title: Genome-wide identification and functional analysis of genes expressed ubiquitously in rice.
abstract: 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 4034 of these genes in rice after studying the results of Agilent 44K and Affymetrix meta-anatomical expression profiles. Among 105 genes that were characterized by loss-of-function analysis, 79 were classified as members of gene families, the majority of which were predominantly expressed. Using T-DNA insertional mutants, we examined 43 genes and found that loss of expression of six genes caused developing seed- or seedling-defective phenotypes. Of these, three are singletons without similar family members and defective phenotypes are expected from mutations. Phylogenomic analyses integrating genome-wide transcriptome data revealed the functional dominance of three ubiquitously expressed family genes. Among them, we investigated the function of Os03g19890, which is involved in ATP generation within the mitochondria during endosperm development. We also created and evaluated functional networks associated with this gene to understand the molecular mechanism. Our study provides a useful strategy for pheonome analysis of ubiquitously expressed genes in rice.
authors.affiliation: Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea; Graduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Korea. Electronic address: khjung2010@khu.ac.kr.
authors.forename: Ki-Hong
authors.initials: KH
authors.lastname: Jung
authors.affiliation: Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea.
authors.forename: Sung-Ruyl
authors.initials: SR
authors.lastname: Kim
authors.affiliation: Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea.
authors.forename: Hoi-Khoanh
authors.initials: HK
authors.lastname: Giong
authors.affiliation: Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea.
authors.forename: Minh Xuan
authors.initials: MX
authors.lastname: Nguyen
authors.affiliation: Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea.
authors.forename: Hyun-Jung
authors.initials: HJ
authors.lastname: Koh
authors.affiliation: Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea; Graduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Korea. Electronic address: genean@khu.ac.kr.
authors.forename: Gynheung
authors.initials: G
authors.lastname: An
mesh_terms: D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant / Q000235:genetics*; D012275:Oryza / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D036226:Seedlings / Q000235:genetics / Q000378:metabolism
chemical_list: D010940:Plant Proteins
keywords: functional redundancy; phylogenomic analysis; rice; systematic phenotype screening; ubiquitously expressed genes