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Combining genetic diversity, informatics and metabolomics to facilitate annotation of plant gene function

Nature Protocols volume 5, pages 1210–1227 (2010)Cite this article

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Abstract

Given the ever-increasing number of species for which full-genome sequencing has been realized, there is a rising burden for gene functional annotation. In this study, we provide a detailed protocol that combines co-response gene analysis (using target genes of known function to allow the identification of nonannotated genes likely to be involved in a certain metabolic process) with the identification of target compounds through metabolomics. Strategies exist for applying this information to populations generated by both forward and reverse genetics approaches, although none of these are facile. This approach can also be used as a tool to identify unknown mass-spectral peaks representing new or unusual secondary metabolites, which is currently the major challenge of this analytical research field.

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Figure 1: An overview of the experimental design of metabolomics-based gene annotation.
Figure 2: A detailed checklist for experimental design for the identification of transcription factor function.
Figure 3: Workflow for peak annotation.
Figure 4: Example coregulation network analysis of the shikimate and phenolic pathways using coexpression database calculated from publicly available microarray data.
Figure 5: An overview of the experimental and bioinformatic-based procedure for pathway prediction.
Figure 6: Timeline for the protocol.
Figure 7: Identification of metabolite quantitative trait loci (QTL) as a means of gene annotation.
Figure 8: An example of an anticipated result of flavonoid profiling of Arabidopsis accessions (Col-0, La-er and Ms-0) for finding new flavonoid glycosyltransferases.

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Acknowledgements

We thank K. Saito, M. Hirai-Yokota and M. Arita of RIKEN PSC and B. Usadel of MPIMP for useful discussions. T.T. was supported by a fellowship from the Alexander von Humboldt foundation.

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  1. Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany

    Takayuki Tohge & Alisdair R Fernie

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  1. Takayuki Tohge
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T.T. and A.R.F. wrote the manuscript.

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Tohge, T., Fernie, A. Combining genetic diversity, informatics and metabolomics to facilitate annotation of plant gene function. Nat Protoc 5, 1210–1227 (2010). https://doi.org/10.1038/nprot.2010.82

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