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RNA sequencing and functional analysis implicate the regulatory role of long non-coding RNAs in tomato fruit ripening.

Zhu B, Yang Y, Li R, Fu D, Wen L, Luo Y, Zhu H - J. Exp. Bot. (2015)

Bottom Line: It was also observed that 490 lncRNAs were significantly up-regulated in ripening mutant fruits, and 187 lncRNAs were down-regulated, indicating that lncRNAs could be involved in the regulation of fruit ripening.In line with this, silencing of two novel tomato intergenic lncRNAs, lncRNA1459 and lncRNA1840, resulted in an obvious delay of ripening of wild-type fruit.Overall, the results indicated that lncRNAs might be essential regulators of tomato fruit ripening, which sheds new light on the regulation of fruit ripening.

View Article: PubMed Central - PubMed

Affiliation: Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.

No MeSH data available.


qRT–qPCR validation of RNA-Seq data on accumulation of 10 arbitrarily selected ripening-related lncRNAs. Down-regulated lncRNAs (A) and up-regulated lncRNAs (B) in rin according to RNA-Seq data were quantified. Actin expression values were used as the internal reference. The relative level of lncRNA transcripts was normalized to that in AC fruits where the amount was arbitrarily assigned a value of 1. Error bars indicate ±SD of three biological replicates, each measured in triplicate. Asterisks indicate a significant difference as determined by Student’s t-test (*P<0.05; **P<0.01).
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Figure 6: qRT–qPCR validation of RNA-Seq data on accumulation of 10 arbitrarily selected ripening-related lncRNAs. Down-regulated lncRNAs (A) and up-regulated lncRNAs (B) in rin according to RNA-Seq data were quantified. Actin expression values were used as the internal reference. The relative level of lncRNA transcripts was normalized to that in AC fruits where the amount was arbitrarily assigned a value of 1. Error bars indicate ±SD of three biological replicates, each measured in triplicate. Asterisks indicate a significant difference as determined by Student’s t-test (*P<0.05; **P<0.01).

Mentions: Because the rin mutant showed a strong non-ripening phenotype compared with AC, it was hypothesized that there might be some novel ripening-related lncRNAs present in rin. Bioinformatics analysis revealed that 3530 of the 3679 tomato lncRNAs were accumulated in both AC and rin (Fig. 5A). Only 23 and 126 lncRNAs were expressed specifically in AC or rin, respectively (Fig. 5A). To identify further ripening-related lncRNAs, the levels of lncRNAs were compared between AC and rin. A total of 677 lncRNAs were significantly differentially expressed between AC and rin. Compared with AC, 490 of 677 lncRNAs were up-regulated in rin, and the other 187 lncRNAs were down-regulated (Fig. 5B). To investigate whether these differentially expressed lncRNAs are engaged in fruit ripening, 10 of them were arbitrarily selected, five from a highly up-regulated group and five from a down-regulated group. The differences in their expression levels observed by RNA-Seq were experimentally validated by qRT–PCR (Fig. 6). In addition, the fold change in the lncRNA expression level of qRT–PCR and RNA-Seq was closely correlated (R2=0.76, P<0.001) (Supplementary Fig. S1 at JXB online). These results indicated that these lncRNAs were indeed ripening-related lncRNAs in tomato fruits, further suggesting that these lncRNAs are likely to play some roles in fruit ripening.


RNA sequencing and functional analysis implicate the regulatory role of long non-coding RNAs in tomato fruit ripening.

Zhu B, Yang Y, Li R, Fu D, Wen L, Luo Y, Zhu H - J. Exp. Bot. (2015)

qRT–qPCR validation of RNA-Seq data on accumulation of 10 arbitrarily selected ripening-related lncRNAs. Down-regulated lncRNAs (A) and up-regulated lncRNAs (B) in rin according to RNA-Seq data were quantified. Actin expression values were used as the internal reference. The relative level of lncRNA transcripts was normalized to that in AC fruits where the amount was arbitrarily assigned a value of 1. Error bars indicate ±SD of three biological replicates, each measured in triplicate. Asterisks indicate a significant difference as determined by Student’s t-test (*P<0.05; **P<0.01).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Figure 6: qRT–qPCR validation of RNA-Seq data on accumulation of 10 arbitrarily selected ripening-related lncRNAs. Down-regulated lncRNAs (A) and up-regulated lncRNAs (B) in rin according to RNA-Seq data were quantified. Actin expression values were used as the internal reference. The relative level of lncRNA transcripts was normalized to that in AC fruits where the amount was arbitrarily assigned a value of 1. Error bars indicate ±SD of three biological replicates, each measured in triplicate. Asterisks indicate a significant difference as determined by Student’s t-test (*P<0.05; **P<0.01).
Mentions: Because the rin mutant showed a strong non-ripening phenotype compared with AC, it was hypothesized that there might be some novel ripening-related lncRNAs present in rin. Bioinformatics analysis revealed that 3530 of the 3679 tomato lncRNAs were accumulated in both AC and rin (Fig. 5A). Only 23 and 126 lncRNAs were expressed specifically in AC or rin, respectively (Fig. 5A). To identify further ripening-related lncRNAs, the levels of lncRNAs were compared between AC and rin. A total of 677 lncRNAs were significantly differentially expressed between AC and rin. Compared with AC, 490 of 677 lncRNAs were up-regulated in rin, and the other 187 lncRNAs were down-regulated (Fig. 5B). To investigate whether these differentially expressed lncRNAs are engaged in fruit ripening, 10 of them were arbitrarily selected, five from a highly up-regulated group and five from a down-regulated group. The differences in their expression levels observed by RNA-Seq were experimentally validated by qRT–PCR (Fig. 6). In addition, the fold change in the lncRNA expression level of qRT–PCR and RNA-Seq was closely correlated (R2=0.76, P<0.001) (Supplementary Fig. S1 at JXB online). These results indicated that these lncRNAs were indeed ripening-related lncRNAs in tomato fruits, further suggesting that these lncRNAs are likely to play some roles in fruit ripening.

Bottom Line: It was also observed that 490 lncRNAs were significantly up-regulated in ripening mutant fruits, and 187 lncRNAs were down-regulated, indicating that lncRNAs could be involved in the regulation of fruit ripening.In line with this, silencing of two novel tomato intergenic lncRNAs, lncRNA1459 and lncRNA1840, resulted in an obvious delay of ripening of wild-type fruit.Overall, the results indicated that lncRNAs might be essential regulators of tomato fruit ripening, which sheds new light on the regulation of fruit ripening.

View Article: PubMed Central - PubMed

Affiliation: Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.

No MeSH data available.