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Alternative splicing during Arabidopsis flower development results in constitutive and stage-regulated isoforms.

Wang H, You C, Chang F, Wang Y, Wang L, Qi J, Ma H - Front Genet (2014)

Bottom Line: We identified approximately 24,000 genes that were expressed at one or more of these stages, and found that nearly 25% of multi-exon genes had two or more spliced variants.Moreover, 337 novel transcribed regions were identified and most of them have a single exon.Taken together, our analyses provide a comprehensive survey of AS in floral development and facilitate further genomic and genetic studies.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Genetic Engineering and Institute of Plant Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai, China ; Institutes of Biomedical Sciences, Fudan University Shanghai, China.

ABSTRACT
Alternative splicing (AS) is a process in eukaryotic gene expression, in which the primary transcript of a multi-exon gene is spliced into two or more different mature transcripts, thereby increasing proteome diversity. AS is often regulated differentially between different tissues or developmental stages. Recent studies suggested that up to 60% of intron-containing genes in Arabidopsis thaliana undergo AS. Yet little is known about this complicated and important process during floral development. To investigate the preferential expression of different isoforms of individual alternatively spliced genes, we used high throughput RNA-Seq technology to explore the transcriptomes of three floral development stages of Arabidopsis thaliana and obtained information of various AS events. We identified approximately 24,000 genes that were expressed at one or more of these stages, and found that nearly 25% of multi-exon genes had two or more spliced variants. This is less frequent than the previously reported 40-60% for multiple organs and stages of A. thaliana, indicating that many genes expressed in floral development function with a single predominant isoform. On the other hand, 1716 isoforms were differentially expressed between the three stages, suggesting that AS might still play important roles in stage transition during floral development. Moreover, 337 novel transcribed regions were identified and most of them have a single exon. Taken together, our analyses provide a comprehensive survey of AS in floral development and facilitate further genomic and genetic studies.

No MeSH data available.


Genes predicted based on RNA-Seq analysis for three floral developmental stages. (A) Number of highly confident genes expressed in each stage. (B) Unique and shared genes among three developmental stages. IM represents inflorescent meristem, F1–9 for flower development stage 1–9, F12 for flower development stage 12.
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Figure 2: Genes predicted based on RNA-Seq analysis for three floral developmental stages. (A) Number of highly confident genes expressed in each stage. (B) Unique and shared genes among three developmental stages. IM represents inflorescent meristem, F1–9 for flower development stage 1–9, F12 for flower development stage 12.

Mentions: To obtain an overview of the transcriptomes of flower development, we examined the distribution of gene expression values for each developmental stage. Each stage contained a group of genes with very low FPKM values, representing low expression or background. Taking a conservative approach, we used a cut-off of FPKM as 0.18 as a minimal expression value to avoid false positive estimation of gene expression, producing a unimodal distribution of genes expressed in each stage (Supplementary Figure 1). We detected 22,626 and 21,392 genes expressed at F12 and F1–9 stages, respectively (Figure 2A), much higher than the 14,833 and 14,460 genes previously reported for the same stages using microarray (Zhang et al., 2005). Compared with microarray technology, high throughput RNA-Seq technology could uncover the expression of many more genes.


Alternative splicing during Arabidopsis flower development results in constitutive and stage-regulated isoforms.

Wang H, You C, Chang F, Wang Y, Wang L, Qi J, Ma H - Front Genet (2014)

Genes predicted based on RNA-Seq analysis for three floral developmental stages. (A) Number of highly confident genes expressed in each stage. (B) Unique and shared genes among three developmental stages. IM represents inflorescent meristem, F1–9 for flower development stage 1–9, F12 for flower development stage 12.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3921568&req=5

Figure 2: Genes predicted based on RNA-Seq analysis for three floral developmental stages. (A) Number of highly confident genes expressed in each stage. (B) Unique and shared genes among three developmental stages. IM represents inflorescent meristem, F1–9 for flower development stage 1–9, F12 for flower development stage 12.
Mentions: To obtain an overview of the transcriptomes of flower development, we examined the distribution of gene expression values for each developmental stage. Each stage contained a group of genes with very low FPKM values, representing low expression or background. Taking a conservative approach, we used a cut-off of FPKM as 0.18 as a minimal expression value to avoid false positive estimation of gene expression, producing a unimodal distribution of genes expressed in each stage (Supplementary Figure 1). We detected 22,626 and 21,392 genes expressed at F12 and F1–9 stages, respectively (Figure 2A), much higher than the 14,833 and 14,460 genes previously reported for the same stages using microarray (Zhang et al., 2005). Compared with microarray technology, high throughput RNA-Seq technology could uncover the expression of many more genes.

Bottom Line: We identified approximately 24,000 genes that were expressed at one or more of these stages, and found that nearly 25% of multi-exon genes had two or more spliced variants.Moreover, 337 novel transcribed regions were identified and most of them have a single exon.Taken together, our analyses provide a comprehensive survey of AS in floral development and facilitate further genomic and genetic studies.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Genetic Engineering and Institute of Plant Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai, China ; Institutes of Biomedical Sciences, Fudan University Shanghai, China.

ABSTRACT
Alternative splicing (AS) is a process in eukaryotic gene expression, in which the primary transcript of a multi-exon gene is spliced into two or more different mature transcripts, thereby increasing proteome diversity. AS is often regulated differentially between different tissues or developmental stages. Recent studies suggested that up to 60% of intron-containing genes in Arabidopsis thaliana undergo AS. Yet little is known about this complicated and important process during floral development. To investigate the preferential expression of different isoforms of individual alternatively spliced genes, we used high throughput RNA-Seq technology to explore the transcriptomes of three floral development stages of Arabidopsis thaliana and obtained information of various AS events. We identified approximately 24,000 genes that were expressed at one or more of these stages, and found that nearly 25% of multi-exon genes had two or more spliced variants. This is less frequent than the previously reported 40-60% for multiple organs and stages of A. thaliana, indicating that many genes expressed in floral development function with a single predominant isoform. On the other hand, 1716 isoforms were differentially expressed between the three stages, suggesting that AS might still play important roles in stage transition during floral development. Moreover, 337 novel transcribed regions were identified and most of them have a single exon. Taken together, our analyses provide a comprehensive survey of AS in floral development and facilitate further genomic and genetic studies.

No MeSH data available.