Article

Plant Molecular Biology

, Volume 65, Issue 1, pp 205-217

Open Access This content is freely available online to anyone, anywhere at any time.

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

  • Xin-Ying RenAffiliated withApplied Bioinformatics, Plant Research International, Plant Sciences Group, Wageningen University and Research CentreLaboratory of Bioinformatics, Plant Sciences Group, Wageningen University and Research Centre
  • , Willem J. StiekemaAffiliated withLaboratory of Bioinformatics, Plant Sciences Group, Wageningen University and Research CentreCentre for BioSystems Genomics
  • , Jan-Peter NapAffiliated withApplied Bioinformatics, Plant Research International, Plant Sciences Group, Wageningen University and Research CentreCentre for BioSystems Genomics Email author 

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 ∼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.

Keywords

Arabidopsis Coexpression domain Higher-order chromatin structures Microsynteny Rice