Abstract
The flower is essential for sexual reproduction of flowering plants and has been extensively studied. However, it is still not clear how many genes are expressed in the flower. Here, we performed RNA-seq analysis as a highly sensitive approach to investigate the Arabidopsis floral transcriptome at three developmental stages. We provide evidence that at least 23, 961 genes are active in the Arabidopsis flower, including 8512 genes that have not been reported as florally expressed previously. We compared gene expression at different stages and found that many genes encoding transcription factors are preferentially expressed in early flower development. Other genes with expression at distinct developmental stages included DUF577 in meiotic cells and DUF220, DUF1216, and Oleosin in stage 12 flowers. DUF1216 and DUF577 are Brassicaceae specific, and together with other families experienced expansion within the Brassicaceae lineage, suggesting novel/greater roles in Brassicaceae floral development than other plants. The large dataset from this study can serve as a resource for expression analysis of genes involved in flower development in Arabidopsis and for comparison with other species. Together, this work provides clues regarding molecular networks underlying flower development.
Highlights
Flower is one of the most complex structures of the angiosperms, and is thought to make great contribution to sexual reproduction in either developmental or evolutionary aspects (Alvarez-Buylla et al, 2010)
The inflorescent meristem (IM), stage 1–9 flowers (F1–9) and stage 12 flowers (F12) samples for RNA sequencing (RNA-seq) were collected in our lab, and the three samples were subjected to 50 bp single-end sequencing on a SOLiD 3 platform; details for the methods were recently described in a study for alternative splicing (Wang et al, 2014a)
GLOBAL GENE EXPRESSION OF FLOWER TRANSCRIPTOMES IN ARABIDOPSIS To obtain more insights about the overall transcriptome landscape during flower development, we analyzed RNA-seq datasets of the Arabidopsis flower at three developmental stages recently generated in our laboratory; these datasets were analyzed for alternative splicing in a separate study (Wang et al, 2014a): inflorescent meristem (IM), stage 1–9 flowers (F1–9) and stage 12 flowers (F12), detecting 21,181 (IM), 22,137 (F1–9), and 22,827 (F12) reliably expressed genes (Table S1, Figure S1)
Summary
Flower is one of the most complex structures of the angiosperms (flowering plants), and is thought to make great contribution to sexual reproduction in either developmental or evolutionary aspects (Alvarez-Buylla et al, 2010). More recently developed RNA sequencing (RNA-seq) technologies can overcome such limitations of hybridization-based approaches and other conventional largescale gene expression analysis methods (Marioni et al, 2008; Xiong et al, 2010). It has great sensitivity, allowing the detection of transcripts with lower expression levels, such as those of many transcription factors (Marioni et al, 2008; Chen et al, 2010). RNA-seq has been used for cell-specific analysis of actively translated mRNAs www.frontiersin.org
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