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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

Alignment results of the clean tags.The figure exhibits the alignment statistics of the tag copy number and the tag type. Note: 1PM (sense or antisense): perfect match to gene (sense or antisense); 1 tag->1 gene: match to one gene; 1 tag->n gene: match to more than one gene; 1 MM (sense or antisense): match to gene (sense or antisense) with 1bp mismatch; PM Genome 1 tag->1 position: perfect match to genome sequence with one best hit; PM Genome 1 tag->n position: perfect match to genome sequence with multiple best hits; 1 MM Genome: match to genome sequence with 1bp mismatch; Unknown Tag: no match to gene (sense and anti-sense) and genome sequence.
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pone-0047810-g004: Alignment results of the clean tags.The figure exhibits the alignment statistics of the tag copy number and the tag type. Note: 1PM (sense or antisense): perfect match to gene (sense or antisense); 1 tag->1 gene: match to one gene; 1 tag->n gene: match to more than one gene; 1 MM (sense or antisense): match to gene (sense or antisense) with 1bp mismatch; PM Genome 1 tag->1 position: perfect match to genome sequence with one best hit; PM Genome 1 tag->n position: perfect match to genome sequence with multiple best hits; 1 MM Genome: match to genome sequence with 1bp mismatch; Unknown Tag: no match to gene (sense and anti-sense) and genome sequence.

Mentions: The distinct tags were compared against the genome and gene sequences of peach using BLASTn. Tags with a complete match or one base-pair mismatch were considered further. The results in Table 1 show that a proportion of tags (26.70% in the PF library and 27.52% in the IF library) matched to the peach genome, but 64,599 (49.72% of unique tags) and 58,309 (46.10% of unique tags) in the PF and IF libraries matched to 17,056 (59.45%) and 16,386 (57.12%) peach genes. Further analysis revealed that 57,871 unique tags (44.54%) in the PF library and 52,144 (41.23%) in the IF library matched to only one gene sequence in the peach genome (Table 1 and Figure 4), including perfect matching to genes and with a 1bp mismatch. These data indicate that approximately 50% of the transcripts predicted in Japanese apricot are expressed in the perfect or imperfect flowers, with more transcripts present in the perfect sample. Figure 4 shows that sense regulation, with clean sequencing tags perfectly mapped to the sense gene being 22.84% (antisense was 11.14%) and 21.39% (antisense was 9.86%) in PF and IF, respectively, was the main regulated model.


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)

Alignment results of the clean tags.The figure exhibits the alignment statistics of the tag copy number and the tag type. Note: 1PM (sense or antisense): perfect match to gene (sense or antisense); 1 tag->1 gene: match to one gene; 1 tag->n gene: match to more than one gene; 1 MM (sense or antisense): match to gene (sense or antisense) with 1bp mismatch; PM Genome 1 tag->1 position: perfect match to genome sequence with one best hit; PM Genome 1 tag->n position: perfect match to genome sequence with multiple best hits; 1 MM Genome: match to genome sequence with 1bp mismatch; Unknown Tag: no match to gene (sense and anti-sense) and genome sequence.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3472986&req=5

pone-0047810-g004: Alignment results of the clean tags.The figure exhibits the alignment statistics of the tag copy number and the tag type. Note: 1PM (sense or antisense): perfect match to gene (sense or antisense); 1 tag->1 gene: match to one gene; 1 tag->n gene: match to more than one gene; 1 MM (sense or antisense): match to gene (sense or antisense) with 1bp mismatch; PM Genome 1 tag->1 position: perfect match to genome sequence with one best hit; PM Genome 1 tag->n position: perfect match to genome sequence with multiple best hits; 1 MM Genome: match to genome sequence with 1bp mismatch; Unknown Tag: no match to gene (sense and anti-sense) and genome sequence.
Mentions: The distinct tags were compared against the genome and gene sequences of peach using BLASTn. Tags with a complete match or one base-pair mismatch were considered further. The results in Table 1 show that a proportion of tags (26.70% in the PF library and 27.52% in the IF library) matched to the peach genome, but 64,599 (49.72% of unique tags) and 58,309 (46.10% of unique tags) in the PF and IF libraries matched to 17,056 (59.45%) and 16,386 (57.12%) peach genes. Further analysis revealed that 57,871 unique tags (44.54%) in the PF library and 52,144 (41.23%) in the IF library matched to only one gene sequence in the peach genome (Table 1 and Figure 4), including perfect matching to genes and with a 1bp mismatch. These data indicate that approximately 50% of the transcripts predicted in Japanese apricot are expressed in the perfect or imperfect flowers, with more transcripts present in the perfect sample. Figure 4 shows that sense regulation, with clean sequencing tags perfectly mapped to the sense gene being 22.84% (antisense was 11.14%) and 21.39% (antisense was 9.86%) in PF and IF, respectively, was the main regulated model.

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