ArticlePlant physiology2011
Comparative network analysis reveals that tissue specificity and gene function are important factors influencing the mode of expression evolution in Arabidopsis and rice.
Article in Plant physiology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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64 citing papers in PubMed, 111 citations in OpenAlex.
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- Cross-species analysis of abiotic stress in hydroponic leafy crops reveals conserved regulatory networks and key divergences.Frontiers in plant science · 2025Article
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- Comparative Coexpression Analysis of Indole Synthase and Tryptophan Synthase A Reveals the Independent Production of Auxin via the Cytosolic Free Indole.Plants (Basel, Switzerland) · 2023Article
- A cross-species co-functional gene network underlying leaf senescence.Horticulture research · 2023Article
- Identification of growth regulators using cross-species network analysis in plants.Plant physiology · 2022Article
- Longer Duration of Active Oil Biosynthesis during Seed Development Is Crucial for High Oil Yield-Lessons from Genome-Wide In Silico Mining and RNA-Seq Validation in Sesame.Plants (Basel, Switzerland) · 2022Article
- Lipidomics-Assisted GWAS (lGWAS) Approach for Improving High-Temperature Stress Tolerance of Crops.International journal of molecular sciences · 2022Review
- Multilevel interactions between native and ectopic isoprenoid pathways affect global metabolism in rice.Transgenic research · 2022Article
- Addressing noise in co-expression network construction.Briefings in bioinformatics · 2022Review
- R2R3-MYBs in Durum Wheat: Genome-Wide Identification, Poaceae-Specific Clusters, Expression, and Regulatory Dynamics Under Abiotic Stresses.Frontiers in plant science · 2022Article
- Conserved co-functional network between maize and Arabidopsis aid in the identification of seed defective genes in maize.Genes & genomics · 2021Article
- A network-based comparative framework to study conservation and divergence of proteomes in plant phylogenies.Nucleic acids research · 2021Article
- TALEN-BasedFrontiers in plant science · 2021Article
- Evidence for the Accumulation of Nonsynonymous Mutations and Favorable Pleiotropic Alleles During Wheat Breeding.G3 (Bethesda, Md.) · 2020Article
4 more citing papers are in PubMed but not listed here.
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3 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Microarray experiments have yielded massive amounts of expression information measured under various conditions for the model species Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). Expression compendia grouping multiple experiments make it possible to define correlated gene expression patterns within one species and to study how expression has evolved between species. We developed a robust framework to measure expression context conservation (ECC) and found, by analyzing 4,630 pairs of orthologous Arabidopsis and rice genes, that 77% showed conserved coexpression. Examples of nonconserved ECC categories suggested a link between regulatory evolution and environmental adaptations and included genes involved in signal transduction, response to different abiotic stresses, and hormone stimuli. To identify genomic features that influence expression evolution, we analyzed the relationship between ECC, tissue specificity, and protein evolution. Tissue-specific genes showed higher expression conservation compared with broadly expressed genes but were fast evolving at the protein level. No significant correlation was found between protein and expression evolution, implying that both modes of gene evolution are not strongly coupled in plants. By integration of cis-regulatory elements, many ECC conserved genes were significantly enriched for shared DNA motifs, hinting at the conservation of ancestral regulatory interactions in both model species. Surprisingly, for several tissue-specific genes, patterns of concerted network evolution were observed, unveiling conserved coexpression in the absence of conservation of tissue specificity. These findings demonstrate that orthologs inferred through sequence similarity in many cases do not share similar biological functions and highlight the importance of incorporating expression information when comparing genes across species.
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