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Title: Prospects and challenges for fungal metatranscriptomes of complex communities

Abstract

We report that the ability to extract and purify messenger RNA directly from plants, decomposing organic matter and soil, followed by high-throughput 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. Finally, 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.

Authors:
 [1];  [1];  [1]; ORCiD logo [2];  [3];  [1];  [4];  [5]
  1. Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Bioscience Division
  2. Michigan State Univ., East Lansing, MI (United States). Dept. of Microbiology and Molecular Genetics
  3. Univ. of Wisconsin, Madison, WI (United States). United States Department of Agriculture, Forest Products Lab.
  4. Concordia Univ., Montreal, QC (Canada). Centre for Structural and Functional Genomics
  5. Duke Univ., Durham, NC (United States). Biological Sciences
Publication Date:
Research Org.:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1329856
Alternate Identifier(s):
OSTI ID: 1357068
Report Number(s):
LA-UR-14-28371
Journal ID: ISSN 1754-5048
Grant/Contract Number:  
AC52-06NA25396; 2014LANLF260; LA-UR-14-28371
Resource Type:
Accepted Manuscript
Journal Name:
Fungal Ecology
Additional Journal Information:
Journal Volume: 14; Journal ID: ISSN 1754-5048
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES; Environmental RNA; Fungal metabolism; Fungal transcriptome; K-mer; Metatranscriptome; Sequence databases

Citation Formats

Kuske, Cheryl Rae, Hesse, Cedar Nelson, Challacombe, Jean Faust, Herr, Joshua R., Cullen, Daniel, Mueller, Rebecca C., Tsang, Adrian, and Vilgalys, Rytas. Prospects and challenges for fungal metatranscriptomes of complex communities. United States: N. p., 2015. Web. doi:10.1016/j.funeco.2014.12.005.
Kuske, Cheryl Rae, Hesse, Cedar Nelson, Challacombe, Jean Faust, Herr, Joshua R., Cullen, Daniel, Mueller, Rebecca C., Tsang, Adrian, & Vilgalys, Rytas. Prospects and challenges for fungal metatranscriptomes of complex communities. United States. doi:10.1016/j.funeco.2014.12.005.
Kuske, Cheryl Rae, Hesse, Cedar Nelson, Challacombe, Jean Faust, Herr, Joshua R., Cullen, Daniel, Mueller, Rebecca C., Tsang, Adrian, and Vilgalys, Rytas. Thu . "Prospects and challenges for fungal metatranscriptomes of complex communities". United States. doi:10.1016/j.funeco.2014.12.005. https://www.osti.gov/servlets/purl/1329856.
@article{osti_1329856,
title = {Prospects and challenges for fungal metatranscriptomes of complex communities},
author = {Kuske, Cheryl Rae and Hesse, Cedar Nelson and Challacombe, Jean Faust and Herr, Joshua R. and Cullen, Daniel and Mueller, Rebecca C. and Tsang, Adrian and Vilgalys, Rytas},
abstractNote = {We report that the ability to extract and purify messenger RNA directly from plants, decomposing organic matter and soil, followed by high-throughput 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. Finally, 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.},
doi = {10.1016/j.funeco.2014.12.005},
journal = {Fungal Ecology},
number = ,
volume = 14,
place = {United States},
year = {2015},
month = {1}
}

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