Limits...
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.

Show MeSH

Related in: MedlinePlus

Histogram showing the Gene Ontology functional enrichment of DEGs.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3472986&req=5

pone-0047810-g005: Histogram showing the Gene Ontology functional enrichment of DEGs.

Mentions: Using the P-value ≤0.05 as the threshold value, 333 differentially expressed genes that could be categorised into 14 functional groups were found (Figure 5), which included four cellular components, four molecular functions and six biological processes. The four component categories were as follows: anchored to membrane (9), ribosome (16), ATPase complex (10) and organelle part (96). Based on molecular function, the genes were finally classified into four categories: ammonia ligase activity (3), acid-ammonia (or amide) ligase activity (3), Rho GTPase activator activity (2) and transferase activity (37). Additionally, six biological processes were identified: nitrogen cycle metabolism (3), proton transport (6), fatty acid metabolism (20), cellular component organisation or biogenesis at the cellular level (44), glutamine metabolism (3) and small molecule metabolism (81). The genes involved in small molecule metabolism [GO: 0044281] were the most significantly enriched in comparison to the other five biological processes. Forty-four differentially expressed genes were involved in the cellular component organisation or biogenesis at the cellular level [GO: 0071841], which is carried out at the cellular level and results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component. Among the significantly enriched transcripts were 20 DEGs associated with the regulation of fatty acid metabolism [GO: 0006631], which includes the chemical reactions and pathways involving fatty acids and aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.


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 showing the Gene Ontology functional enrichment of DEGs.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0047810-g005: Histogram showing the Gene Ontology functional enrichment of DEGs.
Mentions: Using the P-value ≤0.05 as the threshold value, 333 differentially expressed genes that could be categorised into 14 functional groups were found (Figure 5), which included four cellular components, four molecular functions and six biological processes. The four component categories were as follows: anchored to membrane (9), ribosome (16), ATPase complex (10) and organelle part (96). Based on molecular function, the genes were finally classified into four categories: ammonia ligase activity (3), acid-ammonia (or amide) ligase activity (3), Rho GTPase activator activity (2) and transferase activity (37). Additionally, six biological processes were identified: nitrogen cycle metabolism (3), proton transport (6), fatty acid metabolism (20), cellular component organisation or biogenesis at the cellular level (44), glutamine metabolism (3) and small molecule metabolism (81). The genes involved in small molecule metabolism [GO: 0044281] were the most significantly enriched in comparison to the other five biological processes. Forty-four differentially expressed genes were involved in the cellular component organisation or biogenesis at the cellular level [GO: 0071841], which is carried out at the cellular level and results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component. Among the significantly enriched transcripts were 20 DEGs associated with the regulation of fatty acid metabolism [GO: 0006631], which includes the chemical reactions and pathways involving fatty acids and aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.

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