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Plant Mol Biol. 2007 Sep;65(1-2):205-17. Epub 2007 Jul 20.

Local coexpression domains in the genome of rice show no microsynteny with Arabidopsis domains.

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  • 1Applied Bioinformatics, Plant Research International, Plant Sciences Group, Wageningen University and Research Centre, Wageningen, The Netherlands.

Abstract

Chromosomal coexpression domains are found in a number of different genomes under various developmental conditions. The size of these domains and the number of genes they contain vary. Here, we define local coexpression domains as adjacent genes where all possible pair-wise correlations of expression data are higher than 0.7. In rice, such local coexpression domains range from predominantly two genes, up to 4, and make up approximately 5% of the genomic neighboring genes, when examining different expression platforms from the public domain. The genes in local coexpression domains do not fall in the same ontology category significantly more than neighboring genes that are not coexpressed. Duplication, orientation or the distance between the genes does not solely explain coexpression. The regulation of coexpression is therefore thought to be regulated at the level of chromatin structure. The characteristics of the local coexpression domains in rice are strikingly similar to such domains in the Arabidopsis genome. Yet, no microsynteny between local coexpression domains in Arabidopsis and rice could be identified. Although the rice genome is not yet as extensively annotated as the Arabidopsis genome, the lack of conservation of local coexpression domains may indicate that such domains have not played a major role in the evolution of genome structure or in genome conservation.

PMID:
17641976
[PubMed - indexed for MEDLINE]
PMCID:
PMC2039854
Free PMC Article

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