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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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Distribution of tag expression.Left is PF and right is IF. Total clean tags represent the sum of all clean tag numbers; distinct clean tags represent all types of clean tags.
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pone-0047810-g001: Distribution of tag expression.Left is PF and right is IF. Total clean tags represent the sum of all clean tag numbers; distinct clean tags represent all types of clean tags.

Mentions: To identify differentially-expressed genes involved in the pistil development of flowers in Japanese apricot, we used Illumina sequencing on DGE from the perfect (PF) and imperfect (IF) flower buds. A total of 3,476,249 and 3,580,677 tags were obtained from the PF and IF flower bud libraries, respectively (Table 1). To increase the robustness of the approach, single-copy tags in the two libraries (141,270 in the PF and 142,287 in the IF library) were excluded from further analysis (Figure 1). After discarding the low quality tags (tags containing ā€˜Nā€™, adaptor sequences and copy number <2), 3,331,468 and 3,434,800 tags (clean tags) remained in the PF and IF libraries, from which 129,933 (PF) and 126,485 (IF) distinct tags were obtained (Figure 1). There were 3,448 more distinct tags in the PF than in the IF library, possibly representing genes related to pistil development. The percentage of distinct tags rapidly declined as copy number increased, indicating that only a small portion of the transcripts were expressed at a high level under the conditions tested.


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)

Distribution of tag expression.Left is PF and right is IF. Total clean tags represent the sum of all clean tag numbers; distinct clean tags represent all types of clean tags.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0047810-g001: Distribution of tag expression.Left is PF and right is IF. Total clean tags represent the sum of all clean tag numbers; distinct clean tags represent all types of clean tags.
Mentions: To identify differentially-expressed genes involved in the pistil development of flowers in Japanese apricot, we used Illumina sequencing on DGE from the perfect (PF) and imperfect (IF) flower buds. A total of 3,476,249 and 3,580,677 tags were obtained from the PF and IF flower bud libraries, respectively (Table 1). To increase the robustness of the approach, single-copy tags in the two libraries (141,270 in the PF and 142,287 in the IF library) were excluded from further analysis (Figure 1). After discarding the low quality tags (tags containing ā€˜Nā€™, adaptor sequences and copy number <2), 3,331,468 and 3,434,800 tags (clean tags) remained in the PF and IF libraries, from which 129,933 (PF) and 126,485 (IF) distinct tags were obtained (Figure 1). There were 3,448 more distinct tags in the PF than in the IF library, possibly representing genes related to pistil development. The percentage of distinct tags rapidly declined as copy number increased, indicating that only a small portion of the transcripts were expressed at a high level under the conditions tested.

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