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Shared Metabolic Remodeling Processes Characterize the Transcriptome of Arabidopsis thaliana within Various Suborbital Flight Environments

Brandon Califar

Brandon Califar

  • Horticultural Sciences, University of FloridaGainesville,
  • The Genetics Institute, University of FloridaGainesville,
  • Program in Genetics and Genomics, University of FloridaGainesville,
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Califar, Brandon
, 
Agata Zupanska

Agata Zupanska

Horticultural Sciences, University of FloridaGainesville,
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Zupanska, Agata
, 
Jordan A. Callaham

Jordan A. Callaham

Horticultural Sciences, University of FloridaGainesville,
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Callaham, Jordan A.
, 
Matthew T. Bamsey

Matthew T. Bamsey

Canadian Space AgencyMontreal, Canada
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Bamsey, Matthew T.
, 
Thomas Graham

Thomas Graham

  • Canadian Space AgencyMontreal, Canada
  • Environmental Sciences, University of GuelphGuelph, Canada
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Graham, Thomas
, 
Anna-Lisa Paul

Anna-Lisa Paul

  • Horticultural Sciences, University of FloridaGainesville,
  • The Genetics Institute, University of FloridaGainesville,
  • Program in Genetics and Genomics, University of FloridaGainesville,
  • Program in Plant Molecular and Cellular Biology, University of FloridaGainesville,
  • Interdisciplinary Center for Biotechnology and Research, University of FloridaGainesville,
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Paul, Anna-Lisa
 y 
Robert J. Ferl

Robert J. Ferl

  • Horticultural Sciences, University of FloridaGainesville,
  • The Genetics Institute, University of FloridaGainesville,
  • Program in Genetics and Genomics, University of FloridaGainesville,
  • Program in Plant Molecular and Cellular Biology, University of FloridaGainesville,
  • Office of Research, University of FloridaGainesville,
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Ferl, Robert J.
  
29 ene 2021
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Categoría del artículo: Research Note
Publicado en línea: 29 ene 2021
Páginas: 13 - 29
DOI: https://doi.org/10.2478/gsr-2021-0002
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© 2021 Brandon Califar et al., published by Sciendo
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Figure 1

Flight profiles and experimental setup. (A) Basic diagrams of experimental flight profiles with information on fixation time-points, periods of hyper-g and μg, and the genotype(s) used in each experiment. Flight profiles are aligned by the onset of the parabolic stage of flight, designated T0. Harvests are denoted by the identifier used for that time-point, colored according to genotype information. (B) Representative image of Duvetyne-wrapped media plates (indicated by arrow) mounted to the sidewall of the FLEX imager. This setup was used for the BO (imaged) and VG flights. (C) Representative image of the Kennedy Space Center Fixation Tube (KFT) setup used for RNAlater™ fixation of seedlings in the F-104 (imaged), PF2013, and PF2015 experiments. Abbreviations: BO, Blue Origin; FLT, flight condition; GC, ground control; PF, parabolic flight; VG, virgin galactic.
Flight profiles and experimental setup. (A) Basic diagrams of experimental flight profiles with information on fixation time-points, periods of hyper-g and μg, and the genotype(s) used in each experiment. Flight profiles are aligned by the onset of the parabolic stage of flight, designated T0. Harvests are denoted by the identifier used for that time-point, colored according to genotype information. (B) Representative image of Duvetyne-wrapped media plates (indicated by arrow) mounted to the sidewall of the FLEX imager. This setup was used for the BO (imaged) and VG flights. (C) Representative image of the Kennedy Space Center Fixation Tube (KFT) setup used for RNAlater™ fixation of seedlings in the F-104 (imaged), PF2013, and PF2015 experiments. Abbreviations: BO, Blue Origin; FLT, flight condition; GC, ground control; PF, parabolic flight; VG, virgin galactic.

Figure 2

Transcriptomic comparisons. (A) Heatmap comparing DEGs from each experiment, arranged such that DEGs overlapping between the most experiments are located at the top. (B) Venn diagram, showing the DEG overlaps between the three suborbital transcriptomic datasets. (C) Venn diagram, showing the DEG overlaps between the BO WS data, parabolic flight data, and F-104 data. For both (B) and (C), the proportion of the total represented by each section of the diagram is represented as a percentage and by its coloration. Abbreviation: BO, Blue Origin; DEGs, differentially expressed genes.
Transcriptomic comparisons. (A) Heatmap comparing DEGs from each experiment, arranged such that DEGs overlapping between the most experiments are located at the top. (B) Venn diagram, showing the DEG overlaps between the three suborbital transcriptomic datasets. (C) Venn diagram, showing the DEG overlaps between the BO WS data, parabolic flight data, and F-104 data. For both (B) and (C), the proportion of the total represented by each section of the diagram is represented as a percentage and by its coloration. Abbreviation: BO, Blue Origin; DEGs, differentially expressed genes.

Figure 3

GO term enrichment data. Overrepresented GO terms were identified using lists of DEGs for each experiment and time-point, separated by up- and downregulation. The full list of GO terms overrepresented across any of the experiments was trimmed using the REVIGO tool with the “Small” setting, and a subsequent cutoff to retain terms with <1,000 genes (Supek et al., 2011). The −Log10 transform of the q-values for the significance of the terms’ overrepresentation is represented. GO terms are ordered such that those shared between the most experiments are at the top. Abbreviations: DEGs, differentially expressed genes; GO, gene ontology.
GO term enrichment data. Overrepresented GO terms were identified using lists of DEGs for each experiment and time-point, separated by up- and downregulation. The full list of GO terms overrepresented across any of the experiments was trimmed using the REVIGO tool with the “Small” setting, and a subsequent cutoff to retain terms with <1,000 genes (Supek et al., 2011). The −Log10 transform of the q-values for the significance of the terms’ overrepresentation is represented. GO terms are ordered such that those shared between the most experiments are at the top. Abbreviations: DEGs, differentially expressed genes; GO, gene ontology.

Figure 4

KEGG conserved pathways. The KEGG metabolic pathways overview map representing the BO WS, PF2013, PF2015, and F-104 datasets. Pathways associated with DEGs in the datasets are colored based on their conservation, with red representing pathways altered in all four datasets. Black lines reflect lesser degrees of conservation between the experiments, where darker lines equate to higher levels of conservation. Abbreviations: BO, Blue Origin; DEGs, differentially expressed genes; KEGG, Kyoto Encyclopedia of Genes and Genomes; PF, parabolic flight.
KEGG conserved pathways. The KEGG metabolic pathways overview map representing the BO WS, PF2013, PF2015, and F-104 datasets. Pathways associated with DEGs in the datasets are colored based on their conservation, with red representing pathways altered in all four datasets. Black lines reflect lesser degrees of conservation between the experiments, where darker lines equate to higher levels of conservation. Abbreviations: BO, Blue Origin; DEGs, differentially expressed genes; KEGG, Kyoto Encyclopedia of Genes and Genomes; PF, parabolic flight.

Figure 5

KEGG pathway enrichments and pathway-associated DEGs. (A) KEGG pathways enriched within each dataset. The −Log10 transform of the q-values for the significance of the pathways’ enrichment is shown. (B) A heatmap of DEGs associated with enriched KEGG pathways. DEGs from all experiments are represented on the left for pathways enriched in any of the experiments. The KEGG pathways that each DEG is annotated to are indicated on the right side by yellow bars. Abbreviations: BO, Blue Origin; DEGs, differentially expressed genes; KEGG, Kyoto Encyclopedia of Genes and Genomes; PF, parabolic flight; VG, Virgin Galactic.
KEGG pathway enrichments and pathway-associated DEGs. (A) KEGG pathways enriched within each dataset. The −Log10 transform of the q-values for the significance of the pathways’ enrichment is shown. (B) A heatmap of DEGs associated with enriched KEGG pathways. DEGs from all experiments are represented on the left for pathways enriched in any of the experiments. The KEGG pathways that each DEG is annotated to are indicated on the right side by yellow bars. Abbreviations: BO, Blue Origin; DEGs, differentially expressed genes; KEGG, Kyoto Encyclopedia of Genes and Genomes; PF, parabolic flight; VG, Virgin Galactic.

Figure 6

The valine, leucine, and isoleucine degradation KEGG pathway. Nodes associated with DEGs in any of the experiments, also visualized in Figure 5B, were overlaid with a grid colored based on the directionality of DEGs associated with that node in each experiment. This graphic is derived from those generated using the KEGG's Search&Color Pathway tool. Abbreviations: BO, Blue Origin; DEGs, differentially expressed genes; KEGG, Kyoto Encyclopedia of Genes and Genomes; PF, parabolic flight; VG, Virgin Galactic.
The valine, leucine, and isoleucine degradation KEGG pathway. Nodes associated with DEGs in any of the experiments, also visualized in Figure 5B, were overlaid with a grid colored based on the directionality of DEGs associated with that node in each experiment. This graphic is derived from those generated using the KEGG's Search&Color Pathway tool. Abbreviations: BO, Blue Origin; DEGs, differentially expressed genes; KEGG, Kyoto Encyclopedia of Genes and Genomes; PF, parabolic flight; VG, Virgin Galactic.
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