ArticlePlant physiology2008
Comparative analysis of divergent and convergent gene pairs and their expression patterns in rice, Arabidopsis, and populus.
Article in Plant physiology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed, 61 citations in OpenAlex.
- Lineage-associated Human Divergently-paired Genes Exhibit Structural and Regulatory Characteristics.Genomics, proteomics & bioinformatics · 2025Article
- Through the lens of bioenergy crops: advances, bottlenecks, and promises of plant engineering.The Plant journal : for cell and molecular biology · 2025Review
- Plant engineering: advances, bottlenecks, and promise.The Plant journal : for cell and molecular biology · 2025Article
- Genomic Analysis and Functional Validation of Bidirectional Promoters in Medaka (International journal of molecular sciences · 2024Article
- Identification and functional characterization of bidirectional gene pairs and their intergenic regions in cotton.BMC plant biology · 2024Article
- The atypical organization of theJournal of bacteriology · 2024Review
- Genome-Wide Prediction of Transcription Start Sites in Conifers.International journal of molecular sciences · 2022Article
- Distinct Evolutionary Profiles and Functions of microRNA156 and microRNA529 in Land Plants.International journal of molecular sciences · 2021Article
- Metabolic engineering of astaxanthin-rich maize and its use in the production of biofortified eggs.Plant biotechnology journal · 2021Article
- Marchantia TCP transcription factor activity correlates with three-dimensional chromatin structure.Nature plants · 2020Article
- Additional Layer of Regulation via Convergent Gene Orientation in Yeasts.Molecular biology and evolution · 2020Article
- Structural and Functional Analysis of a Bidirectional Promoter fromInternational journal of molecular sciences · 2018Article
- SRARP and HSPB7 are epigenetically regulated gene pairs that function as tumor suppressors and predict clinical outcome in malignancies.Molecular oncology · 2018Article
- Expression of the Intracellular COPT3-Mediated Cu Transport Is Temporally Regulated by the TCP16 Transcription Factor.Frontiers in plant science · 2018Article
- Article
- Analysis of Promoters of Arabidopsis thaliana Divergent Gene Pair SERAT3;2 and IDH-III Shows SERAT3;2 Promoter is Nested Within the IDH-III Promoter.Molecular biotechnology · 2017Article
- Genetic variability of the activity of bidirectional promoters: a pilot study in bovine muscle.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
- The Diversification of Plant NBS-LRR Defense Genes Directs the Evolution of MicroRNAs That Target Them.Molecular biology and evolution · 2016Article
- Histone modifications facilitate the coexpression of bidirectional promoters in rice.BMC genomics · 2016Article
- Functional characterization of open chromatin in bidirectional promoters of rice.Scientific reports · 2016Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Comparative analysis of the organization and expression patterns of divergent and convergent gene pairs in multiple plant genomes can identify patterns that are shared by more than one species or are unique to a particular species. Here, we study the coexpression and interspecies conservation of divergent and convergent gene pairs in three plant species: rice (Oryza sativa), Arabidopsis (Arabidopsis thaliana), and black cottonwood (Populus trichocarpa). Strongly correlated expression levels between divergent and convergent genes were found to be quite common in all three species, and the frequency of strong correlation appears to be independent of intergenic distance. Conservation of divergent or convergent arrangement among these species appears to be quite rare. However, conserved arrangement is significantly more frequent when the genes display strongly correlated expression levels or have one or more Gene Ontology (GO) classes in common. A correlation between intergenic distance in divergent and convergent gene pairs and shared GO classes was observed, in varying degrees, in rice and Populus but not in Arabidopsis. Furthermore, multiple GO classes were either overrepresented or underrepresented in Arabidopsis and Populus gene pairs, while only two GO classes were underrepresented in rice divergent gene pairs. Three cis-regulatory elements common to both Arabidopsis and rice were overrepresented in the intergenic regions of strongly correlated divergent gene pairs compared to those of noncorrelated pairs. Our results suggest that shared as well as unique mechanisms operate in shaping the organization and function of divergent and convergent gene pairs in different plant species.
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