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Serendipitous meta-transcriptomics : the fungal community of Norway spruce (Picea abies)

(2015) PLOS ONE. 10(9).
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Bioinformatics: from nucleotids to networks (N2N)
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.
Keywords
SEQUENCE, RNA-SEQ DATA, REFERENCE GENOME

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Citation

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Chicago
Delhomme, Nicolas, Gorel Sundstrom, Neda Zamani, Henrik Lantz, Yao-Cheng Lin, Torgeir R Hvidsten, Marc P Hoppner, et al. 2015. “Serendipitous Meta-transcriptomics : the Fungal Community of Norway Spruce (Picea Abies).” Plos One 10 (9).
APA
Delhomme, N., Sundstrom, G., Zamani, N., Lantz, H., Lin, Y.-C., Hvidsten, T. R., Hoppner, M. P., et al. (2015). Serendipitous meta-transcriptomics : the fungal community of Norway spruce (Picea abies). PLOS ONE, 10(9).
Vancouver
1.
Delhomme N, Sundstrom G, Zamani N, Lantz H, Lin Y-C, Hvidsten TR, et al. Serendipitous meta-transcriptomics : the fungal community of Norway spruce (Picea abies). PLOS ONE. 2015;10(9).
MLA
Delhomme, Nicolas, Gorel Sundstrom, Neda Zamani, et al. “Serendipitous Meta-transcriptomics : the Fungal Community of Norway Spruce (Picea Abies).” PLOS ONE 10.9 (2015): n. pag. Print.
@article{6970358,
  abstract     = {After performing de novo transcript assembly of {\textrangle}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.},
  articleno    = {e0139080},
  author       = {Delhomme, Nicolas and Sundstrom, Gorel and Zamani, Neda and Lantz, Henrik and Lin, Yao-Cheng and Hvidsten, Torgeir R and Hoppner, Marc P and Jern, Patric and Van de Peer, Yves and Lundeberg, Joakim and Grabherr, Manfred G and Street, Nathaniel R},
  issn         = {1932-6203},
  journal      = {PLOS ONE},
  keyword      = {SEQUENCE,RNA-SEQ DATA,REFERENCE GENOME},
  language     = {eng},
  number       = {9},
  pages        = {9},
  title        = {Serendipitous meta-transcriptomics : the fungal community of Norway spruce (Picea abies)},
  url          = {http://dx.doi.org/10.1371/journal.pone.0139080},
  volume       = {10},
  year         = {2015},
}

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