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Title: Prospects and challenges for fungal metatranscriptomics of complex communities

Source: Fungal Ecology, Corrected proof. 5p.

Author(s)Kuske, Cheryl R.; Hesse, Cedar N.; Challacombe, Jean F.; Cullen, Daniel; Herr, Joshua R.; Mueller, Rebecca C.; Tsang, Adrian; Vilgalys, Rytas

Publication Year: 2015  View PDF »

Category: Journal Articles
Associated Research Project(s):   FPL-4712-4B

Abstract: 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.

Keywords: Environmental RNA; Fungal metabolism; Fungal transcriptome; K-mer; Metatranscriptome; Sequence databases

Publication Review Process: Formally Refereed

File size: 494 kb(s)

Date posted: 02/11/2015

This publication is also viewable on Treesearch:  view
RITS Product ID: 72153
Current FPL Scientist associated with this product
Cullen, Daniel
Research Microbiologist
  

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