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.
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Delhomme, Nicolas; Sundstrom, Gorel; Zamani, Neda; Lantz, Henrik; Lin, Yao-Cheng; Hvidsten, Torgeir R.; Hoppner, Marc P.; Jern, Patric; Van de Peer, Yves; Lundeberg, Joakim; Grabherr, Manfred G.; Street, Nathaniel R.
PLOS ONE, 10 (9):10.1371/journal.pone.0139080 SEP 28 2015