Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies)

PLoS One. 2015 Sep 28;10(9):e0139080. doi: 10.1371/journal.pone.0139080. eCollection 2015.

Abstract

After performing de novo transcript assembly of >1 billion RNA-Sequencing reads obtained from 22 samples of different Norway spruce (Picea abies) tissues that were not surface sterilized, we found that assembled sequences captured a mix of plant, lichen, and fungal transcripts. The latter were likely expressed by endophytic and epiphytic symbionts, indicating that these organisms were present, alive, and metabolically active. Here, we show that these serendipitously sequenced transcripts need not be considered merely as contamination, as is common, but that they provide insight into the plant's phyllosphere. Notably, we could classify these transcripts as originating predominantly from Dothideomycetes and Leotiomycetes species, with functional annotation of gene families indicating active growth and metabolism, with particular regards to glucose intake and processing, as well as gene regulation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Composition / genetics
  • Fungi / genetics*
  • Gene Expression Regulation, Fungal
  • Gene Expression Regulation, Plant
  • Picea / genetics*
  • Picea / microbiology*
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Transcriptome / genetics*

Substances

  • RNA, Messenger

Grants and funding

The authors would like to acknowledge support from the Knut and Alice Wallenberg Foundation. Additional funding was provided by the Swedish Research Council (VR), the Swedish Governmental Agency for Innovation Systems (Vinnova), the Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning (Formas), the Swedish foundation for Strategic Research (SSF), the Trees and Crops for the Future project, and Ghent University (Multidisciplinary Research Partnership “Bioinformatics: from nucleotides to networks”).