U.S. Department of EnergyOffice of Scientific and Technical Information
A KBase Case Study on Genome-wide Transcriptomics and Plant Primary Metabolism 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 allowing them to upload private or public data into the KBase Narrative Interface, empowering them to analyze this data using a rich, extensible array of computational and data-analytics tools, and allows them to securely share 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 that are differentially expressed during drought-stress in Sorghum bicolor, which is an important sustainable production crop plant. We then show how to usemore »
- Authors:
-
- Cold Spring Harbor Laboratory Cold Spring Harbor, NY (United States)
- Publication Date:
- Research Org.:
- Cold Spring Harbor Laboratory Cold Spring Harbor, NY (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
- Keywords:
- transcriptomics, metabolism, sorghum
- OSTI Identifier:
- 1828290
- DOI:
- https://doi.org/10.25982/101788.79/1828290
Citation Formats
Kumari, Sunita. A KBase Case Study on Genome-wide Transcriptomics and Plant Primary Metabolism in Sorghum. United States: N. p., 2021.
Web. doi:10.25982/101788.79/1828290.
Kumari, Sunita. A KBase Case Study on Genome-wide Transcriptomics and Plant Primary Metabolism in Sorghum. United States. doi:https://doi.org/10.25982/101788.79/1828290
Kumari, Sunita. 2021.
"A KBase Case Study on Genome-wide Transcriptomics and Plant Primary Metabolism in Sorghum". United States. doi:https://doi.org/10.25982/101788.79/1828290. https://www.osti.gov/servlets/purl/1828290. Pub date:Mon Nov 01 00:00:00 EDT 2021
@article{osti_1828290,
title = {A KBase Case Study on Genome-wide Transcriptomics and Plant Primary Metabolism in Sorghum},
author = {Kumari, Sunita},
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 allowing them to upload private or public data into the KBase Narrative Interface, empowering them to analyze this data using a rich, extensible array of computational and data-analytics tools, and allows them to securely share 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 that are differentially expressed during drought-stress in Sorghum bicolor, which is an important sustainable production crop plant. We then show how to 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 = {10.25982/101788.79/1828290},
journal = {},
number = ,
volume = ,
place = {United States},
year = {2021},
month = {11}
}
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Escher-FBA: a web application for interactive flux balance analysis
journal, September 2018
- Rowe, Elliot; Palsson, Bernhard O.; King, Zachary A.
- BMC Systems Biology, Vol. 12, Issue 1
High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource
journal, June 2014
- Seaver, Samuel M. D.; Gerdes, Svetlana; Frelin, Océane
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 26
Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways
journal, August 2015
- King, Zachary A.; Dräger, Andreas; Ebrahim, Ali
- PLOS Computational Biology, Vol. 11, Issue 8
Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM
journal, July 2013
- Dreyfuss, Jonathan M.; Zucker, Jeremy D.; Hood, Heather M.
- PLoS Computational Biology, Vol. 9, Issue 7
TopHat: discovering splice junctions with RNA-Seq
journal, March 2009
- Trapnell, Cole; Pachter, Lior; Salzberg, Steven L.
- Bioinformatics, Vol. 25, Issue 9
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
journal, February 2015
- Pertea, Mihaela; Pertea, Geo M.; Antonescu, Corina M.
- Nature Biotechnology, Vol. 33, Issue 3
Ballgown bridges the gap between transcriptome assembly and expression analysis
journal, March 2015
- Frazee, Alyssa C.; Pertea, Geo; Jaffe, Andrew E.
- Nature Biotechnology, Vol. 33, Issue 3
Efficiently gap-filling reaction networks
journal, June 2014
- Latendresse, Mario
- BMC Bioinformatics, Vol. 15, Issue 1
KBase: The United States Department of Energy Systems Biology Knowledgebase
journal, July 2018
- Arkin, Adam P.; Cottingham, Robert W.; Henry, Christopher S.
- Nature Biotechnology, Vol. 36, Issue 7
HISAT: a fast spliced aligner with low memory requirements
journal, March 2015
- Kim, Daehwan; Langmead, Ben; Salzberg, Steven L.
- Nature Methods, Vol. 12, Issue 4
High-throughput generation, optimization and analysis of genome-scale metabolic models
journal, August 2010
- Henry, Christopher S.; DeJongh, Matthew; Best, Aaron A.
- Nature Biotechnology, Vol. 28, Issue 9
Efficiently gap-filling reaction networks
journal, June 2014
- Latendresse, Mario
- BMC Bioinformatics, Vol. 15, Issue 1
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
journal, December 2014
- Love, Michael I.; Huber, Wolfgang; Anders, Simon
- Genome Biology, Vol. 15, Issue 12
Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm
journal, March 2015
- Seaver, Samuel M. D.; Bradbury, Louis M. T.; Frelin, Océane
- Frontiers in Plant Science, Vol. 6
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
journal, November 2013
- Overbeek, Ross; Olson, Robert; Pusch, Gordon D.
- Nucleic Acids Research, Vol. 42, Issue D1
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
journal, January 2013
- Kim, Daehwan; Pertea, Geo; Trapnell, Cole
- Genome Biology, Vol. 14, Issue 4
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
journal, January 2013
- Kim, Daehwan; Pertea, Geo; Trapnell, Cole
- Genome Biology, Vol. 14, Issue 4
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
journal, March 2012
- Trapnell, Cole; Roberts, Adam; Goff, Loyal
- Nature Protocols, Vol. 7, Issue 3
PlantSEED enables automated annotation and reconstruction of plant primary metabolism with improved compartmentalization and comparative consistency
journal, August 2018
- Seaver, Samuel M. D.; Lerma‐Ortiz, Claudia; Conrad, Neal
- The Plant Journal, Vol. 95, Issue 6
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
journal, December 2014
- Love, Michael I.; Huber, Wolfgang; Anders, Simon
- Genome Biology, Vol. 15, Issue 12
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy
journal, August 2015
- Emms, David M.; Kelly, Steven
- Genome Biology, Vol. 16, Issue 1
Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM
journal, July 2013
- Dreyfuss, Jonathan M.; Zucker, Jeremy D.; Hood, Heather M.
- PLoS Computational Biology, Vol. 9, Issue 7