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BBX24 Interacts with DELLA to Regulate UV-B-Induced Photomorphogenesis in Arabidopsis thaliana

Yuewei Huang, Hui Xiong, Yuxin Xie, Suihua Lyu, Tingting Miao, Tingting Li, Guizhen Lyu, Shaoshan Li
2022 International Journal of Molecular Sciences  
Abstracts: UV-B radiation, sensed by the photoreceptor UVR8, induces signal transduction for plant photomorphogenesis [...]  ...  Institutional Review Board Statement: Not applicable. Informed Consent Statement: Not applicable.  ...  We are grateful to Paul Giller from University College Cork, Ireland, for reviewing and suggesting editorial changes of an earlier version of the manuscript.  ... 
doi:10.3390/ijms23137386 pmid:35806395 pmcid:PMC9266986 fatcat:xbmdm74yrzesdctm6fwwx7cgii

Arachis hypogea gene expression atlas (AhGEA) for fastigiata subspecies of cultivated groundnut to accelerate functional and translational genomics applications

Pallavi Sinha, Prasad Bajaj, Lekha T Pazhamala, Spurthi N Nayak, Manish K Pandey, Annapurna Chitikineni, Dongxin Huai, Aamir W Khan, Aarthi Desai, Huifang Jiang, Zhuang Weijian, Baozhu Guo (+2 others)
2020 Plant Biotechnology Journal  
Our in-depth analysis of the global transcriptome sheds light into complex regulatory networks namely, gravitropism and photomorphogenesis, seed development, allergens and oil biosynthesis in groundnut  ...  Approximately 480 million paired-end filtered reads were generated followed by identification of 81,901 transcripts from an early maturing, high-yielding, drought tolerant groundnut variety, ICGV 91114  ...  ICRISAT is a member of CGIAR Consortium.  ... 
doi:10.1111/pbi.13374 pmid:32167667 fatcat:s5uupwiyzbf77fg47ppd77e45m

De Novo Transcriptome Assembly and Analyses of Gene Expression during Photomorphogenesis in Diploid Wheat Triticum monococcum

Samuel E. Fox, Matthew Geniza, Mamatha Hanumappa, Sushma Naithani, Chris Sullivan, Justin Preece, Vijay K. Tiwari, Justin Elser, Jeffrey M. Leonard, Abigail Sage, Cathy Gresham, Arnaud Kerhornou (+6 others)
2014 PLoS ONE  
Triticum monococcum (2n) is a close ancestor of T. urartu, the A-genome progenitor of cultivated hexaploid wheat, and is therefore a useful model for the study of components regulating photomorphogenesis  ...  Differential gene expression analyses revealed 22% more light up-regulated and 35% more light down-regulated transcripts in the G3116 transcriptome compared to DV92.  ...  and potential SNPs and SSRs, which can be used to explore Triticeae genome diversity, co-expression networks involved in photomorphogenesis and to develop stochastic and metabolic networks [22, 48, 49  ... 
doi:10.1371/journal.pone.0096855 pmid:24821410 pmcid:PMC4018402 fatcat:eohusquf7vfbflauwpwlba43zy

Third-generation sequencing and metabolome analysis reveal candidate genes and metabolites with altered levels in albino jackfruit seedlings

Xiangxu Meng, Jiahong Xu, Maoning Zhang, Ruyue Du, Wenxiu Zhao, Qing Zeng, Zhihua Tu, Jinhui Chen, Beibei Chen
2021 BMC Genomics  
Analysis of the TF–DEG network suggested that basic helix-loop-helix (bHLH) and MYB-related TFs regulate the expression of genes involved in carbon fixation and energy metabolism to affect light responses  ...  or photomorphogenesis and normal growth.  ...  Acknowledgements We thank the people in the School of Forestry, Hainan University who helped us find the mutant plants.  ... 
doi:10.1186/s12864-021-07873-y fatcat:pftfwgjdajey3espbtei64akcq

Etiolated Seedling Development Requires Repression of Photomorphogenesis by a Small Cell-Wall-Derived Dark Signal

Scott A. Sinclair, Camille Larue, Laura Bonk, Asif Khan, Hiram Castillo-Michel, Ricardo J. Stein, Daniel Grolimund, Dominik Begerow, Ulla Neumann, Michael J. Haydon, Ute Krämer
2017 Current Biology  
Etiolated growth in darkness or the irreversible transition to photomorphogenesis in the light engages alternative developmental programs operating across all organs of a plant seedling.  ...  In combination with genetic data, we propose a model of spatiotemporally separated photoreceptive and signal-responsive cell types, which contain overlapping subsets of the regulatory network of light-dependent  ...  Germany) for multielement analysis and the Paul Scherrer Institut (Villigen, Switzerland) and the European Synchrotron Radiation Source (ESRF, Grenoble, France) for beamtime at the microXAS beamline of  ... 
doi:10.1016/j.cub.2017.09.063 pmid:29103938 fatcat:z4loin5vlfbg3fyy66x26ncqfi

Genome-wide association study (GWAS) of leaf cuticular wax components in Camelina sativa identifies genetic loci related to intracellular wax transport

Zinan Luo, Pernell Tomasi, Noah Fahlgren, Hussein Abdel-Haleem
2019 BMC Plant Biology  
or Golgi network-mediated transport.  ...  low-input requirements in agriculture practices.  ...  Acknowledgements Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.  ... 
doi:10.1186/s12870-019-1776-0 fatcat:te7iq4vmqrhuvcrtig7ezpnley

Genome-Wide Identification, Evolution, and Comparative Analysis of B-Box Genes in Brassica rapa, B. oleracea, and B. napus and Their Expression Profiling in B. rapa in Response to Multiple Hormones and Abiotic Stresses

Sonam Singh, Sushil Satish Chhapekar, Yinbo Ma, Jana Jeevan Rameneni, Sang Heon Oh, Jusang Kim, Yong Pyo Lim, Su Ryun Choi
2021 International Journal of Molecular Sciences  
Light-responsive cis-regulatory elements were detected in many of the BBX gene promoters.  ...  A whole-genome identification, characterization, and evolutionary analysis (synteny and orthology) of the B-box gene families in the diploid species B. rapa (A genome) and B. oleracea (C genome) and in  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/ijms221910367 pmid:34638707 pmcid:PMC8509055 fatcat:yhiastlezrgkxkgmu323ijhhwa

Identification and integrated analysis of glyphosate stress-responsive microRNAs, lncRNAs, and mRNAs in rice using genome-wide high-throughput sequencing

Rongrong Zhai, Shenghai Ye, Guofu Zhu, Yanting Lu, Jing Ye, Faming Yu, Qiren Chu, Xiaoming Zhang
2020 BMC Genomics  
This study is expected to elucidate the responses of miRNAs, lncRNAs, and mRNAs to glyphosate applications and the potential regulatory mechanisms in response to glyphosate stress in rice.  ...  The glyphosate stress-responsive genes were used for the development of genetically modified crops, while only the EPSPS gene has been used currently in the study on glyphosate-tolerance in rice.  ...  Of which, osa-MIR167f-p3 and osa- Discussion To better understand the global gene expression and the potential regulatory mechanisms involved in the adaptive responses to glyphosate application in rice  ... 
doi:10.1186/s12864-020-6637-6 pmid:32183693 fatcat:yf7f3w2avbatvgqbnt22mzp4qe

Reconstruction of gene regulatory network related to photosynthesis in Arabidopsis thaliana

Xianbin Yu, Guangyong Zheng, Lanlan Shan, Guofeng Meng, Martin Vingron, Qi Liu, Xin-Guang Zhu
2014 Frontiers in Plant Science  
is not only scientifically significant but also holding great potential in agricultural application.  ...  Finally, a gene regulatory network was established by combining TF-targets information generated by these two approaches.  ...  OPP1014417), Ministry of Science and Technology of China (Grant No. 2011DFA31070), and the Young Talent Frontier Program of Shanghai Institutes for Biology Sciences/Chinese Academy of Sciences (Grant No  ... 
doi:10.3389/fpls.2014.00273 pmid:24982665 pmcid:PMC4055858 fatcat:mql2aedeb5epjocklkjnmp23ou

Fused Graphical Lasso Recovers Flowering Time Mutation Genes in Arabidopsis Thaliana

Rajan Kapoor, Aniruddha Datta, Michael Thomson
2021 Inventions  
Observing the network level changes between two phenotypes can also help develop meaningful biological hypotheses regarding the novel functions of these genes.  ...  In this work, we propose the use of the joint graphical lasso for discovering genes responsible for desired phenotypic traits.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/inventions6030052 fatcat:ixcy4w5ehjhc7oqvpwfwgvzv2q

Deciphering Novel Transcriptional Regulators of Soybean Hypocotyl Elongation Based on Gene Co-expression Network Analysis

Zhikang Shen, Min Chen
2022 Frontiers in Plant Science  
To address the problem, bioinformatics approaches along with the weighted gene co-expression network analysis (WGCNA) were carried out to elucidate the regulatory networks and identify key regulators underlying  ...  Taken together, our results constructed the regulatory network and identified novel transcriptional regulators of soybean hypocotyl elongation based on WGCNA, which provide new insights into the global  ...  ORIGINAL RESEARCH article Deciphering Novel Transcriptional Regulators of Soybean Hypocotyl Elongation Based on Gene Co-expression Network Analysis 1 College of Life Science and Technology, Huazhong  ... 
doi:10.3389/fpls.2022.837130 pmid:35273629 pmcid:PMC8902393 fatcat:irxxxha255hrjolvcnq4dxqmhq

Nucleo-plastidic PAP8/pTAC6 couples chloroplast formation with photomorphogenesis [article]

Monique Liebers, François-Xavier Gillet, Abir Israel, Kevin Pounot, Louise Chambon, Maha Chieb, Fabien Chevalier, Rémi Ruedas, Adrien Favier, Pierre Gans, Elisabetta Boeri Erba, David Cobessi (+2 others)
2020 biorxiv/medrxiv   pre-print
In these semi-autonomous organelles, the construction of the photosynthetic apparatus depends on the coordination of nuclear and plastid gene expression.  ...  AbstractThe initial greening of angiosperm occurs upon light-activation of photoreceptors that trigger photomorphogenesis followed with the development of chloroplasts.  ...  of the light-signalling network.  ... 
doi:10.1101/2020.03.10.985002 fatcat:42pm4xl67rcqdnu4lwpmw7dmje

Transcriptome and Metabolomic Analyses Reveal Regulatory Networks Controlling Maize Stomatal Development in Response to Blue Light

Tiedong Liu, Xiwen Zhang
2021 International Journal of Molecular Sciences  
Transcriptome comparisons and correlation signaling network analysis detected 55 genes, and identified 6 genes that work in the regulation of the HY5 module and MAPK cascade, that interact with PTI1, COI1  ...  metabolism of metabolites, and eight obtained genes worked in the HY5 module and MAPK cascade.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/ijms22105393 pmid:34065495 pmcid:PMC8161096 fatcat:df4nqdjnl5e4dijisa4hbiadeq

The Mediator Complex Subunit PFT1 Interferes with COP1 and HY5 in the Regulation of Arabidopsis Light Signaling

C. Klose, C. Buche, A. P. Fernandez, E. Schafer, E. Zwick, T. Kretsch
2012 Plant Physiology  
Expression profile analyses revealed that PFT1(eid3) alters the transcript accumulation of light-regulated genes even in darkness.  ...  of the ELONGATED HYPOCOTYL5 transcription factor, an important positive regulator of light-dependent gene expression.  ...  Thus, regulatory modification of PFT1 is now a known point in the complex network controlling light-regulated gene expression.  ... 
doi:10.1104/pp.112.197319 pmid:22760208 pmcid:PMC3440207 fatcat:cygllt5pqbe6hpe3gxpgvoxtdy

TheArabidopsisC2H2 Zinc Finger INDETERMINATE DOMAIN1/ENHYDROUS Promotes the Transition to Germination by Regulating Light and Hormonal Signaling during Seed Maturation

J. Allan Feurtado, Daiqing Huang, Leigh Wicki-Stordeur, Laura E. Hemstock, Mireille S. Potentier, Edward W.T. Tsang, Adrian J. Cutler
2011 The Plant Cell  
Deciphering gene regulatory networks that control seed development and maturation in Arabidopsis. Plant J. 54: 608-620.  ...  GNC expression is repressed by GA application and elevated in ga-1 and gid1abc mutants.  ... 
doi:10.1105/tpc.111.085134 pmid:21571950 pmcid:PMC3123948 fatcat:mdju225rfjewdj6wuacklryhnm
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