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PMID: 19535473 Published · ppublish English Journal Article

Expansion mechanisms and functional annotations of hypothetical genes in the rice genome.

Plant physiology ·Vol. 150 ·No. 4 ·2009-08-00 ·Pages 1997-2008

Jiang SY, Christoffels A, Ramamoorthy R, Ramachandran S

Abstract

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.

MeSH Terms
Evolution, Molecular Gene Duplication Gene Expression Profiling Gene Expression Regulation, Plant Genes, Plant Oligonucleotide Array Sequence Analysis Oryza/genetics RNA, Antisense/genetics RNA, Plant/genetics Retroelements/genetics Reverse Transcriptase Polymerase Chain Reaction Transcription, Genetic
Chemicals
RNA, Antisense RNA, Plant Retroelements
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Jiang Shu-Ye
Rice Functional Genomics Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604.
Christoffels Alan
Ramamoorthy Rengasamy
Ramachandran Srinivasan
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Article Info
Journal
Plant physiology
Abbr.
Plant Physiol
ISSN
0032-0889
DOI
10.1104/pp.109.139402
Published
2009-08-00
Epub
2009-00-17
Pages
1997-2008
Language
English
Region
United States
NLM ID
0401224
PMCID
PMC2719134
Subset
IM
External Links
PubMed source DOI: 10.1104/pp.109.139402 PMC Full Text View journal details
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