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Patterns of gene expression during Arabidopsis flower development from the time of initiation to maturation

BACKGROUND: The formation of flowers is one of the main model systems to elucidate the molecular mechanisms that control developmental processes in plants. Although several studies have explored gene expression during flower development in the model plant Arabidopsis thaliana on a genome-wide scale,...

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Autores principales: Ryan, Patrick T., Ó’Maoiléidigh, Diarmuid S., Drost, Hajk-Georg, Kwaśniewska, Kamila, Gabel, Alexander, Grosse, Ivo, Graciet, Emmanuelle, Quint, Marcel, Wellmer, Frank
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4488132/
https://www.ncbi.nlm.nih.gov/pubmed/26126740
http://dx.doi.org/10.1186/s12864-015-1699-6
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author Ryan, Patrick T.
Ó’Maoiléidigh, Diarmuid S.
Drost, Hajk-Georg
Kwaśniewska, Kamila
Gabel, Alexander
Grosse, Ivo
Graciet, Emmanuelle
Quint, Marcel
Wellmer, Frank
author_facet Ryan, Patrick T.
Ó’Maoiléidigh, Diarmuid S.
Drost, Hajk-Georg
Kwaśniewska, Kamila
Gabel, Alexander
Grosse, Ivo
Graciet, Emmanuelle
Quint, Marcel
Wellmer, Frank
author_sort Ryan, Patrick T.
collection PubMed
description BACKGROUND: The formation of flowers is one of the main model systems to elucidate the molecular mechanisms that control developmental processes in plants. Although several studies have explored gene expression during flower development in the model plant Arabidopsis thaliana on a genome-wide scale, a continuous series of expression data from the earliest floral stages until maturation has been lacking. Here, we used a floral induction system to close this information gap and to generate a reference dataset for stage-specific gene expression during flower formation. RESULTS: Using a floral induction system, we collected floral buds at 14 different stages from the time of initiation until maturation. Using whole-genome microarray analysis, we identified 7,405 genes that exhibit rapid expression changes during flower development. These genes comprise many known floral regulators and we found that the expression profiles for these regulators match their known expression patterns, thus validating the dataset. We analyzed groups of co-expressed genes for over-represented cellular and developmental functions through Gene Ontology analysis and found that they could be assigned specific patterns of activities, which are in agreement with the progression of flower development. Furthermore, by mapping binding sites of floral organ identity factors onto our dataset, we were able to identify gene groups that are likely predominantly under control of these transcriptional regulators. We further found that the distribution of paralogs among groups of co-expressed genes varies considerably, with genes expressed predominantly at early and intermediate stages of flower development showing the highest proportion of such genes. CONCLUSIONS: Our results highlight and describe the dynamic expression changes undergone by a large number of genes during flower development. They further provide a comprehensive reference dataset for temporal gene expression during flower formation and we demonstrate that it can be used to integrate data from other genomics approaches such as genome-wide localization studies of transcription factor binding sites. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1699-6) contains supplementary material, which is available to authorized users.
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spelling pubmed-44881322015-07-03 Patterns of gene expression during Arabidopsis flower development from the time of initiation to maturation Ryan, Patrick T. Ó’Maoiléidigh, Diarmuid S. Drost, Hajk-Georg Kwaśniewska, Kamila Gabel, Alexander Grosse, Ivo Graciet, Emmanuelle Quint, Marcel Wellmer, Frank BMC Genomics Research Article BACKGROUND: The formation of flowers is one of the main model systems to elucidate the molecular mechanisms that control developmental processes in plants. Although several studies have explored gene expression during flower development in the model plant Arabidopsis thaliana on a genome-wide scale, a continuous series of expression data from the earliest floral stages until maturation has been lacking. Here, we used a floral induction system to close this information gap and to generate a reference dataset for stage-specific gene expression during flower formation. RESULTS: Using a floral induction system, we collected floral buds at 14 different stages from the time of initiation until maturation. Using whole-genome microarray analysis, we identified 7,405 genes that exhibit rapid expression changes during flower development. These genes comprise many known floral regulators and we found that the expression profiles for these regulators match their known expression patterns, thus validating the dataset. We analyzed groups of co-expressed genes for over-represented cellular and developmental functions through Gene Ontology analysis and found that they could be assigned specific patterns of activities, which are in agreement with the progression of flower development. Furthermore, by mapping binding sites of floral organ identity factors onto our dataset, we were able to identify gene groups that are likely predominantly under control of these transcriptional regulators. We further found that the distribution of paralogs among groups of co-expressed genes varies considerably, with genes expressed predominantly at early and intermediate stages of flower development showing the highest proportion of such genes. CONCLUSIONS: Our results highlight and describe the dynamic expression changes undergone by a large number of genes during flower development. They further provide a comprehensive reference dataset for temporal gene expression during flower formation and we demonstrate that it can be used to integrate data from other genomics approaches such as genome-wide localization studies of transcription factor binding sites. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1699-6) contains supplementary material, which is available to authorized users. BioMed Central 2015-07-01 /pmc/articles/PMC4488132/ /pubmed/26126740 http://dx.doi.org/10.1186/s12864-015-1699-6 Text en © Ryan et al. 2015 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Ryan, Patrick T.
Ó’Maoiléidigh, Diarmuid S.
Drost, Hajk-Georg
Kwaśniewska, Kamila
Gabel, Alexander
Grosse, Ivo
Graciet, Emmanuelle
Quint, Marcel
Wellmer, Frank
Patterns of gene expression during Arabidopsis flower development from the time of initiation to maturation
title Patterns of gene expression during Arabidopsis flower development from the time of initiation to maturation
title_full Patterns of gene expression during Arabidopsis flower development from the time of initiation to maturation
title_fullStr Patterns of gene expression during Arabidopsis flower development from the time of initiation to maturation
title_full_unstemmed Patterns of gene expression during Arabidopsis flower development from the time of initiation to maturation
title_short Patterns of gene expression during Arabidopsis flower development from the time of initiation to maturation
title_sort patterns of gene expression during arabidopsis flower development from the time of initiation to maturation
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4488132/
https://www.ncbi.nlm.nih.gov/pubmed/26126740
http://dx.doi.org/10.1186/s12864-015-1699-6
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