Development of bioinformatic tools to support EST-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses.
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.
Küster
Helge
H
Institute for Genome Research, Center for Biotechnology (CeBiTec), Universität Bielefeld, Universitätsstrasse 25, 33594 Bielefeld, Germany. Helge.Kuester@Genetik.Uni-Bielefeld.DE
Becker
Anke
A
Firnhaber
Christian
C
Hohnjec
Natalija
N
Manthey
Katja
K
Perlick
Andreas M
AM
Bekel
Thomas
T
Dondrup
Michael
M
Henckel
Kolja
K
Goesmann
Alexander
A
Meyer
Folker
F
Wipf
Daniel
D
Requena
Natalia
N
Hildebrandt
Ulrich
U
Hampp
Rüdiger
R
Nehls
Uwe
U
Krajinski
Franziska
F
Franken
Philipp
P
Pühler
Alfred
A
D019295:Computational Biology / Q000379:methods*; D020224:Expressed Sequence Tags; D038821:Mycorrhizae / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D013559:Symbiosis / Q000235:genetics*; D014158:Transcription, Genetic / Q000235:genetics*