Ag Data Commons
Browse

File(s) stored somewhere else

Please note: Linked content is NOT stored on Ag Data Commons and we can't guarantee its availability, quality, security or accept any liability.

Data from: Sporobolus stapfianus: Insights into desiccation tolerance in the resurrection grasses from linking transcriptomics to metabolomics

dataset
posted on 2023-12-18, 18:00 authored by Abou Yobi, Karen A. Schlauch, Richard L. Tillett, Won C. Yim, Catherine Espinoza, Bernard W.M. Wone, John C. Cushman, Melvin J. Oliver

Understanding the response of resurrection angiosperms to dehydration and rehydration is critical for deciphering the mechanisms of how plants cope with the rigors of water loss from their vegetative tissues. We have focused our studies on the C4 resurrection grass, Sporobolus stapfianus Gandoger, as a member of a group of important forage grasses. We have combined non-targeted metabolomics with transcriptomics, via a NimbleGen array platform, to develop an understanding of how gene expression and metabolite profiles can be linked to generate a more detailed mechanistic appreciation of the cellular response to both desiccation and rehydration. The rehydration transcriptome and metabolome are primarily geared towards the rapid return of photosynthesis, energy metabolism, protein turnover, and protein synthesis during the rehydration phase. However, there are some metabolites associated with ROS protection that remain elevated during rehydration, most notably the tocopherols. The analysis of the dehydration transcriptome reveals a strong concordance between transcript abundance and the associated metabolite abundance reported earlier, but only in responses that are directly related to cellular protection during dehydration: carbohydrate metabolism and redox homeostasis. The transcriptome response also provides strong support for the involvement of cellular protection processes as exemplified by the increases in the abundance of transcripts encoding late embryogenesis abundant (LEA) proteins, anti-oxidant enzymes, early light-induced proteins (ELIP) proteins, and cell-wall modification enzymes. There is little concordance between transcript and metabolite abundance for processes such as amino acid metabolism that do not appear to contribute directly to cellular protection, but are nonetheless important for the desiccation tolerant phenotype of S. stapfianus. The transcriptomes of both dehydration and rehydration offer insight into the complexity of the regulation of responses to these processes that involve complex signaling pathways and associated transcription factors. ABA appears to be important in the control of gene expression in both the latter stages of the dehydration and the early stages of rehydration. These findings add to the growing body of information detailing how plants tolerate and survive the severe cellular perturbations of dehydration, desiccation, and rehydration.


Resources in this dataset:

  • Resource Title: Pointer to Additional Files.

    File Name: Web Page, url: https://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-017-1013-7#Sec34

    Additional data files at BMC Plant Biology. Files are:

    Additional file 1: Table S1. Non-targeted global metabolite profiles of dehydrating and rehydrating Sporobolus stapfianus leaf tissues. (XLSX 190 kb)

    Additional file 2: Table S2. Gene Ontology (GO) enrichment of SDAT transcripts associated with the dehydration and rehydration of young leaves of Sporobolus stapfianus. (XLSX 24 kb)

    Additional file 3: Table S3. InterProScan protein signatures generated annotation for assembled contigs. (XLSX 306 kb)

    Additional file 4: Table S4a. ANOVA analysis and log2 expression values; 4b. Fold change (log2) in abundance and cluster assignment for SDATs during dehydration; 4c. Fold change (log2) and cluster assignment for SDATs during rehydration. (XLS 1622 kb)

    Additional file 5: Tables S5a, S5b, S5c, S5d. Representative lists of SDATs that have the greatest increase/decrease in abundance during dehydration/rehydration of young leaves of Sporobolus stapfianus. (XLS 78 kb)

    Additional file 6: Tables S6a - S6i. (XLS 308 kb)

    • Table S6a. SDATs encoding antioxidant enzymes and enzymes involved in antioxidant biosynthesis.

    • Table S6b. SDATs encoding enzymes involved in carbohydrate and energy metabolism.

    • Table S6c. SDATs encoding enzymes involved in cell wall biosynthesis and catabolism.

    • Table S6d. SDATs encoding kinases and phosphatases.

    • Table S6e. SDATs encoding transcription factors.

    • Table S6f. SDATs encoding late embryogenesis abundant (LEA) proteins.

    • Table S6g. SDATs encoding heat shock and molecular chaperones.

    • Table S6h. SDATs encoding ABA-induced transcripts.

    • Table S6i. SDATs encoding proteins and enzymes involved in protein biosynthesis and turnover.

    Additional file 7: Figure S1. Predominant clusters of SDATs that share distinct patterns of abundance during dehydration. (PDF 226 kb)

Funding

USDA-NIFA: 2007-55100-18374

National Institute of General Medical Sciences: P20GM103440

History

Data contact name

Oliver, Melvin J.

Data contact email

mel.oliver@ars.usda.gov

Publisher

BMC Plant Biology

Intended use

To help understand how plants tolerate and survive the severe cellular perturbations of dehydration, desiccation, and rehydration.

Theme

  • Not specified

ISO Topic Category

  • biota
  • environment
  • farming

National Agricultural Library Thesaurus terms

Sporobolus stapfianus; drought tolerance; transcriptomics; metabolomics; Angiospermae; rehydration; tissues; C4 plants; forage grasses; gene expression; metabolites; transcriptome; metabolome; photosynthesis; protein synthesis; tocopherols; homeostasis; embryogenesis; antioxidants; enzymes; amino acid metabolism; phenotype; transcription (genetics); signal transduction; transcription factors; abscisic acid; abiotic stress; desiccation (plant physiology)

OMB Program Code

  • 005:000 - (Primary Program Not Available)

Primary article PubAg Handle

Pending citation

  • No

Public Access Level

  • Public

Preferred dataset citation

Yobi, Abou; Schlauch, Karen A.; Tillett, Richard L.; Yim, Won C.; Espinoza, Catherine; Wone, Bernard W.M.; Cushman, John C.; Oliver, Melvin J. (2018). Data from: Sporobolus stapfianus: Insights into desiccation tolerance in the resurrection grasses from linking transcriptomics to metabolomics. BMC Plant Biology. https://doi.org/10.1186/s12870-017-1013-7

Usage metrics

    Licence

    Exports

    RefWorks
    BibTeX
    Ref. manager
    Endnote
    DataCite
    NLM
    DC