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

Medientyp: E-Artikel
Titel: 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
Beteiligte: Tarkka, Mika T.; 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
Erschienen: Wiley, 2013
Erschienen in: New Phytologist
Sprache: Englisch
DOI: 10.1111/nph.12317
ISSN: 0028-646X; 1469-8137
Entstehung:
Anmerkungen:
Beschreibung: <jats:title>Summary</jats:title><jats:p> <jats:list list-type="bullet"> <jats:list-item><jats:p>Oaks (<jats:italic>Quercus</jats:italic> 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 (<jats:styled-content style="fixed-case">EST</jats:styled-content>s) have been characterized in ectomycorrhizal (<jats:styled-content style="fixed-case">EM</jats:styled-content>) symbioses.</jats:p></jats:list-item> <jats:list-item><jats:p>We synthesized seven beneficial and detrimental biotic interactions between microorganisms and animals and a clone (<jats:styled-content style="fixed-case">DF</jats:styled-content>159) of <jats:italic>Quercus robur</jats:italic>. Sixteen 454 and eight Illumina <jats:styled-content style="fixed-case">cDNA</jats:styled-content> libraries from leaves and roots were prepared and merged to establish a reference for <jats:styled-content style="fixed-case">RNA</jats:styled-content>‐Seq transcriptomic analysis of oak EMs with <jats:italic>Piloderma croceum</jats:italic>.</jats:p></jats:list-item> <jats:list-item><jats:p>Using the Mimicking Intelligent Read Assembly (<jats:styled-content style="fixed-case">MIRA</jats:styled-content>) and Trinity assembler, the OakContig<jats:styled-content style="fixed-case">DF</jats:styled-content>159.1 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 <jats:styled-content style="fixed-case">EMs</jats:styled-content>, 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.</jats:p></jats:list-item> <jats:list-item><jats:p>In addition to the first report of remorin expression in <jats:styled-content style="fixed-case">EMs</jats:styled-content>, 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.</jats:p></jats:list-item> </jats:list> </jats:p>
Zugangsstatus: Freier Zugang

Nur in Feld suchen:

Zuletzt gesuchte Begriffe: