A KBase case study on genome-wide transcriptomics and plant primary metabolism in response to drought stress in Sorghum.
Abstract
A better understanding of the genetic and metabolic mechanisms that confer stress resistance and tolerance in plants is key to engineering new crops through advanced breeding technologies. This requires a systems biology approach that builds on a genome-wide understanding of the regulation of gene expression, plant metabolism, physiology and growth. In this study, we examine the response to drought stress in Sorghum, as we leverage the tools for transcriptomics and plant metabolic modeling we have implemented at the U.S. Department of Energy Systems Biology Knowledgebase (KBase). KBase enables researchers worldwide to collaborate and advance research by uploading private or public data into the KBase Narrative Interface, analyzing it using a rich, extensible array of computational and data-analytics tools, and securely sharing scientific workflows and conclusions. We demonstrate how to use the current RNA-seq tools in KBase, applicable to both plants and microbes, to assemble and quantify long transcripts and identify differentially expressed genes effectively. More specifically, we demonstrate the utility of the platform by identifying key genes differentially expressed during drought-stress in Sorghum bicolor, an important sustainable production crop plant. We then show how we can use KBase tools to predict the membership of genes in metabolic pathways and examinemore »
- Authors:
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Argonne National Laboratory (ANL), Argonne, IL (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1829946
- Alternate Identifier(s):
- OSTI ID: 1896982; OSTI ID: 1903003
- Grant/Contract Number:
- AC02-05CH11231; AC02-06CH11357; AC02-98CH10886; AC05–00OR22725; AC05-00OR22725
- Resource Type:
- Published Article
- Journal Name:
- Current plant biology
- Additional Journal Information:
- Journal Name: Current plant biology Journal Volume: 28 Journal Issue: C; Journal ID: ISSN 2214-6628
- Publisher:
- Elsevier
- Country of Publication:
- Netherlands
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; KBase; Transcriptomics; Bioinformatics; Data analysis; Gene expression; RNA-seq; Differential gene expression; ModelSEED; Flux balance analysis model; Primary metabolism; Metabolic network; Pathway viewer; FAIR principles; Sorghum bicolor; FAIR
Citation Formats
Kumari, Sunita, Kumar, Vivek, Beilsmith, Kathleen, Seaver, Samuel M. D., Canon, Shane, Dehal, Paramvir, Gu, Tian, Joachimiak, Marcin, Lerma-Ortiz, Claudia, Liu, Filipe, Lu, Zhenyuan, Pearson, Eric, Ranjan, Priya, Riel, William, Henry, Christopher S., Arkin, Adam P., and Ware, Doreen. A KBase case study on genome-wide transcriptomics and plant primary metabolism in response to drought stress in Sorghum.. Netherlands: N. p., 2021.
Web. doi:10.1016/j.cpb.2021.100229.
Kumari, Sunita, Kumar, Vivek, Beilsmith, Kathleen, Seaver, Samuel M. D., Canon, Shane, Dehal, Paramvir, Gu, Tian, Joachimiak, Marcin, Lerma-Ortiz, Claudia, Liu, Filipe, Lu, Zhenyuan, Pearson, Eric, Ranjan, Priya, Riel, William, Henry, Christopher S., Arkin, Adam P., & Ware, Doreen. A KBase case study on genome-wide transcriptomics and plant primary metabolism in response to drought stress in Sorghum.. Netherlands. https://doi.org/10.1016/j.cpb.2021.100229
Kumari, Sunita, Kumar, Vivek, Beilsmith, Kathleen, Seaver, Samuel M. D., Canon, Shane, Dehal, Paramvir, Gu, Tian, Joachimiak, Marcin, Lerma-Ortiz, Claudia, Liu, Filipe, Lu, Zhenyuan, Pearson, Eric, Ranjan, Priya, Riel, William, Henry, Christopher S., Arkin, Adam P., and Ware, Doreen. Wed .
"A KBase case study on genome-wide transcriptomics and plant primary metabolism in response to drought stress in Sorghum.". Netherlands. https://doi.org/10.1016/j.cpb.2021.100229.
@article{osti_1829946,
title = {A KBase case study on genome-wide transcriptomics and plant primary metabolism in response to drought stress in Sorghum.},
author = {Kumari, Sunita and Kumar, Vivek and Beilsmith, Kathleen and Seaver, Samuel M. D. and Canon, Shane and Dehal, Paramvir and Gu, Tian and Joachimiak, Marcin and Lerma-Ortiz, Claudia and Liu, Filipe and Lu, Zhenyuan and Pearson, Eric and Ranjan, Priya and Riel, William and Henry, Christopher S. and Arkin, Adam P. and Ware, Doreen},
abstractNote = {A better understanding of the genetic and metabolic mechanisms that confer stress resistance and tolerance in plants is key to engineering new crops through advanced breeding technologies. This requires a systems biology approach that builds on a genome-wide understanding of the regulation of gene expression, plant metabolism, physiology and growth. In this study, we examine the response to drought stress in Sorghum, as we leverage the tools for transcriptomics and plant metabolic modeling we have implemented at the U.S. Department of Energy Systems Biology Knowledgebase (KBase). KBase enables researchers worldwide to collaborate and advance research by uploading private or public data into the KBase Narrative Interface, analyzing it using a rich, extensible array of computational and data-analytics tools, and securely sharing scientific workflows and conclusions. We demonstrate how to use the current RNA-seq tools in KBase, applicable to both plants and microbes, to assemble and quantify long transcripts and identify differentially expressed genes effectively. More specifically, we demonstrate the utility of the platform by identifying key genes differentially expressed during drought-stress in Sorghum bicolor, an important sustainable production crop plant. We then show how we can use KBase tools to predict the membership of genes in metabolic pathways and examine expression data in the context of metabolic subsystems. We demonstrate the power of the platform by making the data, analysis and interpretation available to the biologists in the reproducible, re-usable, point-and-click format of a KBase Narrative thus promoting FAIR (Findable, Accessible, Interoperable and Reusable) guiding principles for scientific data management and stewardship.},
doi = {10.1016/j.cpb.2021.100229},
journal = {Current plant biology},
number = C,
volume = 28,
place = {Netherlands},
year = {Wed Dec 01 00:00:00 EST 2021},
month = {Wed Dec 01 00:00:00 EST 2021}
}
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