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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.


Silencing of novel intergenic lncRNAs delayed the ripening of fruits. After 2 or 3 weeks, tomato fruits infiltrated with TRV-RIN (B), TRV-lncRNA1459 (C), and TRV-lncRNA1840 (D) showed partial ripening compared with TRV control tomato fruit (A). Black arrows indicated the sites of injection on the carpopodium of tomato fruits. (D–G) Close up of TRV control, RIN silenced, lncRNA1459 silenced, and lncRNA1840 silenced fruits, respectively. (H) qRT–PCR analysis of RIN transcript in TRV control and TRV-RIN tomato fruits (yellow sections). (I) qRT–PCR analysis of lncRNA1459 transcript in TRV control and TRV-lncRNA1459 tomato fruits (red and green sections). (J) qRT–PCR analysis of lncRNA1840 transcript in TRV control and TRV-lncRNA1840 tomato fruits (red and yellow sections). Actin expression values were used for internal reference. The relative level of lncRNA transcripts was normalized to that in TRV control plants where the amount was arbitrarily assigned a value of 1. Error bars indicate ±SD of three biological replicates, each measured in triplicate. Data in columns with different letters are statistically different according to Duncan’s multiple range test at P<0.01. Asterisks indicate a significant difference as determined by Student’s t-test (*P<0.01).
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Figure 7: Silencing of novel intergenic lncRNAs delayed the ripening of fruits. After 2 or 3 weeks, tomato fruits infiltrated with TRV-RIN (B), TRV-lncRNA1459 (C), and TRV-lncRNA1840 (D) showed partial ripening compared with TRV control tomato fruit (A). Black arrows indicated the sites of injection on the carpopodium of tomato fruits. (D–G) Close up of TRV control, RIN silenced, lncRNA1459 silenced, and lncRNA1840 silenced fruits, respectively. (H) qRT–PCR analysis of RIN transcript in TRV control and TRV-RIN tomato fruits (yellow sections). (I) qRT–PCR analysis of lncRNA1459 transcript in TRV control and TRV-lncRNA1459 tomato fruits (red and green sections). (J) qRT–PCR analysis of lncRNA1840 transcript in TRV control and TRV-lncRNA1840 tomato fruits (red and yellow sections). Actin expression values were used for internal reference. The relative level of lncRNA transcripts was normalized to that in TRV control plants where the amount was arbitrarily assigned a value of 1. Error bars indicate ±SD of three biological replicates, each measured in triplicate. Data in columns with different letters are statistically different according to Duncan’s multiple range test at P<0.01. Asterisks indicate a significant difference as determined by Student’s t-test (*P<0.01).

Mentions: Compared with AC fruits, accumulation of intergenic lncRNA1459 and lncRNA1840 was lower in the rin mutant than in AC (Fig. 6A). It was hypothesized that lncRNA1459 and lncRNA1840 may regulate the ripening process of tomato fruits. To test this hypothesis, VIGS was performed to silence lncRNA1459 and lncRNA1840 in Micro-Tom fruits. VIGS of RIN was used as a positive control. Intriguingly, 2 or 3 weeks after infiltration, compared with TRV control fruits (already ripening) (Fig. 7A, D), tomato fruits injected with TRV-RIN, TRV-lncRNA1459, or TRV-lncRNA1840 showed partial ripening, with a ripening section (red) and a non-ripening section (green or yellow) (Fig. 7B–D, E–G). Semi-quantitative PCR analysis suggested that a recombinant virus could spread from carpopodiums to fruits (Supplementary Fig. S2 at JXB online), and then induce the VIGS of lncRNAs or RIN in tomato fruits. For positive VIGS control, the expression of RIN was decreased to 20% in the yellow section of tomato fruits (Fig. 7H). Compared with TRV control fruits, the transcript level of lncRNA1459 in the green sections of TRV-lncRNA1459 fruits was dramatically decreased by 65% (Fig. 7I). On the other hand, the expression of lncRNA1459 in the red sections of TRV-lncRNA1459 fruits was comparable with that in TRV control fruits. Similarly, the level of lncRNA1840 in yellow sections of TRV-lncRNA1840 fruits decreased to 18% compared with TRV control fruits (Fig. 7J). Therefore, the non-ripening phenotype of TRV-lncRNA1459 or TRV-lncRNA1840 fruits clearly resulted from the silencing of lncRNA1459 or lncRNA1840. The result strongly suggested that the two novel lncRNAs were involved in the regulation of tomato fruit ripening and might play an essential role 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)

Silencing of novel intergenic lncRNAs delayed the ripening of fruits. After 2 or 3 weeks, tomato fruits infiltrated with TRV-RIN (B), TRV-lncRNA1459 (C), and TRV-lncRNA1840 (D) showed partial ripening compared with TRV control tomato fruit (A). Black arrows indicated the sites of injection on the carpopodium of tomato fruits. (D–G) Close up of TRV control, RIN silenced, lncRNA1459 silenced, and lncRNA1840 silenced fruits, respectively. (H) qRT–PCR analysis of RIN transcript in TRV control and TRV-RIN tomato fruits (yellow sections). (I) qRT–PCR analysis of lncRNA1459 transcript in TRV control and TRV-lncRNA1459 tomato fruits (red and green sections). (J) qRT–PCR analysis of lncRNA1840 transcript in TRV control and TRV-lncRNA1840 tomato fruits (red and yellow sections). Actin expression values were used for internal reference. The relative level of lncRNA transcripts was normalized to that in TRV control plants where the amount was arbitrarily assigned a value of 1. Error bars indicate ±SD of three biological replicates, each measured in triplicate. Data in columns with different letters are statistically different according to Duncan’s multiple range test at P<0.01. Asterisks indicate a significant difference as determined by Student’s t-test (*P<0.01).
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Figure 7: Silencing of novel intergenic lncRNAs delayed the ripening of fruits. After 2 or 3 weeks, tomato fruits infiltrated with TRV-RIN (B), TRV-lncRNA1459 (C), and TRV-lncRNA1840 (D) showed partial ripening compared with TRV control tomato fruit (A). Black arrows indicated the sites of injection on the carpopodium of tomato fruits. (D–G) Close up of TRV control, RIN silenced, lncRNA1459 silenced, and lncRNA1840 silenced fruits, respectively. (H) qRT–PCR analysis of RIN transcript in TRV control and TRV-RIN tomato fruits (yellow sections). (I) qRT–PCR analysis of lncRNA1459 transcript in TRV control and TRV-lncRNA1459 tomato fruits (red and green sections). (J) qRT–PCR analysis of lncRNA1840 transcript in TRV control and TRV-lncRNA1840 tomato fruits (red and yellow sections). Actin expression values were used for internal reference. The relative level of lncRNA transcripts was normalized to that in TRV control plants where the amount was arbitrarily assigned a value of 1. Error bars indicate ±SD of three biological replicates, each measured in triplicate. Data in columns with different letters are statistically different according to Duncan’s multiple range test at P<0.01. Asterisks indicate a significant difference as determined by Student’s t-test (*P<0.01).
Mentions: Compared with AC fruits, accumulation of intergenic lncRNA1459 and lncRNA1840 was lower in the rin mutant than in AC (Fig. 6A). It was hypothesized that lncRNA1459 and lncRNA1840 may regulate the ripening process of tomato fruits. To test this hypothesis, VIGS was performed to silence lncRNA1459 and lncRNA1840 in Micro-Tom fruits. VIGS of RIN was used as a positive control. Intriguingly, 2 or 3 weeks after infiltration, compared with TRV control fruits (already ripening) (Fig. 7A, D), tomato fruits injected with TRV-RIN, TRV-lncRNA1459, or TRV-lncRNA1840 showed partial ripening, with a ripening section (red) and a non-ripening section (green or yellow) (Fig. 7B–D, E–G). Semi-quantitative PCR analysis suggested that a recombinant virus could spread from carpopodiums to fruits (Supplementary Fig. S2 at JXB online), and then induce the VIGS of lncRNAs or RIN in tomato fruits. For positive VIGS control, the expression of RIN was decreased to 20% in the yellow section of tomato fruits (Fig. 7H). Compared with TRV control fruits, the transcript level of lncRNA1459 in the green sections of TRV-lncRNA1459 fruits was dramatically decreased by 65% (Fig. 7I). On the other hand, the expression of lncRNA1459 in the red sections of TRV-lncRNA1459 fruits was comparable with that in TRV control fruits. Similarly, the level of lncRNA1840 in yellow sections of TRV-lncRNA1840 fruits decreased to 18% compared with TRV control fruits (Fig. 7J). Therefore, the non-ripening phenotype of TRV-lncRNA1459 or TRV-lncRNA1840 fruits clearly resulted from the silencing of lncRNA1459 or lncRNA1840. The result strongly suggested that the two novel lncRNAs were involved in the regulation of tomato fruit ripening and might play an essential role 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.