We are analyzing https://link.springer.com/article/10.1186/1471-2164-12-514.

Title:
Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid | BMC Genomics
Description:
Background Higher plants exhibit remarkable phenotypic plasticity allowing them to adapt to an extensive range of environmental conditions. Sorghum is a cereal crop that exhibits exceptional tolerance to adverse conditions, in particular, water-limiting environments. This study utilized next generation sequencing (NGS) technology to examine the transcriptome of sorghum plants challenged with osmotic stress and exogenous abscisic acid (ABA) in order to elucidate genes and gene networks that contribute to sorghum
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Keywords {🔍}

pubmed, genes, article, google, scholar, cas, plant, gene, stress, sorghum, aba, expression, file, response, additional, drought, pathways, analysis, proteins, osmotic, central, arabidopsis, acid, pathway, biosynthesis, function, data, rnaseq, treatment, figure, number, plants, expressed, enrichment, tolerance, transcription, roots, cell, differentially, family, biol, root, rice, physiol, species, maize, shoots, responses, cdna, counts,

Topics {✒️}

helix-loop-helix-loop-helix domains late embryogenesis abundant org/pub/jgi_data/phytozome/v6 amino-acid-loop-extension class zinc-dependent dna-binding protein open access article heterotrimeric ccaat-box-binding complex blue long-dashed lines cn/download/gene_model_family/sbi ccgac cis-acting element helix-loop-helix article download pdf injured/infected potato tubers agriculture-agricultural research service represent background signal stressed genomics-bringing relief abre-binding bzip factor genome-wide targeted prediction repeated ap2/erf domains c-terminal tubby domains ap2/erebp transcription factors phosphoethanolamine n-methyltransferase results org/pub/gramene/pathways/sorghumcyc ß-alanine betaine biosynthesis temperature-sensitive male sterility riaño-pachón dm ap2-erebp tf family dtdp-l-rhamnose biosynthesis tata-box binding protein cis-acting elements found udp-n-acetylgalactosamine biosynthesis low-temperature-responsive elements repeated ap2/erf domain rna gel-blot analyses conserved dna-binding homeodomain dehydration-responsive elements dre2corezmrab17 rna-seq results differed putative leucine-zipper motif conserved c-terminal domain cytokinins-o-glucoside biosynthesis indole-3-acetic acid single ap2/erf domain protein-binding dna sequences c3/c4/cam photosynthesis central hypergeometric distribution full-length cdna microarray existing rna-seq resources sorghum cdna-array analyses cis-acting element full size image

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WebPage:
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         headline:Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid
         description:Higher plants exhibit remarkable phenotypic plasticity allowing them to adapt to an extensive range of environmental conditions. Sorghum is a cereal crop that exhibits exceptional tolerance to adverse conditions, in particular, water-limiting environments. This study utilized next generation sequencing (NGS) technology to examine the transcriptome of sorghum plants challenged with osmotic stress and exogenous abscisic acid (ABA) in order to elucidate genes and gene networks that contribute to sorghum's tolerance to water-limiting environments with a long-term aim of developing strategies to improve plant productivity under drought. RNA-Seq results revealed transcriptional activity of 28,335 unique genes from sorghum root and shoot tissues subjected to polyethylene glycol (PEG)-induced osmotic stress or exogenous ABA. Differential gene expression analyses in response to osmotic stress and ABA revealed a strong interplay among various metabolic pathways including abscisic acid and 13-lipoxygenase, salicylic acid, jasmonic acid, and plant defense pathways. Transcription factor analysis indicated that groups of genes may be co-regulated by similar regulatory sequences to which the expressed transcription factors bind. We successfully exploited the data presented here in conjunction with published transcriptome analyses for rice, maize, and Arabidopsis to discover more than 50 differentially expressed, drought-responsive gene orthologs for which no function had been previously ascribed. The present study provides an initial assemblage of sorghum genes and gene networks regulated by osmotic stress and hormonal treatment. We are providing an RNA-Seq data set and an initial collection of transcription factors, which offer a preliminary look into the cascade of global gene expression patterns that arise in a drought tolerant crop subjected to abiotic stress. These resources will allow scientists to query gene expression and functional annotation in response to drought.
         datePublished:2011-10-18T00:00:00Z
         dateModified:2011-10-18T00:00:00Z
         pageStart:1
         pageEnd:21
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         keywords:
            Gene Ontology
            Osmotic Stress
            Differentially Express
            Differentially Express Gene
            Late Embryogenesis Abundant
            Life Sciences
            general
            Microarrays
            Proteomics
            Animal Genetics and Genomics
            Microbial Genetics and Genomics
            Plant Genetics and Genomics
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                     address:
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      headline:Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid
      description:Higher plants exhibit remarkable phenotypic plasticity allowing them to adapt to an extensive range of environmental conditions. Sorghum is a cereal crop that exhibits exceptional tolerance to adverse conditions, in particular, water-limiting environments. This study utilized next generation sequencing (NGS) technology to examine the transcriptome of sorghum plants challenged with osmotic stress and exogenous abscisic acid (ABA) in order to elucidate genes and gene networks that contribute to sorghum's tolerance to water-limiting environments with a long-term aim of developing strategies to improve plant productivity under drought. RNA-Seq results revealed transcriptional activity of 28,335 unique genes from sorghum root and shoot tissues subjected to polyethylene glycol (PEG)-induced osmotic stress or exogenous ABA. Differential gene expression analyses in response to osmotic stress and ABA revealed a strong interplay among various metabolic pathways including abscisic acid and 13-lipoxygenase, salicylic acid, jasmonic acid, and plant defense pathways. Transcription factor analysis indicated that groups of genes may be co-regulated by similar regulatory sequences to which the expressed transcription factors bind. We successfully exploited the data presented here in conjunction with published transcriptome analyses for rice, maize, and Arabidopsis to discover more than 50 differentially expressed, drought-responsive gene orthologs for which no function had been previously ascribed. The present study provides an initial assemblage of sorghum genes and gene networks regulated by osmotic stress and hormonal treatment. We are providing an RNA-Seq data set and an initial collection of transcription factors, which offer a preliminary look into the cascade of global gene expression patterns that arise in a drought tolerant crop subjected to abiotic stress. These resources will allow scientists to query gene expression and functional annotation in response to drought.
      datePublished:2011-10-18T00:00:00Z
      dateModified:2011-10-18T00:00:00Z
      pageStart:1
      pageEnd:21
      license:https://creativecommons.org/licenses/by/2.0
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      keywords:
         Gene Ontology
         Osmotic Stress
         Differentially Express
         Differentially Express Gene
         Late Embryogenesis Abundant
         Life Sciences
         general
         Microarrays
         Proteomics
         Animal Genetics and Genomics
         Microbial Genetics and Genomics
         Plant Genetics and Genomics
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                  address:
                     name:USDA-ARS, Southern Plains Agricultural Research Center, College Station, USA
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Sunita Kumari
            affiliation:
                  name:Cold Spring Harbor
                  address:
                     name:Cold Spring Harbor Laboratory, Cold Spring Harbor, USA
                     type:PostalAddress
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            affiliation:
                  name:Cold Spring Harbor
                  address:
                     name:Cold Spring Harbor Laboratory, Cold Spring Harbor, USA
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         type:PostalAddress
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         type:PostalAddress
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         type:PostalAddress
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         type:PostalAddress
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            type:Organization
      name:Marcela K Monaco
      affiliation:
            name:Cold Spring Harbor
            address:
               name:Cold Spring Harbor Laboratory, Cold Spring Harbor, USA
               type:PostalAddress
            type:Organization
      name:Andrew Olson
      affiliation:
            name:Cold Spring Harbor
            address:
               name:Cold Spring Harbor Laboratory, Cold Spring Harbor, USA
               type:PostalAddress
            type:Organization
      name:Robert R Klein
      affiliation:
            name:Southern Plains Agricultural Research Center
            address:
               name:USDA-ARS, Southern Plains Agricultural Research Center, College Station, USA
               type:PostalAddress
            type:Organization
      name:Sunita Kumari
      affiliation:
            name:Cold Spring Harbor
            address:
               name:Cold Spring Harbor Laboratory, Cold Spring Harbor, USA
               type:PostalAddress
            type:Organization
      name:Doreen Ware
      affiliation:
            name:Cold Spring Harbor
            address:
               name:Cold Spring Harbor Laboratory, Cold Spring Harbor, USA
               type:PostalAddress
            type:Organization
            name:Cornell University
            address:
               name:USDA-ARS, Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, USA
               type:PostalAddress
            type:Organization
      name:Patricia E Klein
      affiliation:
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      name:Cold Spring Harbor Laboratory, Cold Spring Harbor, USA
      name:Cold Spring Harbor Laboratory, Cold Spring Harbor, USA
      name:USDA-ARS, Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, USA
      name:Department of Horticulture, Texas A&M University, College Station, USA

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