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

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

© 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

Bibliographische Detailangaben
Veröffentlicht in:The New phytologist. - 1979. - 199(2013), 2 vom: 11. Juli, Seite 529-540
1. Verfasser: Tarkka, Mika T (VerfasserIn)
Weitere Verfasser: Herrmann, Sylvie, Wubet, Tesfaye, Feldhahn, Lasse, Recht, Sabine, Kurth, Florence, Mailänder, Sarah, Bönn, Markus, Neef, Maren, Angay, Oguzhan, Bacht, Michael, Graf, Marcel, Maboreke, Hazel, Fleischmann, Frank, Grams, Thorsten E E, Ruess, Liliane, Schädler, Martin, Brandl, Roland, Scheu, Stefan, Schrey, Silvia D, Grosse, Ivo, Buscot, François
Format: Online-Aufsatz
Sprache:English
Veröffentlicht: 2013
Zugriff auf das übergeordnete Werk:The New phytologist
Schlagworte:Journal Article Research Support, Non-U.S. Gov't
Beschreibung
Zusammenfassung:© 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.
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
Beschreibung:Date Completed 15.01.2014
Date Revised 18.04.2021
published: Print-Electronic
CommentIn: New Phytol. 2013 Jul;199(2):308-10. - PMID 23782153
Citation Status MEDLINE
ISSN:1469-8137
DOI:10.1111/nph.12317