ArticleBMC genomics2020
Interspecific analysis of diurnal gene regulation in panicoid grasses identifies known and novel regulatory motifs.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed, 43 citations in OpenAlex.
- Diurnal dynamics of maize gene expression is associated with phyllosphere microbiome composition.International microbiology : the official journal of the Spanish Society for Microbiology · 2026Article
- Genome Wide Identification and Characterization ofInternational journal of genomics · 2026Article
- The blue light receptor ZmFKF1a recruits ZmGI1 to the nucleus to accelerate shoot apex development and flowering in maize.The Plant cell · 2025Article
- Rhythmic lipid and gene expression responses to chilling in panicoid grasses.Journal of experimental botany · 2024Article
- Compartmentation of photosynthesis gene expression in C4 maize depends on time of day.Plant physiology · 2023Article
- Transcriptomic and metabolic studies on the role of inorganic and organic iodine compounds in lettuce plants.Scientific reports · 2023Article
- Wheat EARLY FLOWERING 3 affects heading date without disrupting circadian oscillations.Plant physiology · 2023Article
- A Transferable Machine Learning Framework for Predicting Transcriptional Responses of Genes Across Species.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Article
- Time of Day Analysis over a Field Grown Developmental Time Course in Rice.Plants (Basel, Switzerland) · 2022Article
- Core circadian clock and light signaling genes brought into genetic linkage across the green lineage.Plant physiology · 2022Article
- CAST-R: An application to visualize circadian and heat stress-responsive genes in plants.Plant physiology · 2022Article
- Differential timing of gene expression and recruitment in independent origins of CAM in the Agavoideae (Asparagaceae).The New phytologist · 2022Article
- Review
- Genomic Architecture and Evolution of theFrontiers in plant science · 2022Article
- ZmCCT regulates photoperiod-dependent flowering and response to stresses in maize.BMC plant biology · 2021Article
- Predicting transcriptional responses to cold stress across plant species.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- 72-h diurnal RNA-seq analysis of fully expanded third leaves from maize, sorghum, and foxtail millet at 3-h resolution.BMC research notes · 2021Article
- Using single-plant-omics in the field to link maize genes to functions and phenotypes.Molecular systems biology · 2020Article
- A sorghumPlant direct · 2020Article
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundThe circadian clock drives endogenous 24-h rhythms that allow organisms to adapt and prepare for predictable and repeated changes in their environment throughout the day-night (diurnal) cycle. Many components of the circadian clock in Arabidopsis thaliana have been functionally characterized, but comparatively little is known about circadian clocks in grass species including major crops like maize and sorghum.
resultsComparative research based on protein homology and diurnal gene expression patterns suggests the function of some predicted clock components in grasses is conserved with their Arabidopsis counterparts, while others have diverged in function. Our analysis of diurnal gene expression in three panicoid grasses sorghum, maize, and foxtail millet revealed conserved and divergent evolution of expression for core circadian clock genes and for the overall transcriptome. We find that several classes of core circadian clock genes in these grasses differ in copy number compared to Arabidopsis, but mostly exhibit conservation of both protein sequence and diurnal expression pattern with the notable exception of maize paralogous genes. We predict conserved cis-regulatory motifs shared between maize, sorghum, and foxtail millet through identification of diurnal co-expression clusters for a subset of 27,196 orthologous syntenic genes. In this analysis, a Cochran-Mantel-Haenszel based method to control for background variation identified significant enrichment for both expected and novel 6-8 nucleotide motifs in the promoter regions of genes with shared diurnal regulation predicted to function in common physiological activities.
conclusionsThis study illustrates the divergence and conservation of circadian clocks and diurnal regulatory networks across syntenic orthologous genes in panacoid grass species. Further, conserved local regulatory sequences contribute to the architecture of these diurnal regulatory networks that produce conserved patterns of diurnal gene expression.
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