ArticleNucleic acids research2009
Structure and expression analysis of rice paleo duplications.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Ancient allopolyploidy and specific subgenomic evolution drove the radiation of poplars and willows.Nature communications · 2025Article
- Genome-wide identification ofPeerJ · 2023Article
- The complex genome and adaptive evolution of polyploid Chinese pepper (Zanthoxylum armatum and Zanthoxylum bungeanum).Plant biotechnology journal · 2023Article
- Evolution of the DEHYDRATION-RESPONSIVE ELEMENT-BINDING PROTEIN subfamily in green plants.Plant physiology · 2022Article
- Rapid functional divergence after small-scale gene duplication in grasses.BMC evolutionary biology · 2019Article
- Hierarchically Aligning 10 Legume Genomes Establishes a Family-Level Genomics Platform.Plant physiology · 2017Article
- Expression Pattern Similarities Support the Prediction of Orthologs Retaining Common Functions after Gene Duplication Events.Plant physiology · 2016Article
- Evolution of Gene Duplication in Plants.Plant physiology · 2016Review
- MYB31/MYB42 Syntelogs Exhibit Divergent Regulation of Phenylpropanoid Genes in Maize, Sorghum and Rice.Scientific reports · 2016Article
- Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum.BMC genomics · 2016Article
- Structure, phylogeny, allelic haplotypes and expression of sucrose transporter gene families in Saccharum.BMC genomics · 2016Article
- Impacts of Whole-Genome Triplication on MIRNA Evolution in Brassica rapa.Genome biology and evolution · 2015Article
- Article
- Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence.Genome biology and evolution · 2014Article
- Diversification of the plant-specific hybrid glycine-rich protein (HyGRP) genes in cereals.Frontiers in plant science · 2014Article
- The barley UNICULM2 gene resides in a centromeric region and may be associated with signaling and stress responses.Functional & integrative genomics · 2013Article
- Construction of a rice glycoside hydrolase phylogenomic database and identification of targets for biofuel research.Frontiers in plant science · 2013Article
- Identification, nomenclature, and evolutionary relationships of mitogen-activated protein kinase (MAPK) genes in soybean.Evolutionary bioinformatics online · 2013Article
- Grass microRNA gene paleohistory unveils new insights into gene dosage balance in subgenome partitioning after whole-genome duplication.The Plant cell · 2012Article
- Emerging knowledge from genome sequencing of crop species.Molecular biotechnology · 2012Review
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Having a well-known history of genome duplication, rice is a good model for studying structural and functional evolution of paleo duplications. Improved sequence alignment criteria were used to characterize 10 major chromosome-to-chromosome duplication relationships associated with 1440 paralogous pairs, covering 47.8% of the rice genome, with 12.6% of genes that are conserved within sister blocks. Using a micro-array experiment, a genome-wide expression map has been produced, in which 2382 genes show significant differences of expression in root, leaf and grain. By integrating both structural (1440 paralogous pairs) and functional information (2382 differentially expressed genes), we identified 115 paralogous gene pairs for which at least one copy is differentially expressed in one of the three tissues. A vast majority of the 115 paralogous gene pairs have been neofunctionalized or subfunctionalized as 88%, 89% and 96% of duplicates, respectively, expressed in grain, leaf and root show distinct expression patterns. On the basis of a Gene Ontology analysis, we have identified and characterized the gene families that have been structurally and functionally preferentially retained in the duplication showing that the vast majority (>85%) of duplicated have been either lost or have been subfunctionalized or neofunctionalized during 50-70 million years of evolution.
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