These authors contributed equally to this work.
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
Article first published online: 15 MAY 2013
© 2013 The Authors. New Phytologist © 2013 New Phytologist Trust
Volume 199, Issue 2, pages 529–540, July 2013
How to Cite
Tarkka, M. T., Herrmann, S., Wubet, T., Feldhahn, L., Recht, S., Kurth, F., Mailänder, S., Bönn, M., Neef, M., Angay, O., Bacht, M., Graf, M., Maboreke, H., Fleischmann, F., Grams, T. E. E., Ruess, L., Schädler, M., Brandl, R., Scheu, S., Schrey, S. D., Grosse, I. and Buscot, F. (2013), 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. New Phytologist, 199: 529–540. doi: 10.1111/nph.12317
- Issue published online: 19 JUN 2013
- Article first published online: 15 MAY 2013
- Manuscript Accepted: 2 APR 2013
- Manuscript Received: 26 FEB 2013
- German Science Foundation (DFG). Grant Numbers: BU 941/20-1, GR 1881/3-1, RU 780/5-1, SCHA 1242/4-1, SCHE 376/26-1, SCHR 1257/1-1, TA 290/4-1
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Fig. S1 Strategy for removing reads from oak-interacting organisms.
Fig. S2 Representation of reads with homology to Arabidopsis accessions in 16 pedunculate oak Roche 454 transcript libraries.
Fig. S3 Comparison of the oak assemblies generated by the MIRA and Trinity assembly programs with reference databases.
Fig. S4 Relatedness of the contigs in the OakContigDF159.1 reference transcriptome to sequences in the GenBank nr database.
Fig. S5 Classification of contigs in the OakContigDF159.1 reference transcriptome by Gene Ontology terms.
Fig. S6 Comparison of coverage of global KEGG metabolic pathways by the OakContigDF159.1 reference transcriptome relative to the Arabidopsis thaliana proteome.
Fig. S7 Mycorrhiza formation on oak roots leads to increased transcript abundances of contigs associated with starch metabolism in comparison with the abundance in fine roots.
Table S1 Quantitative polymerase chain reaction primers
Table S2 Numbers and lengths of oak transcripts obtained by Roche 454 sequencing
Table S3 Transcripts in roots and leaves of oak DF159 microcuttings and in EMs synthesized with Piloderma croceum as revealed by Illumina sequencing
Table S4 GO annotation of contigs in the OakContigDF159.1 reference transcriptome
Table S5 GO enrichment analysis of EMs synthesized between pedunculate oak DF159 microcuttings and Piloderma croceum
Table S6 Differentially expressed transcripts in EMs synthesized between microcuttings of the pedunculate oak clone DF159 and Piloderma croceum
Methods S1 Supporting methods.