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.
Highlights
To aid gene prediction within the Norway spruce genome project [1], we sequenced more than half a billion paired end reads (2 x 100 bps) using the oligo(dT) protocol from samples collected from various tree tissues
We identified striking differences between plant and fungal transcripts: plant sequences were on average longer (N50: 1,823 vs 453bp), exhibited higher total Fragments Per Kilobase per Million mapped reads (FPKM) expression values (79.3M vs. 0.7M), and were lower in average GC content (44.5%, vs. 53.1%, Fig 1A)
The expression specificity across samples, as measured by the tau score [8] was lower for plants, indicating that many genes were expressed in multiple tissues or samples, while fungal transcripts exhibited almost complete specificity
Summary
To aid gene prediction within the Norway spruce genome project [1], we sequenced more than half a billion paired end reads (2 x 100 bps) using the oligo(dT) protocol from samples collected from various tree tissues. All samples (see S1 Fig, detailed in S1 Table) were collected with full permission from mature Norway spruce individuals within a national, clonal archive of breeding material maintained by Skogforsk (the Forestry Research Institute of Sweden). Metatranscriptomics of Norway Spruce (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”)
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