title: Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies).
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.
authors.affiliation: Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Delhomme
authors.affiliation: Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden; Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
authors.forename: Görel
authors.initials: G
authors.lastname: Sundström
authors.affiliation: Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden; Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
authors.forename: Neda
authors.initials: N
authors.lastname: Zamani
authors.affiliation: Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden; Bioinformatics Infrastructure for Life Sciences (BILS), Uppsala, Sweden.
authors.forename: Henrik
authors.initials: H
authors.lastname: Lantz
authors.affiliation: Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics (Ghent University), Ghent, Belgium.
authors.forename: Yao-Cheng
authors.initials: YC
authors.lastname: Lin
authors.affiliation: Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden; Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
authors.forename: Torgeir R
authors.initials: TR
authors.lastname: Hvidsten
authors.affiliation: Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden; Bioinformatics Infrastructure for Life Sciences (BILS), Uppsala, Sweden.
authors.forename: Marc P
authors.initials: MP
authors.lastname: Höppner
authors.affiliation: Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
authors.forename: Patric
authors.initials: P
authors.lastname: Jern
authors.affiliation: Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics (Ghent University), Ghent, Belgium; Genomics Research Institute, University of Pretoria, Pretoria, South Africa.
authors.forename: Yves
authors.initials: Y
authors.lastname: Van de Peer
authors.affiliation: School of Biotechnology, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden.
authors.forename: Joakim
authors.initials: J
authors.lastname: Lundeberg
authors.affiliation: Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden; Bioinformatics Infrastructure for Life Sciences (BILS), Uppsala, Sweden.
authors.forename: Manfred G
authors.initials: MG
authors.lastname: Grabherr
authors.affiliation: Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden.
authors.forename: Nathaniel R
authors.initials: NR
authors.lastname: Street
mesh_terms: D001482:Base Composition / Q000235:genetics; D005658:Fungi / Q000235:genetics*; D015966:Gene Expression Regulation, Fungal; D018506:Gene Expression Regulation, Plant; D028222:Picea / Q000235:genetics* / Q000382:microbiology*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome / Q000235:genetics*
chemical_list: D012333:RNA, Messenger