Development of bioinformatic tools to support EST-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses

Küster H, Becker A, Firnhaber C, Hohnjec N, Manthey K, Perlick AM, Bekel T, Dondrup M, Henckel K, Goesmann A, Meyer F, et al. (2007)
Phytochemistry 68(1): 19-32.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Abstract / Bemerkung
The great majority of terrestrial plants enters a beneficial arbuscular mycorrhiza (AM) or ectomycorrhiza (ECM) symbiosis with soil fungi. In the SPP 1084 "MolMyk: Molecular Basics of Mycorrhizal Symbioses", high-throughput EST-sequencing was performed to obtain snapshots of the plant and fungal transcriptome in mycorrhizal roots and in extraradical hyphae. To focus activities, the interactions between Medicago truncatula and Glomus intraradices as well as Populus tremula and Amanita muscaria were selected as models for AM and ECM symbioses, respectively. Together, almost, 20.000 expressed sequence tags (ESTs) were generated from different random and suppressive subtractive hybridization (SSH) cDNA libraries, providing a comprehensive overview of the mycorrhizal transcriptome. To automatically cluster and annotate EST-sequences, the BioMake and SAMS software tools were developed. In connection with the eNorthern software SteN, plant genes with a predicted mycorrhiza-induced expression were identified. To support experimental transcriptome profiling, macro- and microarray tools have been constructed for the two model mycorrhizae, based either on PCR-amplified cDNAs or 70mer oligonucleotides. These arrays were used to profile the transcriptome of AM and ECM roots under different conditions, and the data obtained were uploaded to the ArrayLIMS and EMMA databases that are designed to store and evaluate expression profiles from DNA arrays. Together, the EST- and transcriptome databases can be mined to identify candidate genes for targeted functional studies.
Stichworte
macroarrays; microarrays; mycorrhiza; bioinformatics; EST-sequencing; Glomus intraradices; transcriptome database; in silico profiling; EST-clustering; ectomycorrhizal fungi; Populus tremula; ectomycorrhiza; Transcriptome database; Arbuscular; Medicago truncatula
Erscheinungsjahr
2007
Zeitschriftentitel
Phytochemistry
Band
68
Ausgabe
1
Seite(n)
19-32
ISSN
0031-9422
Page URI
https://pub.uni-bielefeld.de/record/1894739

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Küster H, Becker A, Firnhaber C, et al. Development of bioinformatic tools to support EST-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses. Phytochemistry. 2007;68(1):19-32.
Küster, H., Becker, A., Firnhaber, C., Hohnjec, N., Manthey, K., Perlick, A. M., Bekel, T., et al. (2007). Development of bioinformatic tools to support EST-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses. Phytochemistry, 68(1), 19-32. doi:10.1016/j.phytochem.2006.09.026
Küster, H., Becker, A., Firnhaber, C., Hohnjec, N., Manthey, K., Perlick, A. M., Bekel, T., Dondrup, M., Henckel, K., Goesmann, A., et al. (2007). Development of bioinformatic tools to support EST-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses. Phytochemistry 68, 19-32.
Küster, H., et al., 2007. Development of bioinformatic tools to support EST-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses. Phytochemistry, 68(1), p 19-32.
H. Küster, et al., “Development of bioinformatic tools to support EST-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses”, Phytochemistry, vol. 68, 2007, pp. 19-32.
Küster, H., Becker, A., Firnhaber, C., Hohnjec, N., Manthey, K., Perlick, A.M., Bekel, T., Dondrup, M., Henckel, K., Goesmann, A., Meyer, F., Wipf, D., Requena, N., Hildebrandt, U., Hampp, R., Nehls, U., Krajinski, F., Franken, P., Pühler, A.: Development of bioinformatic tools to support EST-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses. Phytochemistry. 68, 19-32 (2007).
Küster, Helge, Becker, Anke, Firnhaber, Christian, Hohnjec, Natalija, Manthey, Katja, Perlick, Andreas M., Bekel, Thomas, Dondrup, Michael, Henckel, Kolja, Goesmann, Alexander, Meyer, Folker, Wipf, Daniel, Requena, Natalia, Hildebrandt, Ulrich, Hampp, Rüdiger, Nehls, Uwe, Krajinski, Franziska, Franken, Philipp, and Pühler, Alfred. “Development of bioinformatic tools to support EST-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses”. Phytochemistry 68.1 (2007): 19-32.

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