title: OakContigDF159.1, a reference library for studying differential gene expression in Quercus robur during controlled biotic interactions: use for quantitative transcriptomic profiling of oak roots in ectomycorrhizal symbiosis.
abstract: Oaks (Quercus spp.), which are major forest trees in the northern hemisphere, host many biotic interactions, but molecular investigation of these interactions is limited by fragmentary genome data. To date, only 75 oak expressed sequence tags (ESTs) have been characterized in ectomycorrhizal (EM) symbioses. We synthesized seven beneficial and detrimental biotic interactions between microorganisms and animals and a clone (DF159) of Quercus robur. Sixteen 454 and eight Illumina cDNA libraries from leaves and roots were prepared and merged to establish a reference for RNA-Seq transcriptomic analysis of oak EMs with Piloderma croceum. Using the Mimicking Intelligent Read Assembly (MIRA) and Trinity assembler, the OakContigDF159.1 hybrid assembly, containing 65 712 contigs with a mean length of 1003 bp, was constructed, giving broad coverage of metabolic pathways. This allowed us to identify 3018 oak contigs that were differentially expressed in EMs, with genes encoding proline-rich cell wall proteins and ethylene signalling-related transcription factors showing up-regulation while auxin and defence-related genes were down-regulated. In addition to the first report of remorin expression in EMs, the extensive coverage provided by the study permitted detection of differential regulation within large gene families (nitrogen, phosphorus and sugar transporters, aquaporins). This might indicate specific mechanisms of genome regulation in oak EMs compared with other trees.
authors.affiliation: Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle/Saale, Germany.
authors.forename: Mika T
authors.initials: MT
authors.lastname: Tarkka
authors.affiliation: Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle/Saale, Germany.|Department of Community Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle/Saale, Germany.
authors.forename: Sylvie
authors.initials: S
authors.lastname: Herrmann
authors.affiliation: Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle/Saale, Germany.
authors.forename: Tesfaye
authors.initials: T
authors.lastname: Wubet
authors.affiliation: Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle/Saale, Germany.|Institute of Computer Science, Martin-Luther University, Von-Seckendorff-Platz 1, 06120, Halle/Saale, Germany.
authors.forename: Lasse
authors.initials: L
authors.lastname: Feldhahn
authors.affiliation: Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle/Saale, Germany.
authors.forename: Sabine
authors.initials: S
authors.lastname: Recht
authors.affiliation: Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle/Saale, Germany.
authors.forename: Florence
authors.initials: F
authors.lastname: Kurth
authors.affiliation: IMIT-Physiological Ecology of Plants, Auf der Morgenstelle 1, 72076, Tübingen, Germany.
authors.forename: Sarah
authors.initials: S
authors.lastname: Mailänder
authors.affiliation: Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle/Saale, Germany.|Institute of Computer Science, Martin-Luther University, Von-Seckendorff-Platz 1, 06120, Halle/Saale, Germany.
authors.forename: Markus
authors.initials: M
authors.lastname: Bönn
authors.affiliation: IMIT-Physiological Ecology of Plants, Auf der Morgenstelle 1, 72076, Tübingen, Germany.
authors.forename: Maren
authors.initials: M
authors.lastname: Neef
authors.affiliation: Section Pathology of Woody Plants, Technische Universität München, Hans-Carl-von-Carlowitz-Platz 2, 85354, Freising, Germany.|TEEG: Ecophysiology of Plants, Technische Universität München, Hans-Carl-von-Carlowitz-Platz 2, 85354, Freising, Germany.
authors.forename: Oguzhan
authors.initials: O
authors.lastname: Angay
authors.affiliation: Animal Ecology, Department of Ecology, Faculty of Biology, Philipps-Universität Marburg, Karl-von-Frisch Str. 8, 35032, Marburg, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Bacht
authors.affiliation: J.F. Blumenbach Institute of Zoology and Anthropology, Georg August University Göttingen, Berliner Str. 28, 37073, Göttingen, Germany.
authors.forename: Marcel
authors.initials: M
authors.lastname: Graf
authors.affiliation: Ecology Group, Institute of Biology, Humboldt-Universität zu Berlin, Philippstr. 13, 10115, Berlin, Germany.
authors.forename: Hazel
authors.initials: H
authors.lastname: Maboreke
authors.affiliation: Section Pathology of Woody Plants, Technische Universität München, Hans-Carl-von-Carlowitz-Platz 2, 85354, Freising, Germany.
authors.forename: Frank
authors.initials: F
authors.lastname: Fleischmann
authors.affiliation: TEEG: Ecophysiology of Plants, Technische Universität München, Hans-Carl-von-Carlowitz-Platz 2, 85354, Freising, Germany.
authors.forename: Thorsten E E
authors.initials: TEE
authors.lastname: Grams
authors.affiliation: Ecology Group, Institute of Biology, Humboldt-Universität zu Berlin, Philippstr. 13, 10115, Berlin, Germany.
authors.forename: Liliane
authors.initials: L
authors.lastname: Ruess
authors.affiliation: Department of Community Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle/Saale, Germany.|Animal Ecology, Department of Ecology, Faculty of Biology, Philipps-Universität Marburg, Karl-von-Frisch Str. 8, 35032, Marburg, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Schädler
authors.affiliation: Animal Ecology, Department of Ecology, Faculty of Biology, Philipps-Universität Marburg, Karl-von-Frisch Str. 8, 35032, Marburg, Germany.
authors.forename: Roland
authors.initials: R
authors.lastname: Brandl
authors.affiliation: J.F. Blumenbach Institute of Zoology and Anthropology, Georg August University Göttingen, Berliner Str. 28, 37073, Göttingen, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Scheu
authors.affiliation: IMIT-Physiological Ecology of Plants, Auf der Morgenstelle 1, 72076, Tübingen, Germany.
authors.forename: Silvia D
authors.initials: SD
authors.lastname: Schrey
authors.affiliation: Institute of Computer Science, Martin-Luther University, Von-Seckendorff-Platz 1, 06120, Halle/Saale, Germany.
authors.forename: Ivo
authors.initials: I
authors.lastname: Grosse
authors.affiliation: Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle/Saale, Germany.|Institute of Biology, Leipzig University, Johannisallee 21-23, 04103, Leipzig, Germany.
authors.forename: François
authors.initials: F
authors.lastname: Buscot
mesh_terms: D058448:Biota; D015536:Down-Regulation / Q000235:genetics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D038821:Mycorrhizae / Q000502:physiology*; D029963:Quercus / Q000235:genetics* / Q000382:microbiology*; D060888:Real-Time Polymerase Chain Reaction; D012015:Reference Standards; D017423:Sequence Analysis, RNA; D013559:Symbiosis / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics; D015854:Up-Regulation / Q000235:genetics