mer, Metatranscriptome, Sequence databases

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