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

Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies). Delhomme, N., Sundstrom, G., Zamani, N., Lantz, H., Lin, Y. C., Hvidsten, T. R., Hoppner, M. P., Jern, P., Van de Peer, Y., Lundeberg, J., Grabherr, M. G., & Street, N. R. PLoS One, 10(9):e0139080, September, 2015. Edition: 2015/09/29

Paper doi abstract bibtex

After performing de novo transcript assembly of \textgreater1 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.

@article{delhomme_serendipitous_2015,
	title = {Serendipitous {Meta}-{Transcriptomics}: {The} {Fungal} {Community} of {Norway} {Spruce} ({Picea} abies)},
	volume = {10},
	issn = {1932-6203 (Electronic) 1932-6203 (Linking)},
	shorttitle = {Serendipitous {Meta}-{Transcriptomics}},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26413905},
	doi = {10/f3m8d5},
	abstract = {After performing de novo transcript assembly of {\textgreater}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.},
	language = {en},
	number = {9},
	urldate = {2021-06-07},
	journal = {PLoS One},
	author = {Delhomme, N. and Sundstrom, G. and Zamani, N. and Lantz, H. and Lin, Y. C. and Hvidsten, T. R. and Hoppner, M. P. and Jern, P. and Van de Peer, Y. and Lundeberg, J. and Grabherr, M. G. and Street, N. R.},
	month = sep,
	year = {2015},
	note = {Edition: 2015/09/29},
	keywords = {Base Composition/genetics, Fungi/*genetics, Gene Expression Regulation, Fungal, Gene Expression Regulation, Plant, Picea/*genetics/*microbiology, RNA, Messenger/genetics/metabolism, Transcriptome/*genetics},
	pages = {e0139080},
}

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