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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.


LncRNAs are shorter and have fewer exons than protein-coding transcripts. The distribution of length (A) and numbers of exons (B) of 3679 lncRNAs in comparison with 34 726 protein-coding transcripts of tomato (SL2.50 genome).
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Figure 3: LncRNAs are shorter and have fewer exons than protein-coding transcripts. The distribution of length (A) and numbers of exons (B) of 3679 lncRNAs in comparison with 34 726 protein-coding transcripts of tomato (SL2.50 genome).

Mentions: Previous studies have shown that both plant and animal lncRNAs are shorter and harbour fewer exons than protein-coding genes (Pauli et al., 2012; Li et al., 2014; Shuai et al., 2014). To determine whether tomato lncRNAs share these features, the distribution of length and exon number of 3679 lncRNAs were analysed compared with all tomato predicted protein-coding transcripts (34,726 genes from the SL2.50 genome). Figure 3A shows that ~78% of lncRNAs ranged in size from 200 to 1000 nucleotides, with only 22% >1000 nucleotides. In contrast, for the protein-coding transcripts, ~50% of them were >1000 nucleotides. Interestingly, most (90%) of the genes encoding tomato lncRNAs only contained one or two exons, while the number of exons for the protein-coding genes ranged from one to ≥10 (Fig. 3B). These results together indicated that, unlike protein-coding genes, the majority of the tomato lncRNAs are relatively shorter and contain fewer exons.


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)

LncRNAs are shorter and have fewer exons than protein-coding transcripts. The distribution of length (A) and numbers of exons (B) of 3679 lncRNAs in comparison with 34 726 protein-coding transcripts of tomato (SL2.50 genome).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4507755&req=5

Figure 3: LncRNAs are shorter and have fewer exons than protein-coding transcripts. The distribution of length (A) and numbers of exons (B) of 3679 lncRNAs in comparison with 34 726 protein-coding transcripts of tomato (SL2.50 genome).
Mentions: Previous studies have shown that both plant and animal lncRNAs are shorter and harbour fewer exons than protein-coding genes (Pauli et al., 2012; Li et al., 2014; Shuai et al., 2014). To determine whether tomato lncRNAs share these features, the distribution of length and exon number of 3679 lncRNAs were analysed compared with all tomato predicted protein-coding transcripts (34,726 genes from the SL2.50 genome). Figure 3A shows that ~78% of lncRNAs ranged in size from 200 to 1000 nucleotides, with only 22% >1000 nucleotides. In contrast, for the protein-coding transcripts, ~50% of them were >1000 nucleotides. Interestingly, most (90%) of the genes encoding tomato lncRNAs only contained one or two exons, while the number of exons for the protein-coding genes ranged from one to ≥10 (Fig. 3B). These results together indicated that, unlike protein-coding genes, the majority of the tomato lncRNAs are relatively shorter and contain fewer exons.

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.