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

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.

我们对未经过表面灭菌的22份不同挪威云杉（*Picea abies*）组织样本的逾10亿条RNA测序（RNA-seq）读长开展从头转录组组装（de novo transcript assembly）后，发现组装得到的序列包含植物、地衣与真菌的转录本。其中真菌转录本大概率由内生及附生共生体表达，表明这类生物真实存在、具有活性且代谢活跃。本研究表明，这些偶然测得的转录本不必如常规做法般仅被视为污染序列，反而能够为植物叶际（phyllosphere）研究提供重要见解。值得注意的是，我们可将这些转录本归类为主要源自座囊菌纲（Dothideomycetes）与盘菌纲（Leotiomycetes）物种；对基因家族的功能注释结果显示，这些共生体存在活跃的生长与代谢活动，尤其涉及葡萄糖摄取与代谢过程，以及基因调控。