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Session 3 – Tools and Bioengineering
S3.4- BradiNet: co-expression platform and comparative transcriptomics for
Brachypodium
Marek Mutwil 1, Richard Sibout 2, Herman Höfte 2 and Staffan Persson 1
1 Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam –
Golm, Germany
2 Institut Jean-Pierre Bourgin, UMR1318-INRA-AgroParisTech, Centre de Versailles-Grignon,
Route de St-Cyr, 78026 Versailles Cedex-France
mutwil@mpimp-golm.mpg.de
Abstract
It is well documented that transcriptionally coordinated genes tend to be functionally
related and that such relationships may be conserved across different species and even
kingdoms. To exploit such relationships, we have performed microarray analysis of all
major tissues during different developmental stages of Brachypodium distachyon. The
data was used to create co-expression network for Brachypodium and included into
PlaNet database (http://aranet.mpimp-golm.mpg.de/bradinet). One major problem
with transferring knowledge from a model organism is that since plants harbor large gene
families, standard phylogenetic methods might not be sufficient to identify functional
homologs. To remedy this, we implemented a comparative network algorithm that
estimates similarities between network structures. Thus, the platform can be used to swiftly
infer similar coexpressed network vicinities within and across species and can predict the
identity of functional homologs. We exemplify this with comparative analysis of
Brachypodium cellulose synthase gene networks to find corresponding functional
homologs between Arabidopsis, Brachypodium, Medicago, poplar, rice, soybean and
wheat. The data support the contention that this platform will considerably improve
transfer of knowledge between model organisms Arabidopsis and Brachypodium and
crop species such as rice and wheat.
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