This Article Full Text Full Text (PDF) Supplemental Data All Versions of this Article: 150/4/1997    most recent pp.109.139402v1 Alert me when this article is cited Alert me if a correction is posted Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via CrossRef Citing Articles via Google Scholar Google Scholar Articles by Jiang, S.-Y. Articles by Ramachandran, S. Search for Related Content PubMed PubMed Citation Articles by Jiang, S.-Y. Articles by Ramachandran, S. Agricola Articles by Jiang, S.-Y. Articles by Ramachandran, S. Related Collections The Grasses

GENETICS, GENOMICS, AND MOLECULAR EVOLUTION

Expansion Mechanisms and Functional Annotations of Hypothetical Genes in the Rice Genome^[W]

Rice Functional Genomics Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604 (S.-Y.J., R.R., S.R.); and South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa (A.C.)

In each completely sequenced genome, 30% to 50% of genes are annotated as uncharacterized hypothetical genes. In the rice (Oryza sativa) genome, 10,918 hypothetical genes were annotated in the latest version (release 6) of the Michigan State University rice genome annotation. We have implemented an integrative approach to analyze their duplication/expansion and function. The analyses show that tandem/segmental duplication and transposition/retrotransposition have significantly contributed to the expansion of hypothetical genes despite their different contribution rates. A total of 3,769 hypothetical genes have been detected from retrogene, tandem, segmental, Pack-MULE, or long terminated direct repeat-related duplication/expansion. The nonsynonymous substitutions per site and synonymous substitutions per site analyses showed that 21.65% of them were still functional, accounting for 7.47% of total hypothetical genes. Global expression analyses have identified 1,672 expressed hypothetical genes. Among them, 415 genes might function in a developmental stage-specific manner. Antisense strand expression and small RNA analyses have demonstrated that a high percentage of these hypothetical genes might play important roles in negatively regulating gene expression. Homologous searches against Arabidopsis (Arabidopsis thaliana), maize (Zea mays), sorghum (Sorghum bicolor), and indica rice genomes suggest that most of the hypothetical genes could be annotated from recently evolved genomic sequences. These data advance the understanding of rice hypothetical genes as being involved in lineage-specific expansion and that they function in a specific developmental stage. Our analyses also provide a valuable means to facilitate the characterization and functional annotation of hypothetical genes in other organisms.

^[W] The online version of this article contains Web-only data.

www.plantphysiol.org/cgi/doi/10.1104/pp.109.139402

^* Corresponding author; e-mail sri{at}tll.org.sg.

Received April 2, 2009; accepted June 15, 2009; published June 17, 2009.