Determination, Optimization and Taxonomy of Regulatory Networks: The Example of Arabidopsis thaliana Flower Morphogenesis

2011 ◽  
Author(s):  
Nicolas Glade ◽  
Adrien Elena ◽  
Fabien Corblin ◽  
Eric Fanchon ◽  
Jacques Demongeot ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Regulatory Networks ◽  
Flower Morphogenesis

scholarly journals Genome-scale cold stress response regulatory networks in ten Arabidopsis thaliana ecotypes

BMC Genomics ◽  
2013 ◽  
Vol 14 (1) ◽  
pp. 722 ◽  
Author(s):  
Pankaj Barah ◽  
Naresh Jayavelu ◽  
Simon Rasmussen ◽  
Henrik Nielsen ◽  
John Mundy ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Stress Response ◽  
Cold Stress ◽  
Regulatory Networks ◽  
Genome Scale

The effects of fluctuations in the nutrient supply on the expression of ANR1 and 11 other MADS box genes in shoots and roots of Arabidopsis thaliana

Botany ◽  
2010 ◽  
Vol 88 (12) ◽  
pp. 1023-1031 ◽  
Author(s):  
Yinbo Gan ◽  
Zhongjing Zhou ◽  
Lijun An ◽  
Shengjie Bao ◽  
Qing Liu ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Regulatory Networks ◽  
Nutrient Supply ◽  
The Other ◽  
Plant Responses ◽  
Similar Response ◽  
Mads Box ◽  
Mads Box Genes ◽  
Nutrient Condition ◽  
N Starvation

We previously reported that the response of ANR1 expression in shoots to nitrogen (N) starvation and resupply was different from its response in roots. However, how the other root-expressed MADS box genes respond to different N fluctuations in the shoot, and how these MADS box genes respond to complete nutrient fluctuations in the root, were unknown. Results from this study have shown that some members of these root-expressed MADS box genes have different responses in the shoot and root to N treatments, whereas others have similar responses or no responses to the N treatments. Among these 12 root-expressed MADS box genes, AGL16 was the only gene to show a similar response to N fluctuation in both shoots and roots in the same way as ANR1. Results from this study have also shown that ANR1, AGL12, AGL16, AGL19, and SOC1 responded to changes of the complete nutrient condition, which might indicate that they could play key roles in general nutrient stress. These novel findings will help us to further characterize these 12 MADS box genes to uncover the complex regulatory networks that integrate plant responses to changes in nutrient availability.

scholarly journals Characterization of novel pollen-expressed transcripts reveals their potential roles in pollen heat stress response in Arabidopsis thaliana

2020 ◽  
Author(s):  
Nicholas Rutley ◽  
Laetitia Poidevin ◽  
Tirza Doniger ◽  
Richard Tillet ◽  
Abhishek Rath ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Heat Stress ◽  
Regulatory Networks ◽  
Male Gametophyte ◽  
Open Reading Frames ◽  
Heat Stress Response ◽  
Rna Fragments ◽  
Response To Stress ◽  
Small Open Reading Frames

ABSTRACTThe male gametophyte is the most heat-sensitive of all plant tissues. In recent years, long noncoding RNAs (lncRNAs) have emerged as important components of cellular regulatory networks involved in most biological processes, including response to stress. While examining RNAseq datasets of developing and germinating Arabidopsis thaliana pollen exposed to heat stress (HS), we identified 66 novel and 246 recently-annotated intergenic expressed loci (XLOCs) of unknown function, with the majority encoding lncRNAs. Comparison to HS in cauline leaves and other RNAseq experiments, indicated 74% of the 312 XLOCs are pollen-specific, and at least 42% are HS-responsive. Phylogenetic analysis revealed 96% of the genes evolved recently in Brassicaceae. We found that 50 genes are putative targets of microRNAs, and that 30% of the XLOCs contain small open reading frames (ORFs) with homology to protein sequences. Finally, RNAseq of ribosome-protected RNA fragments together with predictions of periodic footprint of the ribosome P-sites indicated that 23 of these ORFs are likely to be translated. Our findings indicate that many of the 312 unknown genes might be functional, and play significant role in pollen biology, including the HS response.

scholarly journals Dynamic Transcriptional Profiles of Arabidopsis thaliana Infected by Tomato spotted wilt virus

2020 ◽  
Vol 110 (1) ◽  
pp. 153-163 ◽  
Author(s):  
Min Xu ◽  
Jing Chen ◽  
Ying Huang ◽  
Danyu Shen ◽  
Peng Sun ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Regulatory Networks ◽  
Tomato Spotted Wilt Virus ◽  
Rna Virus ◽  
Economic Loss ◽  
Immune Defense ◽  
Tomato Spotted Wilt ◽  
Deep Sequencing Technology ◽  
Photosynthesis Pathway ◽  
Wilt Virus

Tomato spotted wilt virus (TSWV) is a negative-stranded RNA virus that infects hundreds of plant species, causing great economic loss. Infected Arabidopsis thaliana plants develop symptoms including chlorosis and wilt, which can lead to cell death. From 9 to 15 days after TSWV infection, symptoms progress through a three-stage process of appearance, severity, and death. In this study, deep sequencing technology was first used to explore gene expression in response to TSWV infection in model plant A. thaliana at different symptom development stages. We found that plant immune defense and protein degradation are induced by TSWV infection and that both inductions became stronger over time. The photosynthesis pathway was attenuated with TSWV infection. Cell wall metabolism had a large extent of downregulation while some genes were upregulated. These results illustrate the dynamic nature of TSWV infection in A. thaliana at the whole-transcriptome level. The link between biological processes and subpathway metabolism was further analyzed. Our study provides new insight into host regulatory networks and dynamic processes in response to TSWV infection.

scholarly journals Large-effect flowering time mutations reveal conditionally adaptive paths through fitness landscapes in Arabidopsis thaliana

2019 ◽  
Vol 116 (36) ◽  
pp. 17890-17899 ◽  
Author(s):  
Mark A. Taylor ◽  
Amity M. Wilczek ◽  
Judith L. Roe ◽  
Stephen M. Welch ◽  
Daniel E. Runcie ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Flowering Time ◽  
Environmental Conditions ◽  
Regulatory Networks ◽  
Evolutionary Dynamics ◽  
Natural Populations ◽  
Fitness Landscapes ◽  
Natural Environments ◽  
Multiple Phenotypes ◽  
Mutant Phenotypes

Contrary to previous assumptions that most mutations are deleterious, there is increasing evidence for persistence of large-effect mutations in natural populations. A possible explanation for these observations is that mutant phenotypes and fitness may depend upon the specific environmental conditions to which a mutant is exposed. Here, we tested this hypothesis by growing large-effect flowering time mutants of Arabidopsis thaliana in multiple field sites and seasons to quantify their fitness effects in realistic natural conditions. By constructing environment-specific fitness landscapes based on flowering time and branching architecture, we observed that a subset of mutations increased fitness, but only in specific environments. These mutations increased fitness via different paths: through shifting flowering time, branching, or both. Branching was under stronger selection, but flowering time was more genetically variable, pointing to the importance of indirect selection on mutations through their pleiotropic effects on multiple phenotypes. Finally, mutations in hub genes with greater connectedness in their regulatory networks had greater effects on both phenotypes and fitness. Together, these findings indicate that large-effect mutations may persist in populations because they influence traits that are adaptive only under specific environmental conditions. Understanding their evolutionary dynamics therefore requires measuring their effects in multiple natural environments.

scholarly journals Evolution of cis-regulatory elements and regulatory networks in duplicated genes of Arabidopsis thaliana

2015 ◽  
pp. pp.00717.2015 ◽  
Author(s):  
Andrej A Arsovski ◽  
Julian Pradinuk ◽  
Xu Qiu Guo ◽  
Sishuo Wang ◽  
Keith L Adams
Keyword(s):  
Arabidopsis Thaliana ◽  
Regulatory Networks ◽  
Regulatory Elements ◽  
Duplicated Genes

scholarly journals The evolution of gene regulatory networks controlling Arabidopsis thaliana L. trichome development

2019 ◽  
Vol 19 (S1) ◽  
Author(s):  
Alexey V. Doroshkov ◽  
Dmitrii K. Konstantinov ◽  
Dmitrij A. Afonnikov ◽  
Konstantin V. Gunbin
Keyword(s):  
Arabidopsis Thaliana ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Trichome Development ◽  
Gene Regulatory

Regulatory networks of glucosinolates shape Arabidopsis thaliana fitness

2010 ◽  
Vol 13 (3) ◽  
pp. 347-352 ◽  
Author(s):  
Meike Burow ◽  
Barbara A Halkier ◽  
Daniel J Kliebenstein
Keyword(s):  
Arabidopsis Thaliana ◽  
Regulatory Networks
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