title: Development of bioinformatic tools to support EST-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses.
abstract: 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.
authors.affiliation: Institute for Genome Research, Center for Biotechnology (CeBiTec), Universität Bielefeld, Universitätsstrasse 25, 33594 Bielefeld, Germany. Helge.Kuester@Genetik.Uni-Bielefeld.DE
authors.forename: Helge
authors.initials: H
authors.lastname: Küster
authors.forename: Anke
authors.initials: A
authors.lastname: Becker
authors.forename: Christian
authors.initials: C
authors.lastname: Firnhaber
authors.forename: Natalija
authors.initials: N
authors.lastname: Hohnjec
authors.forename: Katja
authors.initials: K
authors.lastname: Manthey
authors.forename: Andreas M
authors.initials: AM
authors.lastname: Perlick
authors.forename: Thomas
authors.initials: T
authors.lastname: Bekel
authors.forename: Michael
authors.initials: M
authors.lastname: Dondrup
authors.forename: Kolja
authors.initials: K
authors.lastname: Henckel
authors.forename: Alexander
authors.initials: A
authors.lastname: Goesmann
authors.forename: Folker
authors.initials: F
authors.lastname: Meyer
authors.forename: Daniel
authors.initials: D
authors.lastname: Wipf
authors.forename: Natalia
authors.initials: N
authors.lastname: Requena
authors.forename: Ulrich
authors.initials: U
authors.lastname: Hildebrandt
authors.forename: Rüdiger
authors.initials: R
authors.lastname: Hampp
authors.forename: Uwe
authors.initials: U
authors.lastname: Nehls
authors.forename: Franziska
authors.initials: F
authors.lastname: Krajinski
authors.forename: Philipp
authors.initials: P
authors.lastname: Franken
authors.forename: Alfred
authors.initials: A
authors.lastname: Pühler
mesh_terms: 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*