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Identification of differentially-expressed genes associated with pistil abortion in Japanese apricot by genome-wide transcriptional analysis.

Shi T, Gao Z, Wang L, Zhang Z, Zhuang W, Sun H, Zhong W - PLoS ONE (2012)

Bottom Line: There were 689 significant differentially-expressed genes between the two libraries.GO annotation revealed that highly ranked genes were those implicated in small molecule metabolism, cellular component organisation or biogenesis at the cellular level and fatty acid metabolism.The expression patterns of 36 differentially expressed genes were confirmed by real-time (RT)-PCR.

View Article: PubMed Central - PubMed

Affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, People's Republic China.

ABSTRACT
The phenomenon of pistil abortion widely occurs in Japanese apricot, and imperfect flowers with pistil abortion seriously decrease the yield in production. Although transcriptome analyses have been extensively studied in the past, a systematic study of differential gene expression has not been performed in Japanese apricot. To investigate genes related to the pistil development of Japanese apricot, high-throughput sequencing technology (Illumina) was employed to survey gene expression profiles from perfect and imperfect Japanese apricot flower buds. 3,476,249 and 3,580,677 tags were sequenced from two libraries constructed from perfect and imperfect flower buds of Japanese apricot, respectively. There were 689 significant differentially-expressed genes between the two libraries. GO annotation revealed that highly ranked genes were those implicated in small molecule metabolism, cellular component organisation or biogenesis at the cellular level and fatty acid metabolism. According to the results, we assumed that late embryogenesis abundant protein (LEA), Dicer-like 3 (DCL3) Xyloglucan endotransglucosylase/hydrolase 2 (XTH2), Pectin lyase-like superfamily protein (PPME1), Lipid transfer protein 3 (LTP3), Fatty acid biosynthesis 1 (FAB1) and Fatty acid desaturase 5 (FAD5) might have relationships with the pistil abortion in Japanese apricot. The expression patterns of 36 differentially expressed genes were confirmed by real-time (RT)-PCR. This is the first report of the Illumina RNA-seq technique being used for the analysis of differentially-expressed gene profiles related to pistil abortion that both computationally and experimentally provides valuable information for the further functional characterisation of genes associated with pistil development in woody plants.

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Related in: MedlinePlus

Digital gene expression tag profiling and quantitative real-time PCR analysis of the expression of randomly selected genes.All real-time PCR reactions were repeated three times and the data are presented as the mean ± SD. The x-axis indicates the different genes. The y-axis shows the expression levels: the left shows the relative expression level by qRT-PCR and the right shows tag number per million tags by DGE.
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pone-0047810-g009: Digital gene expression tag profiling and quantitative real-time PCR analysis of the expression of randomly selected genes.All real-time PCR reactions were repeated three times and the data are presented as the mean ± SD. The x-axis indicates the different genes. The y-axis shows the expression levels: the left shows the relative expression level by qRT-PCR and the right shows tag number per million tags by DGE.

Mentions: To confirm the reliability of Illumina sequencing technology, 36 genes were randomly selected for quantitative RT-PCR assays. The actual melting curves of 36 genes are showed in the Table S2. The expression level of each gene in the perfect and imperfect flower buds was compared with its abundance from the sequencing data of DGE sequencing (Figure 9). The apparent discrepancies with respect to ratio can be attributed to the essentially different algorithms determined by the two techniques. In the analysis of gene profiles, the DGE method generates absolute rather than relative expression measurements. However, the results showed that expression of these 36 genes was consistent between the qRT-PCR and the DGE analyses. Transcripts from highly abundant Illumina tags appeared at the expected high expression level in the quantitative PCR analyses. Additionally, high-fold changes were observed for genes that showed low copy-numbers in the PF library but high abundances in the IF library. For example, CPK13 (calcium-dependent protein kinase 13; ppa004141m) showed no expression in the PF library, whereas it was detected at levels of 8.86-fold in the IF library. It was significantly up-regulated by more than 15-fold in the RT-PCR analysis. Similarly, DCL3 (ppa021659m) was induced by more than 5-fold. In addition, FAD5 (ppa027208m) showed no expression in the IF library, while it was detected 14.26-fold in the IF library, and was significantly down-regulated in the RT-PCR analysis. These results confirmed the reliability of the transcriptome analysis.


Identification of differentially-expressed genes associated with pistil abortion in Japanese apricot by genome-wide transcriptional analysis.

Shi T, Gao Z, Wang L, Zhang Z, Zhuang W, Sun H, Zhong W - PLoS ONE (2012)

Digital gene expression tag profiling and quantitative real-time PCR analysis of the expression of randomly selected genes.All real-time PCR reactions were repeated three times and the data are presented as the mean ± SD. The x-axis indicates the different genes. The y-axis shows the expression levels: the left shows the relative expression level by qRT-PCR and the right shows tag number per million tags by DGE.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3472986&req=5

pone-0047810-g009: Digital gene expression tag profiling and quantitative real-time PCR analysis of the expression of randomly selected genes.All real-time PCR reactions were repeated three times and the data are presented as the mean ± SD. The x-axis indicates the different genes. The y-axis shows the expression levels: the left shows the relative expression level by qRT-PCR and the right shows tag number per million tags by DGE.
Mentions: To confirm the reliability of Illumina sequencing technology, 36 genes were randomly selected for quantitative RT-PCR assays. The actual melting curves of 36 genes are showed in the Table S2. The expression level of each gene in the perfect and imperfect flower buds was compared with its abundance from the sequencing data of DGE sequencing (Figure 9). The apparent discrepancies with respect to ratio can be attributed to the essentially different algorithms determined by the two techniques. In the analysis of gene profiles, the DGE method generates absolute rather than relative expression measurements. However, the results showed that expression of these 36 genes was consistent between the qRT-PCR and the DGE analyses. Transcripts from highly abundant Illumina tags appeared at the expected high expression level in the quantitative PCR analyses. Additionally, high-fold changes were observed for genes that showed low copy-numbers in the PF library but high abundances in the IF library. For example, CPK13 (calcium-dependent protein kinase 13; ppa004141m) showed no expression in the PF library, whereas it was detected at levels of 8.86-fold in the IF library. It was significantly up-regulated by more than 15-fold in the RT-PCR analysis. Similarly, DCL3 (ppa021659m) was induced by more than 5-fold. In addition, FAD5 (ppa027208m) showed no expression in the IF library, while it was detected 14.26-fold in the IF library, and was significantly down-regulated in the RT-PCR analysis. These results confirmed the reliability of the transcriptome analysis.

Bottom Line: There were 689 significant differentially-expressed genes between the two libraries.GO annotation revealed that highly ranked genes were those implicated in small molecule metabolism, cellular component organisation or biogenesis at the cellular level and fatty acid metabolism.The expression patterns of 36 differentially expressed genes were confirmed by real-time (RT)-PCR.

View Article: PubMed Central - PubMed

Affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, People's Republic China.

ABSTRACT
The phenomenon of pistil abortion widely occurs in Japanese apricot, and imperfect flowers with pistil abortion seriously decrease the yield in production. Although transcriptome analyses have been extensively studied in the past, a systematic study of differential gene expression has not been performed in Japanese apricot. To investigate genes related to the pistil development of Japanese apricot, high-throughput sequencing technology (Illumina) was employed to survey gene expression profiles from perfect and imperfect Japanese apricot flower buds. 3,476,249 and 3,580,677 tags were sequenced from two libraries constructed from perfect and imperfect flower buds of Japanese apricot, respectively. There were 689 significant differentially-expressed genes between the two libraries. GO annotation revealed that highly ranked genes were those implicated in small molecule metabolism, cellular component organisation or biogenesis at the cellular level and fatty acid metabolism. According to the results, we assumed that late embryogenesis abundant protein (LEA), Dicer-like 3 (DCL3) Xyloglucan endotransglucosylase/hydrolase 2 (XTH2), Pectin lyase-like superfamily protein (PPME1), Lipid transfer protein 3 (LTP3), Fatty acid biosynthesis 1 (FAB1) and Fatty acid desaturase 5 (FAD5) might have relationships with the pistil abortion in Japanese apricot. The expression patterns of 36 differentially expressed genes were confirmed by real-time (RT)-PCR. This is the first report of the Illumina RNA-seq technique being used for the analysis of differentially-expressed gene profiles related to pistil abortion that both computationally and experimentally provides valuable information for the further functional characterisation of genes associated with pistil development in woody plants.

Show MeSH
Related in: MedlinePlus