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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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Histogram illustrating pathway enrichment analyses.
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pone-0047810-g006: Histogram illustrating pathway enrichment analyses.

Mentions: A Q-value of ≤0.05 defined those genes that were significantly differentially expressed (enriched). 227 differentially expressed genes associated with 12 metabolic and signal transduction pathways were found (Figure 6). The pathways with the most unique genes were metabolic pathways (250 genes), cellular process (66 genes) and genetic information processing (20 genes). We believe that these pathways are significant in the pistil abortion of Japanese apricot, in particular metabolic pathways and cellular processes. In our study, metabolic pathways (ko01100) are large complexes comprising several metabolic patterns, including: the biosynthesis of secondary metabolites (ko01110, 66 genes); flavonoid biosynthesis (ko00941, 15); oxidative phosphorylation (ko00190, 10 genes); arginine and proline metabolism (ko00330, eight genes); galactose metabolism (ko00052, seven genes); the biosynthesis of unsaturated fatty acids (ko01040, seven genes); pyruvate metabolism (ko00620, seven genes); nitrogen metabolism (ko00910, six genes) and alanine, aspartate and glutamate metabolism (ko00330, six genes). Cellular processes included phagosome (ko04145, 14 genes) and endocytosis (ko04144, nine genes). Genetic information processing only included protein processing in the endoplasmic reticulum (ko04141, 20 genes).


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)

Histogram illustrating pathway enrichment analyses.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0047810-g006: Histogram illustrating pathway enrichment analyses.
Mentions: A Q-value of ≤0.05 defined those genes that were significantly differentially expressed (enriched). 227 differentially expressed genes associated with 12 metabolic and signal transduction pathways were found (Figure 6). The pathways with the most unique genes were metabolic pathways (250 genes), cellular process (66 genes) and genetic information processing (20 genes). We believe that these pathways are significant in the pistil abortion of Japanese apricot, in particular metabolic pathways and cellular processes. In our study, metabolic pathways (ko01100) are large complexes comprising several metabolic patterns, including: the biosynthesis of secondary metabolites (ko01110, 66 genes); flavonoid biosynthesis (ko00941, 15); oxidative phosphorylation (ko00190, 10 genes); arginine and proline metabolism (ko00330, eight genes); galactose metabolism (ko00052, seven genes); the biosynthesis of unsaturated fatty acids (ko01040, seven genes); pyruvate metabolism (ko00620, seven genes); nitrogen metabolism (ko00910, six genes) and alanine, aspartate and glutamate metabolism (ko00330, six genes). Cellular processes included phagosome (ko04145, 14 genes) and endocytosis (ko04144, nine genes). Genetic information processing only included protein processing in the endoplasmic reticulum (ko04141, 20 genes).

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