Ryan, Patrick T. and Ó'Maoiléidigh, Diarmuid S. and Drost, Hajk-Georg and Kwasniewska, Kamila and Gabel, Alexander and Grosse, Ivo and Graciet, Emmanuelle and Quint, Marcel and Wellmer, Frank (2015) Patterns of gene expression during Arabidopsis flower development from the time of initiation to maturation. BMC Genomics, 16 (488). ISSN 1471-2164

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Abstract

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.

Item Type:	Article
Additional Information:	© 2015 Ryan et al. 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.
Keywords:	Arabidopsis thaliana; Flower development; Organ specification; Transcriptomics; Temporal gene expression; Paralog; Gene expression atlas;
Academic Unit:	Faculty of Science and Engineering > Biology
Item ID:	7424
Identification Number:	https://doi.org/10.1186/s12864-015-1699-6
Depositing User:	Emanuelle Graciet
Date Deposited:	02 Sep 2016 08:31
Journal or Publication Title:	BMC Genomics
Publisher:	Biomed Central
Refereed:	Yes
URI:
Use Licence:	This item is available under a Creative Commons Attribution Non Commercial Share Alike Licence (CC BY-NC-SA). Details of this licence are available here

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