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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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Saturation evaluation of differential expression.The left figure is PF and the right figure is IF.
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pone-0047810-g002: Saturation evaluation of differential expression.The left figure is PF and the right figure is IF.

Mentions: The saturation of the library was determined by the identification of unique tags. Sequencing was considered to have reached saturation when no new unique tags were detected. The results shown in Figure 2 indicate that the PF and IF libraries were sequenced to saturation, producing a full representation of the transcripts in the conditions tested. In both libraries, fewer unique tags were identified as the number of sequencing tags increased, reaching a plateau shortly after 1 M tags were sequenced. No new unique tags were identified as the total tag number approached 3 M in the PF library and 2.5 M in the IF library.


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)

Saturation evaluation of differential expression.The left figure is PF and the right figure is IF.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0047810-g002: Saturation evaluation of differential expression.The left figure is PF and the right figure is IF.
Mentions: The saturation of the library was determined by the identification of unique tags. Sequencing was considered to have reached saturation when no new unique tags were detected. The results shown in Figure 2 indicate that the PF and IF libraries were sequenced to saturation, producing a full representation of the transcripts in the conditions tested. In both libraries, fewer unique tags were identified as the number of sequencing tags increased, reaching a plateau shortly after 1 M tags were sequenced. No new unique tags were identified as the total tag number approached 3 M in the PF library and 2.5 M in the IF library.

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