A KBase case study on genome-wide transcriptomics and plant primary metabolism in response to drought stress in Sorghum.
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 e...
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Elsevier
2021
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oai:doaj.org-article:2087d5b2f21344b089f1fda6604a0faf2021-12-02T05:01:43ZA KBase case study on genome-wide transcriptomics and plant primary metabolism in response to drought stress in Sorghum.2214-662810.1016/j.cpb.2021.100229https://doaj.org/article/2087d5b2f21344b089f1fda6604a0faf2021-12-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S2214662821000347https://doaj.org/toc/2214-6628A 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.Sunita KumariVivek KumarKathleen BeilsmithSamuel M.D. SeaverShane CanonParamvir DehalTian GuMarcin JoachimiakClaudia Lerma-OrtizFilipe LiuZhenyuan LuEric PearsonPriya RanjanWilliam RielChristopher S. HenryAdam P. ArkinDoreen WareElsevierarticleKBaseTranscriptomicsBioinformaticsData analysisGene expressionRNA-seqBotanyQK1-989ENCurrent Plant Biology, Vol 28, Iss , Pp 100229- (2021) |
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| collection |
DOAJ |
| language |
EN |
| topic |
KBase Transcriptomics Bioinformatics Data analysis Gene expression RNA-seq Botany QK1-989 |
| spellingShingle |
KBase Transcriptomics Bioinformatics Data analysis Gene expression RNA-seq Botany QK1-989 Sunita Kumari Vivek Kumar Kathleen Beilsmith Samuel M.D. Seaver Shane Canon Paramvir Dehal Tian Gu Marcin Joachimiak Claudia Lerma-Ortiz Filipe Liu Zhenyuan Lu Eric Pearson Priya Ranjan William Riel Christopher S. Henry Adam P. Arkin Doreen Ware A KBase case study on genome-wide transcriptomics and plant primary metabolism in response to drought stress in Sorghum. |
| description |
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. |
| format |
article |
| author |
Sunita Kumari Vivek Kumar Kathleen Beilsmith Samuel M.D. Seaver Shane Canon Paramvir Dehal Tian Gu Marcin Joachimiak Claudia Lerma-Ortiz Filipe Liu Zhenyuan Lu Eric Pearson Priya Ranjan William Riel Christopher S. Henry Adam P. Arkin Doreen Ware |
| author_facet |
Sunita Kumari Vivek Kumar Kathleen Beilsmith Samuel M.D. Seaver Shane Canon Paramvir Dehal Tian Gu Marcin Joachimiak Claudia Lerma-Ortiz Filipe Liu Zhenyuan Lu Eric Pearson Priya Ranjan William Riel Christopher S. Henry Adam P. Arkin Doreen Ware |
| author_sort |
Sunita Kumari |
| title |
A KBase case study on genome-wide transcriptomics and plant primary metabolism in response to drought stress in Sorghum. |
| title_short |
A KBase case study on genome-wide transcriptomics and plant primary metabolism in response to drought stress in Sorghum. |
| title_full |
A KBase case study on genome-wide transcriptomics and plant primary metabolism in response to drought stress in Sorghum. |
| title_fullStr |
A KBase case study on genome-wide transcriptomics and plant primary metabolism in response to drought stress in Sorghum. |
| title_full_unstemmed |
A KBase case study on genome-wide transcriptomics and plant primary metabolism in response to drought stress in Sorghum. |
| title_sort |
kbase case study on genome-wide transcriptomics and plant primary metabolism in response to drought stress in sorghum. |
| publisher |
Elsevier |
| publishDate |
2021 |
| url |
https://doaj.org/article/2087d5b2f21344b089f1fda6604a0faf |
| work_keys_str_mv |
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