Transcriptional dynamics of two seed compartments with opposing roles in Arabidopsis seed germination. / Dekkers, Bas JW; Pearce, Simon; van Bolderen-Veldkamp, R.P. (Marieke); Marshall, Alex; Widera, Pawel; Gilbert, James; Drost, Hajk-Georg; Bassel, Georg W.; Müller, Kerstin; King, John R.; Wood, Andrew T.A.; Quint, Marcel; Krasnogor, Natalio; Leubner-Metzger, Gerhard; Holdsworth, Mike; Bentsink, Leonie.

In: Plant physiology, Vol. 163, 13.07.2013, p. 205-215.

Research output: Contribution to journalArticlepeer-review

Published

Standard

Transcriptional dynamics of two seed compartments with opposing roles in Arabidopsis seed germination. / Dekkers, Bas JW; Pearce, Simon; van Bolderen-Veldkamp, R.P. (Marieke); Marshall, Alex; Widera, Pawel; Gilbert, James; Drost, Hajk-Georg; Bassel, Georg W.; Müller, Kerstin; King, John R.; Wood, Andrew T.A.; Quint, Marcel; Krasnogor, Natalio; Leubner-Metzger, Gerhard; Holdsworth, Mike; Bentsink, Leonie.

In: Plant physiology, Vol. 163, 13.07.2013, p. 205-215.

Research output: Contribution to journalArticlepeer-review

Harvard

Dekkers, BJW, Pearce, S, van Bolderen-Veldkamp, RPM, Marshall, A, Widera, P, Gilbert, J, Drost, H-G, Bassel, GW, Müller, K, King, JR, Wood, ATA, Quint, M, Krasnogor, N, Leubner-Metzger, G, Holdsworth, M & Bentsink, L 2013, 'Transcriptional dynamics of two seed compartments with opposing roles in Arabidopsis seed germination', Plant physiology, vol. 163, pp. 205-215. https://doi.org/http:/?/?dx.?doi.?org/?10.?1104/?pp.?113.?223511

APA

Dekkers, B. JW., Pearce, S., van Bolderen-Veldkamp, R. P. M., Marshall, A., Widera, P., Gilbert, J., Drost, H-G., Bassel, G. W., Müller, K., King, J. R., Wood, A. T. A., Quint, M., Krasnogor, N., Leubner-Metzger, G., Holdsworth, M., & Bentsink, L. (2013). Transcriptional dynamics of two seed compartments with opposing roles in Arabidopsis seed germination. Plant physiology, 163, 205-215. https://doi.org/http:/?/?dx.?doi.?org/?10.?1104/?pp.?113.?223511

Vancouver

Dekkers BJW, Pearce S, van Bolderen-Veldkamp RPM, Marshall A, Widera P, Gilbert J et al. Transcriptional dynamics of two seed compartments with opposing roles in Arabidopsis seed germination. Plant physiology. 2013 Jul 13;163:205-215. https://doi.org/http:/?/?dx.?doi.?org/?10.?1104/?pp.?113.?223511

Author

Dekkers, Bas JW ; Pearce, Simon ; van Bolderen-Veldkamp, R.P. (Marieke) ; Marshall, Alex ; Widera, Pawel ; Gilbert, James ; Drost, Hajk-Georg ; Bassel, Georg W. ; Müller, Kerstin ; King, John R. ; Wood, Andrew T.A. ; Quint, Marcel ; Krasnogor, Natalio ; Leubner-Metzger, Gerhard ; Holdsworth, Mike ; Bentsink, Leonie. / Transcriptional dynamics of two seed compartments with opposing roles in Arabidopsis seed germination. In: Plant physiology. 2013 ; Vol. 163. pp. 205-215.

BibTeX

@article{9d02f14727ed41c8bfb14ee56502da99,
title = "Transcriptional dynamics of two seed compartments with opposing roles in Arabidopsis seed germination",
abstract = "Seed germination is a critical stage in the plant life cycle and the first step towards successful plant establishment. Understanding germination is therefore of important ecological and agronomical relevance. Previous research revealed that different seed compartments (testa, endosperm and embryo) control germination, but little is known about the underlying spatial and temporal transcriptome changes that lead to seed germination. We analyzed genome-wide expression in germinating Arabidopsis thaliana seeds with both temporal and spatial detail and provide web accessible visualizations of the data reported (vseed.nottingham.ac.uk). We show the potential of this high resolution data set for the construction of meaningful co-expression networks, which provide insight into the genetic control of germination. The data set reveals two transcriptional phases during germination that are separated by testa rupture. The first phase is marked by large transcriptome changes as the seed switches from a dry, quiescent state to a hydrated and active state. At the end of this first transcriptional phase the number of differentially expressed genes between consecutive time points drop. This increases again at testa rupture, the start of the second transcriptional phase. Transcriptome data indicates a role for mechano-induced signalling at this stage, and subsequently highlights the fates of the endosperm and radicle; senescence and growth respectively. Finally, using a phylotranscriptomic approach we show that expression levels of evolutionary young genes drop during the first transcriptional phase and increase during the second phase. Evolutionary old genes show an opposite pattern, suggesting a more conserved transcriptome prior to the completion of germination.",
author = "Dekkers, {Bas JW} and Simon Pearce and {van Bolderen-Veldkamp}, {R.P. (Marieke)} and Alex Marshall and Pawel Widera and James Gilbert and Hajk-Georg Drost and Bassel, {Georg W.} and Kerstin M{\"u}ller and King, {John R.} and Wood, {Andrew T.A.} and Marcel Quint and Natalio Krasnogor and Gerhard Leubner-Metzger and Mike Holdsworth and Leonie Bentsink",
note = "Joint senior authors: Gerhard Leubner-Metzger, Michael J. Holdsworth, Leonie Bentsink",
year = "2013",
month = jul,
day = "13",
doi = "http:/?/?dx.?doi.?org/?10.?1104/?pp.?113.?223511",
language = "English",
volume = "163",
pages = "205--215",
journal = "Plant physiology",
issn = "0032-0889",
publisher = "American Society of Plant Biologists",

}

RIS

TY - JOUR

T1 - Transcriptional dynamics of two seed compartments with opposing roles in Arabidopsis seed germination

AU - Dekkers, Bas JW

AU - Pearce, Simon

AU - van Bolderen-Veldkamp, R.P. (Marieke)

AU - Marshall, Alex

AU - Widera, Pawel

AU - Gilbert, James

AU - Drost, Hajk-Georg

AU - Bassel, Georg W.

AU - Müller, Kerstin

AU - King, John R.

AU - Wood, Andrew T.A.

AU - Quint, Marcel

AU - Krasnogor, Natalio

AU - Leubner-Metzger, Gerhard

AU - Holdsworth, Mike

AU - Bentsink, Leonie

N1 - Joint senior authors: Gerhard Leubner-Metzger, Michael J. Holdsworth, Leonie Bentsink

PY - 2013/7/13

Y1 - 2013/7/13

N2 - Seed germination is a critical stage in the plant life cycle and the first step towards successful plant establishment. Understanding germination is therefore of important ecological and agronomical relevance. Previous research revealed that different seed compartments (testa, endosperm and embryo) control germination, but little is known about the underlying spatial and temporal transcriptome changes that lead to seed germination. We analyzed genome-wide expression in germinating Arabidopsis thaliana seeds with both temporal and spatial detail and provide web accessible visualizations of the data reported (vseed.nottingham.ac.uk). We show the potential of this high resolution data set for the construction of meaningful co-expression networks, which provide insight into the genetic control of germination. The data set reveals two transcriptional phases during germination that are separated by testa rupture. The first phase is marked by large transcriptome changes as the seed switches from a dry, quiescent state to a hydrated and active state. At the end of this first transcriptional phase the number of differentially expressed genes between consecutive time points drop. This increases again at testa rupture, the start of the second transcriptional phase. Transcriptome data indicates a role for mechano-induced signalling at this stage, and subsequently highlights the fates of the endosperm and radicle; senescence and growth respectively. Finally, using a phylotranscriptomic approach we show that expression levels of evolutionary young genes drop during the first transcriptional phase and increase during the second phase. Evolutionary old genes show an opposite pattern, suggesting a more conserved transcriptome prior to the completion of germination.

AB - Seed germination is a critical stage in the plant life cycle and the first step towards successful plant establishment. Understanding germination is therefore of important ecological and agronomical relevance. Previous research revealed that different seed compartments (testa, endosperm and embryo) control germination, but little is known about the underlying spatial and temporal transcriptome changes that lead to seed germination. We analyzed genome-wide expression in germinating Arabidopsis thaliana seeds with both temporal and spatial detail and provide web accessible visualizations of the data reported (vseed.nottingham.ac.uk). We show the potential of this high resolution data set for the construction of meaningful co-expression networks, which provide insight into the genetic control of germination. The data set reveals two transcriptional phases during germination that are separated by testa rupture. The first phase is marked by large transcriptome changes as the seed switches from a dry, quiescent state to a hydrated and active state. At the end of this first transcriptional phase the number of differentially expressed genes between consecutive time points drop. This increases again at testa rupture, the start of the second transcriptional phase. Transcriptome data indicates a role for mechano-induced signalling at this stage, and subsequently highlights the fates of the endosperm and radicle; senescence and growth respectively. Finally, using a phylotranscriptomic approach we show that expression levels of evolutionary young genes drop during the first transcriptional phase and increase during the second phase. Evolutionary old genes show an opposite pattern, suggesting a more conserved transcriptome prior to the completion of germination.

U2 - http:/?/?dx.?doi.?org/?10.?1104/?pp.?113.?223511

DO - http:/?/?dx.?doi.?org/?10.?1104/?pp.?113.?223511

M3 - Article

VL - 163

SP - 205

EP - 215

JO - Plant physiology

JF - Plant physiology

SN - 0032-0889

ER -