Details
| Original language | English |
|---|---|
| Pages (from-to) | 19-32 |
| Number of pages | 14 |
| Journal | PHYTOCHEMISTRY |
| Volume | 68 |
| Issue number | 1 |
| Publication status | Published - Jan 2007 |
| Externally published | Yes |
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.
Keywords
- Arbuscular mycorrhiza, Bioinformatics, Ectomycorrhiza, Ectomycorrhizal fungi, EST-Clustering, EST-Sequencing, Glomus intraradices, in silico Profiling, Macroarrays, Medicago truncatula, Microarrays, Populus tremula, Transcriptome database
ASJC Scopus subject areas
- Biochemistry, Genetics and Molecular Biology(all)
- Biochemistry
- Biochemistry, Genetics and Molecular Biology(all)
- Molecular Biology
- Agricultural and Biological Sciences(all)
- Plant Science
- Agricultural and Biological Sciences(all)
- Horticulture
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In: PHYTOCHEMISTRY, Vol. 68, No. 1, 01.2007, p. 19-32.
Research output: Contribution to journal › Review article › Research › peer review
}
TY - JOUR
T1 - Development of bioinformatic tools to support EST-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses
AU - Küster, Helge
AU - Becker, Anke
AU - Firnhaber, Christian
AU - Hohnjec, Natalija
AU - Manthey, Katja
AU - Perlick, Andreas M.
AU - Bekel, Thomas
AU - Dondrup, Michael
AU - Henckel, Kolja
AU - Goesmann, Alexander
AU - Meyer, Folker
AU - Wipf, Daniel
AU - Requena, Natalia
AU - Hildebrandt, Ulrich
AU - Hampp, Rüdiger
AU - Nehls, Uwe
AU - Krajinski, Franziska
AU - Franken, Philipp
AU - Pühler, Alfred
N1 - Funding information: The transcriptomics work was supported by the Deutsche Forschungsgemeinschaft in the SPP 1084 “Mykorrhiza” projects Pu-28/22-1, KU1478/1-2, and Pu-28/25-3 as well as by the European Union projects MEDICAGO (QLG-CT2000-00676) and GRAIN LEGUMES (FOOD-CT-2004-506223). Helge Küster, Michael Dondrup and Natalija Hohnjec received financial support from the International Graduate School in Bioinformatics and Genome Research. We are thankful to Vivienne Gianinazzi-Pearson and Diederik van Tuinen (both INRA, Dijon, France) as well as to Jerôme Gouzy and Pascal Gamas (all CNRS-INRA, Toulouse, France) for long-lasting, fruitful collaborations in the field of M. truncatula transcriptomics. Greg May (Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA) and Chris Town (TIGR, Rockville, Maryland, USA) are acknowledged for the cooperation during the setup of a M. truncatula 16 k 70mer oligonucleotide set. We are grateful to Manuela Meyer, Eva Schulte-Berndt, and Tanja Thias (Institute for Genome Research, Center for Biotechnology, Universität Bielefeld) for their excellent technical support throughout the project.
PY - 2007/1
Y1 - 2007/1
N2 - 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.
AB - 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.
KW - Arbuscular mycorrhiza
KW - Bioinformatics
KW - Ectomycorrhiza
KW - Ectomycorrhizal fungi
KW - EST-Clustering
KW - EST-Sequencing
KW - Glomus intraradices
KW - in silico Profiling
KW - Macroarrays
KW - Medicago truncatula
KW - Microarrays
KW - Populus tremula
KW - Transcriptome database
UR - http://www.scopus.com/inward/record.url?scp=33845669590&partnerID=8YFLogxK
U2 - 10.1016/j.phytochem.2006.09.026
DO - 10.1016/j.phytochem.2006.09.026
M3 - Review article
C2 - 17081576
AN - SCOPUS:33845669590
VL - 68
SP - 19
EP - 32
JO - PHYTOCHEMISTRY
JF - PHYTOCHEMISTRY
SN - 0031-9422
IS - 1
ER -