Skip to Main Content
U.S. Forest Service
Caring for the land and serving people

United States Department of Agriculture

Home > Search > Publication Information

  1. Share via EmailShare on FacebookShare on LinkedInShare on Twitter
    Dislike this pubLike this pub
    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)

    Description

    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.

    Publication Notes

    • We recommend that you also print this page and attach it to the printout of the article, to retain the full citation information.
    • This article was written and prepared by U.S. Government employees on official time, and is therefore in the public domain.

    Citation

    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.

    Cited

    Google Scholar

    Keywords

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

    Related Search


    XML: View XML
Show More
Show Fewer
Jump to Top of Page
https://www.fs.usda.gov/treesearch/pubs/47689