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The Tomato Expression Atlas

Noe Fernandez-Pozo, Yi Zheng, Stephen I Snyder, Philippe Nicolas, Yoshihito Shinozaki, Zhangjun Fei, Carmen Catala, James J Giovannoni, Jocelyn K.C Rose, Lukas A Mueller, Janet Kelso
2017 Bioinformatics  
Using tomato fruit as a model, we have developed the Tomato Expression Atlas to facilitate effective data analysis, allowing the simultaneous visualization of groups of genes at a cell/tissue level of  ...  This atlas can be adapted to different types of expression data from diverse multicellular species.  ...  This work has been supported by a grant from the US National Science Foundation (Plant Genome Research Program; IOS-1339287) and a Grant-in-Aid for JSPS Fellows from the Japan Society for the Promotion  ... 
doi:10.1093/bioinformatics/btx190 pmid:28379331 pmcid:PMC5860121 fatcat:2zudeh5z4bfvhhgonifeuixr4u

Over-Expression, Purification, and Characterization of Plant LeGST01, the Mammalian GST-Omega Homolog that Interacts with LeTPX1 from a Tomato cDNA Library

Firas Fohely, Khaled Sabarna Sabarna
2021 Atlas Journal of Biology  
The study focuses on an in vivo GST- omega homologue (pCRT7/TPxII intB4) over-expression, purification and characterization.  ...  Upon specific expression, the proteins exerted, differential protective effects in yeast cells treated with lethal doses of the prooxidants hydrogen peroxide, t-butyl hydroperoxide, and cumene hydroperoxide  ...  Acknowledgments The Authors would like to sincerely thank all the parties that collaborate in this work.  ... 
doi:10.5147/ajb.vi0.221 fatcat:q34772n47zfrzdfnx5sr2rkyz4

Integrated Network Analysis Identifies Fight-Club Nodes as a Class of Hubs Encompassing Key Putative Switch Genes That Induce Major Transcriptome Reprogramming during Grapevine Development

Maria Concetta Palumbo, Sara Zenoni, Marianna Fasoli, Mélanie Massonnet, Lorenzo Farina, Filippo Castiglione, Mario Pezzotti, Paola Paci
2014 The Plant Cell  
By studying grapevine (Vitis vinifera) and tomato (Solanum lycopersicum) gene expression atlases and a grapevine berry transcriptomic data set during the transition from immature to mature growth, we identified  ...  Finally, our analysis of tomato gene expression data sets showed that wild-type switch genes are downregulated in ripening-deficient mutants.  ...  (A) The correlation network obtained using the grapevine gene expression atlas (Fasoli et al., 2012) .  ... 
doi:10.1105/tpc.114.133710 pmid:25490918 fatcat:2ejb3sdg7nd6tly2fvo46gaowu

Comparative Analysis of Developmental Transcriptome Maps of Arabidopsis thaliana and Solanum lycopersicum

Aleksey A. Penin, Anna V. Klepikova, Artem S. Kasianov, Evgeny S. Gerasimov, Maria D. Logacheva
2019 Genes  
Here, we present a transcriptome atlas of tomato (Solanum lycopersicum) consisting of 30 samples of different organs and developmental stages.  ...  In this paper, we demonstrate the potential of comparing transcriptome maps for inferring shifts in the expression of paralogous genes.  ...  Acknowledgments: The authors express gratitude to D.D. Sokoloff for the help with tomato meristem collection. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/genes10010050 pmid:30650673 pmcid:PMC6356586 fatcat:scy6enziqjhtrex566k44fdcc4

Transcriptome profiling of cytokinin and auxin regulation in tomato root

Sarika Gupta, Xiuling Shi, Ingrid E. Lindquist, Nicholas Devitt, Joann Mudge, Aaron M. Rashotte
2013 Journal of Experimental Botany  
This study examined the transcriptome atlas of tomato root regions (root tip, lateral roots, and whole roots) and the transcriptional regulation of each root region in response to the plant hormones cytokinin  ...  Overall this study presents the first global expression patterns of hormone-regulated transcripts in tomato roots, which will be functionally relevant for future studies directed towards tomato root growth  ...  This work Transcriptome profiling of cytokinin and auxin regulation in tomato root | 703 was funded by the USDA-NRI (grant 2008-35304-04457), the AAES-HATCH (grants 370220-310007-2055, and 103600-310010  ... 
doi:10.1093/jxb/ers365 pmid:23307920 pmcid:PMC3542057 fatcat:swy7yg3jwrevtnmsgc67ugj2o4

Page 210 of Law Reporter Vol. 24, Issue 5 [page]

1981 Law Reporter  
The disease resulted in substantial destruction both to the crops raised from the purchased seedlings and to the farmers’ domestically-grown tomato plants.  ...  The roofer admitted liability and joined with the school in a suit against GAF Corp., the na- tion’s largest asphalt roofing manufacturer, claiming breach of express and implied warranties in selling defective  ... 

NexGenEx-Tom: a gene expression platform to investigate the functionalities of the tomato genome

Hamed Bostan, Maria Chiusano
2015 BMC Plant Biology  
However, the resulting collections are heterogeneous in terms of experimental approaches, genotypes and conditions, making the data far from representing a gene expression atlas for the species.  ...  The gene expression of tomato tissues has been widely investigated in the years, thanks to both EST sequencing and different microarray platforms.  ...  This work is also supported by the Genopom PRO Projects (Ministero dell'Istruzione, dell'Università e della Ricerca (MIUR), Italy) and is in the frame of the Cost Action FA1106. We acknowledge Dr.  ... 
doi:10.1186/s12870-014-0412-2 pmid:25849067 pmcid:PMC4340097 fatcat:kek7ikoxlfdlng6o5w5cuw6uom

Gramene database: Navigating plant comparative genomics resources

Parul Gupta, Sushma Naithani, Marcela Karey Tello-Ruiz, Kapeel Chougule, Peter D'Eustachio, Antonio Fabregat, Yinping Jiao, Maria Keays, Young Koung Lee, Sunita Kumari, Joseph Mulvaney, Andrew Olson (+10 others)
2016 Current Plant Biology  
Here we briefly describe the functions and uses of the Gramene database.  ...  It consists of an integrated portal for querying, visualizing and analyzing data for 44 plant reference genomes, genetic variation data sets for 12 species, expression data for 16 species, curated rice  ...  of the resources and tools.  ... 
doi:10.1016/j.cpb.2016.12.005 pmid:28713666 pmcid:PMC5509230 fatcat:gmdx6rggmjgpbptvme75fmf7d4

Screening of tissue-specific genes and promoters in tomato by comparing genome wide expression profiles of Arabidopsis orthologues

Chan Ju Lim, Ha Yeon Lee, Woong Bom Kim, Bok-Sim Lee, Jungeun Kim, Raza Ahmad, Hyun A. Kim, So Young Yi, Cheol-Goo Hur, Suk-Yoon Kwon
2012 Molecules and Cells  
After thoroughly examining the expression patterns of these five promoter::GUS transgenic lines, we evaluated the similarities in expressional specificities between tomato promoter activities and the expression  ...  These unexpected minor expressional differences in tomato and Arabidopsis tissues may be a demerit for mining the tissue specific promoters by using orthologue search.  ...  Tissue-Specific Promoters in Tomato Chan Ju Lim et al.  ... 
doi:10.1007/s10059-012-0068-4 pmid:22699756 pmcid:PMC3887779 fatcat:ncpaam2osbbvrgyiaygwv2nwce

An Intracellular Transcriptomic Atlas of the Giant Coenocyte Caulerpa taxifolia

Aashish Ranjan, Brad T. Townsley, Yasunori Ichihashi, Neelima R. Sinha, Daniel H. Chitwood, Gregory P. Copenhaver
2015 PLoS Genetics  
The analysis of the intersection of transcriptomic atlases of a land plant and Caulerpa suggests the recurrent recruitment of transcript accumulation patterns to organs over large evolutionary distances  ...  Here, we present a de novo assembled, intracellular transcriptomic atlas for the giant coenocyte Caulerpa taxifolia.  ...  Wrote the paper: DHC NRS.  ... 
doi:10.1371/journal.pgen.1004900 pmid:25569326 pmcid:PMC4287348 fatcat:7owiokvawbddnok63bfhcrxvsq

Single-nucleus RNA-seq resolves spatiotemporal developmental trajectories in the tomato shoot apex [article]

Caihuan Tian, Qingwei Du, Mengxue Xu, Fei Du, Yuling Jiao
2020 bioRxiv   pre-print
Collectively, this study demonstrates the power of snRNA-seq to plant research and provides an unprecedented spatiotemporal gene expression atlas of heterogeneous shoot cells.  ...  The obtained high-resolution expression atlas identifies numerous distinct cell types covering major shoot tissues and developmental stages, delineates developmental trajectories of mesophyll cells, vasculature  ...  We 186 have applied snRNA-seq to obtain a high-resolution cellular expression atlas of the tomato 187shoot.  ... 
doi:10.1101/2020.09.20.305029 fatcat:hntpkiu4nfgvjicdd7pomrmkvm

LncRNA regulates tomato fruit cracking by coordinating gene expression via a hormone-redox-cell wall network

Lingzi Xue, Mintao Sun, Zhen Wu, Lu Yu, Qinghui Yu, Yaping Tang, Fangling Jiang
2020 BMC Plant Biology  
In addition, the lncRNAs (XLOC_16662 and XLOC_033910, etc) regulated the expression of their neighbouring genes, and genes related to tomato cracking were selected to construct a lncRNA-mRNA network influencing  ...  This study provides insight into the responsive network for water-induced cracking in tomato fruit.  ...  The differences in gene expression in this experiment and Tomato Gene Expression Atlas might be due to different varieties, treatment and detection standards (Fig. 5b) .  ... 
doi:10.1186/s12870-020-02373-9 pmid:32293294 pmcid:PMC7161180 fatcat:dzibzi4nbrcutbamu4v6tigdsa

RNA Profiling of the Human and Mouse Spinal Cord Stem Cell Niches Reveals an Embryonic-like Regionalization with MSX1+ Roof-Plate-Derived Cells

Hussein Ghazale, Chantal Ripoll, Nicolas Leventoux, Laurent Jacob, Safa Azar, Daria Mamaeva, Yael Glasson, Charles-Felix Calvo, Jean-Leon Thomas, Sarah Meneceur, Yvan Lallemand, Valérie Rigau (+6 others)
2019 Stem Cell Reports  
This uncovered the conserved expression of 1,200 genes including 120 transcription factors.  ...  The dorsal EZ expresses a high level of Bmp6 and Gdf10 genes and harbors a subpopulation of radial quiescent cells expressing MSX1 and ID4 transcription factors.  ...  The authors declare that there is no conflict of interest regarding the publication of this article.  ... 
doi:10.1016/j.stemcr.2019.04.001 pmid:31031189 pmcid:PMC6524006 fatcat:wkouxzyu6zaptfp2lp3aku7mva

BREADING NEW LOCAL TOMATO HYBRIDS AT WEST-DELTA REGION OF EGYPT

A. Kansouh
2014 Journal of Plant Production  
Then, the overall evaluation must be depended on the mean performance and higher heterotic expression based on top parent (top heterosis)and commercial hybrid (commercial or standard heterosis).  ...  The hybrid breeding method can be used efficiently to improve yield and quality in tomato.  ... 
doi:10.21608/jpp.2014.64670 fatcat:p35tgtbir5aablv5hjn5szp5li

Development of a Gene-Centered SSR Atlas as a Resource for Papaya (Carica papaya) Marker-Assisted Selection and Population Genetic Studies

Newton Medeiros Vidal, Ana Laura Grazziotin, Helaine Christine Cancela Ramos, Messias Gonzaga Pereira, Thiago Motta Venancio, Chunxian Chen
2014 PLoS ONE  
In the present study we report the development and validation of an atlas of papaya simple sequence repeat (SSR) markers.  ...  The SSR atlas presented here is the first comprehensive gene-centered collection of annotated and genome positioned papaya SSRs.  ...  To achieve this goal, tomato gene expression and tomato/papaya orthology data were integrated.  ... 
doi:10.1371/journal.pone.0112654 pmid:25393538 pmcid:PMC4231050 fatcat:dxhfz3ehgbhuhjmm2era7ff6fm
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