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Expression pattern similarities support the prediction of orthologs retaining common functions after gene duplication events.
Plant Physiol. 171, 2343-2357 (2016)
Identification of functionally equivalent, orthologous genes (functional orthologs) across genomes is necessary for accurate transfer of experimental knowledge from well-characterized organisms to others. This frequently relies on automated, coding sequence-based approaches such as OrthoMCL, Inparanoid, KOG, which usually work well for one-to-one homologous states. However, this strategy does not reliably work for plants due to the occurrence of extensive gene/genome duplication. Frequently, for one query gene multiple orthologous genes are predicted in the other genome and it is not clear a priori from sequence comparison and similarity which one preserves the ancestral function. We have studied eleven organ-dependent and stress-induced gene expression patterns of 286 A. lyrata duplicated gene groups and compared them to the respective A. thaliana genes to predict putative expressologs and non-expressologs based on gene expression similarity. Promoter sequence divergence as an additional tool to substantiate functional orthology only partially overlapped with expressolog classification. By cloning eight A. lyrata homologs and complementing them in the respective four A. thaliana loss-of-function mutants we experimentally proved that predicted expressologs are indeed functional orthologs, while non-expressologs or non-functionalized orthologs are not. Our study demonstrates that even a small set of gene expression data in addition to sequence homologies are instrumental in the assignment of functional orthologs in the presence of multiple orthologs.
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Publication type
Article: Journal article
Document type
Scientific Article
Keywords
Arabidopsis-thaliana; Ribonucleotide Reductase; Leaf Development; Brassica-napus; Plant Genomes; Large Subunit; Evolution; Protein; Identification; Divergence
ISSN (print) / ISBN
0032-0889
e-ISSN
1532-2548
Journal
Plant Physiology
Quellenangaben
Volume: 171,
Issue: 4,
Pages: 2343-2357
Publisher
American Society of Plant Biologists (ASPB)
Publishing Place
Rockville
Non-patent literature
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Reviewing status
Peer reviewed