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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

Distribution of clean tag copy number.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-g003: Distribution of clean tag copy number.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: The distribution of the clean tag copy number is shown in figure 3. The copy number of clean tags between 2 and 5 was 208,111, between 6 and 10 was 153,194, between 11 and 20 was 213,051, between 21 and 50 was 396,739, between 51 and 100 was 382,603, and >100 was 1,977,770 in the PF library. In contrast, the copy number of distinct clean tags was mostly distributed between 2 and 5, with 55.45% of the total clean tags in the PF library (Figure 3). In the IF library, the copy number of clean tags between 2 and 5 was 199,910, between 6 and 10 was 147,600, between 11 and 20 was 205,594, between 21 and 50 was 395,033, between 51 and 100 was 392,318, and >100 was 2,094,345. Similar to the PF library, the copy number of distinct clean tags was mostly distributed between 2 and 5, with 54.88% of the total clean tags in the IF library (Figure 3).


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 clean tag copy number.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-g003: Distribution of clean tag copy number.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: The distribution of the clean tag copy number is shown in figure 3. The copy number of clean tags between 2 and 5 was 208,111, between 6 and 10 was 153,194, between 11 and 20 was 213,051, between 21 and 50 was 396,739, between 51 and 100 was 382,603, and >100 was 1,977,770 in the PF library. In contrast, the copy number of distinct clean tags was mostly distributed between 2 and 5, with 55.45% of the total clean tags in the PF library (Figure 3). In the IF library, the copy number of clean tags between 2 and 5 was 199,910, between 6 and 10 was 147,600, between 11 and 20 was 205,594, between 21 and 50 was 395,033, between 51 and 100 was 392,318, and >100 was 2,094,345. Similar to the PF library, the copy number of distinct clean tags was mostly distributed between 2 and 5, with 54.88% of the total clean tags in the IF library (Figure 3).

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