Genome-wide Identification and Functional Analysis of Genes Expressed Ubiquitously in Rice

Genes that are expressed ubiquitously throughout all developmental stages are thought to be necessary for basic biological or cellular functions. Therefore, determining their biological roles is a great challenge. We identified 4,034 of these genes in rice after studying the results of Agilent 44K and Affymetrix meta-anatomical expression profiles. Among the 105 that were characterized by loss-of-function analysis, 79 were classified as members of gene families, with the majority of them being predominantly expressed. Using T-DNA insertional mutants, we examined 43 genes and found that loss-of-expression in six caused developing seed- or seedling-defective phenotypes. Of them, three are singletons without same family members and easily expect the defective phenotypes by the mutations. Phylogenomic analyses integrating genome-wide transcriptome data revealed the functional dominance of three ubiquitously expressed family genes. From them, we investigated the role of Os03g19890, which is involved in ATP generation within the mitochondria during endosperm development. We also created and evaluated functional networks associated with that gene to understand the molecular mechanism. Our study will provide useful strategy for pheonome analysis of ubiquitously expressed genes.