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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

Comparison of gene expression levels between the two libraries.For comparing gene expression levels between the two libraries, each library was normalised to 1 million tags. Red dots represent transcripts more prevalent in the infected leaf library, green dots show those present at a lower frequency in the infected tissue and blue dots indicate transcripts that did not change significantly. The parameters FDR <0.001 and log2 ratio ≥ 1 were used as the threshold to judge the significance of gene expression difference.
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pone-0047810-g007: Comparison of gene expression levels between the two libraries.For comparing gene expression levels between the two libraries, each library was normalised to 1 million tags. Red dots represent transcripts more prevalent in the infected leaf library, green dots show those present at a lower frequency in the infected tissue and blue dots indicate transcripts that did not change significantly. The parameters FDR <0.001 and log2 ratio ≥ 1 were used as the threshold to judge the significance of gene expression difference.

Mentions: Differences in the tag frequencies that appeared in the PF and IF libraries were used to estimate gene expression levels in response to pistil abortion. The transcripts detected with at least a two-fold difference between the two libraries are shown in Figure 7 (FDR <0.001). The red dots (468) and green dots (221) represent transcripts with a higher or lower abundance of more than two-fold than in the PF library, respectively. The blue dots represent transcripts that differed less than two-fold between the two libraries, which were arbitrarily designated as “no difference in expression”. The differentially-expressed genes with five-fold or greater differences in accumulation are shown in Figure 8 and Table 2. About 0.23% total unique tags increased by at least five-fold, and about 0.47% total unique tags were decreased by at least five-fold in the IF library, while the expression level of 99.3% unique tags was within the five-fold difference between the two samples.


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)

Comparison of gene expression levels between the two libraries.For comparing gene expression levels between the two libraries, each library was normalised to 1 million tags. Red dots represent transcripts more prevalent in the infected leaf library, green dots show those present at a lower frequency in the infected tissue and blue dots indicate transcripts that did not change significantly. The parameters FDR <0.001 and log2 ratio ≥ 1 were used as the threshold to judge the significance of gene expression difference.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0047810-g007: Comparison of gene expression levels between the two libraries.For comparing gene expression levels between the two libraries, each library was normalised to 1 million tags. Red dots represent transcripts more prevalent in the infected leaf library, green dots show those present at a lower frequency in the infected tissue and blue dots indicate transcripts that did not change significantly. The parameters FDR <0.001 and log2 ratio ≥ 1 were used as the threshold to judge the significance of gene expression difference.
Mentions: Differences in the tag frequencies that appeared in the PF and IF libraries were used to estimate gene expression levels in response to pistil abortion. The transcripts detected with at least a two-fold difference between the two libraries are shown in Figure 7 (FDR <0.001). The red dots (468) and green dots (221) represent transcripts with a higher or lower abundance of more than two-fold than in the PF library, respectively. The blue dots represent transcripts that differed less than two-fold between the two libraries, which were arbitrarily designated as “no difference in expression”. The differentially-expressed genes with five-fold or greater differences in accumulation are shown in Figure 8 and Table 2. About 0.23% total unique tags increased by at least five-fold, and about 0.47% total unique tags were decreased by at least five-fold in the IF library, while the expression level of 99.3% unique tags was within the five-fold difference between the two samples.

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