Evidence map›Paper›PMID 27208254›Full record

ArticlePlant physiology2016

Transcriptomes of Eight Arabidopsis thaliana Accessions Reveal Core Conserved, Genotype- and Organ-Specific Responses to Flooding Stress.

Hans van Veen, Divya Vashisht, Melis Akman, Thomas Girke, Angelika Mustroph, Emilie Reinen, Sjon Hartman, Maarten Kooiker, Peter van Tienderen, M Eric Schranz and 3 more

Open access · bronzeAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Plant physiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
54citing papers in PubMed, 1 pooled it
25.4field-weighted citation impact, top 1% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

54 citing papers in PubMed, 1 synthesis or guideline pooled it, 109 citations in OpenAlex.

  1. Pooled it
  2. Article
  3. Article
  4. Article
  5. Article
  6. Article
  7. Article
  8. Article
  9. Article
  10. Article
  11. Review
  12. Article
  13. Article
  14. Article
  15. Article
  16. Article
  17. Article
  18. Article
  19. Article
  20. Alternative Splicing and Its Roles in Plant Metabolism.International journal of molecular sciences · 2022
    Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

13 authors at 5 institutions in 4 countries.

Hans van VeenPlant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands (H.v.V., D.V., E.R., S.H., M.K., J.B.-S., L.A.C.J.V., R.S.);Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (H.v.V.);Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands (M.A., P.v.T.);Center for Plant Cell Biology, Botany, and Plant Sciences, University of California, Riverside, California 92521 (T.G., J.B.-S.);Department of Plant Physiology, Bayreuth University, 95447 Bayreuth, Germany (A.M.); andBiosystematics Group, Wageningen University, 6708 PB Wageningen, The Netherlands (M.E.S.).
Divya VashishtPlant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands (H.v.V., D.V., E.R., S.H., M.K., J.B.-S., L.A.C.J.V., R.S.);Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (H.v.V.);Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands (M.A., P.v.T.);Center for Plant Cell Biology, Botany, and Plant Sciences, University of California, Riverside, California 92521 (T.G., J.B.-S.);Department of Plant Physiology, Bayreuth University, 95447 Bayreuth, Germany (A.M.); andBiosystematics Group, Wageningen University, 6708 PB Wageningen, The Netherlands (M.E.S.).
Melis AkmanPlant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands (H.v.V., D.V., E.R., S.H., M.K., J.B.-S., L.A.C.J.V., R.S.);Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (H.v.V.);Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands (M.A., P.v.T.);Center for Plant Cell Biology, Botany, and Plant Sciences, University of California, Riverside, California 92521 (T.G., J.B.-S.);Department of Plant Physiology, Bayreuth University, 95447 Bayreuth, Germany (A.M.); andBiosystematics Group, Wageningen University, 6708 PB Wageningen, The Netherlands (M.E.S.).
Thomas GirkePlant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands (H.v.V., D.V., E.R., S.H., M.K., J.B.-S., L.A.C.J.V., R.S.);Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (H.v.V.);Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands (M.A., P.v.T.);Center for Plant Cell Biology, Botany, and Plant Sciences, University of California, Riverside, California 92521 (T.G., J.B.-S.);Department of Plant Physiology, Bayreuth University, 95447 Bayreuth, Germany (A.M.); andBiosystematics Group, Wageningen University, 6708 PB Wageningen, The Netherlands (M.E.S.).
Angelika MustrophPlant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands (H.v.V., D.V., E.R., S.H., M.K., J.B.-S., L.A.C.J.V., R.S.);Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (H.v.V.);Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands (M.A., P.v.T.);Center for Plant Cell Biology, Botany, and Plant Sciences, University of California, Riverside, California 92521 (T.G., J.B.-S.);Department of Plant Physiology, Bayreuth University, 95447 Bayreuth, Germany (A.M.); andBiosystematics Group, Wageningen University, 6708 PB Wageningen, The Netherlands (M.E.S.).
Emilie ReinenPlant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands (H.v.V., D.V., E.R., S.H., M.K., J.B.-S., L.A.C.J.V., R.S.);Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (H.v.V.);Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands (M.A., P.v.T.);Center for Plant Cell Biology, Botany, and Plant Sciences, University of California, Riverside, California 92521 (T.G., J.B.-S.);Department of Plant Physiology, Bayreuth University, 95447 Bayreuth, Germany (A.M.); andBiosystematics Group, Wageningen University, 6708 PB Wageningen, The Netherlands (M.E.S.).
Sjon HartmanPlant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands (H.v.V., D.V., E.R., S.H., M.K., J.B.-S., L.A.C.J.V., R.S.);Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (H.v.V.);Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands (M.A., P.v.T.);Center for Plant Cell Biology, Botany, and Plant Sciences, University of California, Riverside, California 92521 (T.G., J.B.-S.);Department of Plant Physiology, Bayreuth University, 95447 Bayreuth, Germany (A.M.); andBiosystematics Group, Wageningen University, 6708 PB Wageningen, The Netherlands (M.E.S.).ORCID 0000-0002-6709-6436
Maarten KooikerPlant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands (H.v.V., D.V., E.R., S.H., M.K., J.B.-S., L.A.C.J.V., R.S.);Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (H.v.V.);Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands (M.A., P.v.T.);Center for Plant Cell Biology, Botany, and Plant Sciences, University of California, Riverside, California 92521 (T.G., J.B.-S.);Department of Plant Physiology, Bayreuth University, 95447 Bayreuth, Germany (A.M.); andBiosystematics Group, Wageningen University, 6708 PB Wageningen, The Netherlands (M.E.S.).
Peter van TienderenPlant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands (H.v.V., D.V., E.R., S.H., M.K., J.B.-S., L.A.C.J.V., R.S.);Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (H.v.V.);Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands (M.A., P.v.T.);Center for Plant Cell Biology, Botany, and Plant Sciences, University of California, Riverside, California 92521 (T.G., J.B.-S.);Department of Plant Physiology, Bayreuth University, 95447 Bayreuth, Germany (A.M.); andBiosystematics Group, Wageningen University, 6708 PB Wageningen, The Netherlands (M.E.S.).
M Eric SchranzPlant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands (H.v.V., D.V., E.R., S.H., M.K., J.B.-S., L.A.C.J.V., R.S.);Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (H.v.V.);Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands (M.A., P.v.T.);Center for Plant Cell Biology, Botany, and Plant Sciences, University of California, Riverside, California 92521 (T.G., J.B.-S.);Department of Plant Physiology, Bayreuth University, 95447 Bayreuth, Germany (A.M.); andBiosystematics Group, Wageningen University, 6708 PB Wageningen, The Netherlands (M.E.S.).ORCID 0000-0001-6777-6565
Julia Bailey-SerresPlant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands (H.v.V., D.V., E.R., S.H., M.K., J.B.-S., L.A.C.J.V., R.S.);Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (H.v.V.);Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands (M.A., P.v.T.);Center for Plant Cell Biology, Botany, and Plant Sciences, University of California, Riverside, California 92521 (T.G., J.B.-S.);Department of Plant Physiology, Bayreuth University, 95447 Bayreuth, Germany (A.M.); andBiosystematics Group, Wageningen University, 6708 PB Wageningen, The Netherlands (M.E.S.).ORCID 0000-0002-8568-7125
Laurentius A C J VoesenekPlant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands (H.v.V., D.V., E.R., S.H., M.K., J.B.-S., L.A.C.J.V., R.S.);Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (H.v.V.);Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands (M.A., P.v.T.);Center for Plant Cell Biology, Botany, and Plant Sciences, University of California, Riverside, California 92521 (T.G., J.B.-S.);Department of Plant Physiology, Bayreuth University, 95447 Bayreuth, Germany (A.M.); andBiosystematics Group, Wageningen University, 6708 PB Wageningen, The Netherlands (M.E.S.).
Rashmi SasidharanPlant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands (H.v.V., D.V., E.R., S.H., M.K., J.B.-S., L.A.C.J.V., R.S.);Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy (H.v.V.);Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands (M.A., P.v.T.);Center for Plant Cell Biology, Botany, and Plant Sciences, University of California, Riverside, California 92521 (T.G., J.B.-S.);Department of Plant Physiology, Bayreuth University, 95447 Bayreuth, Germany (A.M.); andBiosystematics Group, Wageningen University, 6708 PB Wageningen, The Netherlands (M.E.S.) r.sasidharan@uu.nl.ORCID 0000-0002-6940-0657
Utrecht University · NLUniversity of Amsterdam · NLUniversity of California, Riverside · USUniversity of Bayreuth · DEWageningen University & Research · NL

Funding

Acquisition of a Scalable Storage Cluster for Data Intensive NIH ResearchS10OD016290 · OD · UNIVERSITY OF CALIFORNIA RIVERSIDE · PI GIRKE, THOMAS · 2014 to 2014
$593k
6 · The paper itself

Abstract

Climate change has increased the frequency and severity of flooding events, with significant negative impact on agricultural productivity. These events often submerge plant aerial organs and roots, limiting growth and survival due to a severe reduction in light reactions and gas exchange necessary for photosynthesis and respiration, respectively. To distinguish molecular responses to the compound stress imposed by submergence, we investigated transcriptomic adjustments to darkness in air and under submerged conditions using eight Arabidopsis (Arabidopsis thaliana) accessions differing significantly in sensitivity to submergence. Evaluation of root and rosette transcriptomes revealed an early transcriptional and posttranscriptional response signature that was conserved primarily across genotypes, although flooding susceptibility-associated and genotype-specific responses also were uncovered. Posttranscriptional regulation encompassed darkness- and submergence-induced alternative splicing of transcripts from pathways involved in the alternative mobilization of energy reserves. The organ-specific transcriptome adjustments reflected the distinct physiological status of roots and shoots. Root-specific transcriptome changes included marked up-regulation of chloroplast-encoded photosynthesis and redox-related genes, whereas those of the rosette were related to the regulation of development and growth processes. We identified a novel set of tolerance genes, recognized mainly by quantitative differences. These included a transcriptome signature of more pronounced gluconeogenesis in tolerant accessions, a response that included stress-induced alternative splicing. This study provides organ-specific molecular resolution of genetic variation in submergence responses involving interactions between darkness and low-oxygen constraints of flooding stress and demonstrates that early transcriptome plasticity, including alternative splicing, is associated with the ability to cope with a compound environmental stress.

Indexed as

FloodsTranscriptomeAdaptation, PhysiologicalArabidopsisDarknessGene Expression ProfilingGene Expression Regulation, PlantGene OntologyGenotypeOrgan SpecificityPhotosynthesisPlant RootsPlant ShootsReverse Transcriptase Polymerase Chain ReactionSignal TransductionSpecies SpecificityWater

Identifiers

PMID27208254
PMCPMC5047075
OpenAlexW2369934933

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.