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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.


Related in: MedlinePlus

Detailed schematic diagram of the informatics pipeline for identification of tomato lncRNAs. Paired-end strand-specific RNA-Seq was performed for AC and rin fruits at the BR stage. Clean reads were mapped and assembled according to the known tomato genome using TopHat and Cufflinks. Transcripts were filtered with the six criteria for identification of putative lncRNAs. (i) Not tomato coding genes; (2) length >200 nucleotides and ORF <100 amino acids; (iii) not encoding known protein domains; (iv) little coding potential; (v) not housekeeping ncRNAs; and (vi) not miRNA precursors. At each step, a green arrow indicates those transcripts which were passed by the filter; a red arrow, those that were excluded. The number of transcripts that di not pass the filter is shown.
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Figure 1: Detailed schematic diagram of the informatics pipeline for identification of tomato lncRNAs. Paired-end strand-specific RNA-Seq was performed for AC and rin fruits at the BR stage. Clean reads were mapped and assembled according to the known tomato genome using TopHat and Cufflinks. Transcripts were filtered with the six criteria for identification of putative lncRNAs. (i) Not tomato coding genes; (2) length >200 nucleotides and ORF <100 amino acids; (iii) not encoding known protein domains; (iv) little coding potential; (v) not housekeeping ncRNAs; and (vi) not miRNA precursors. At each step, a green arrow indicates those transcripts which were passed by the filter; a red arrow, those that were excluded. The number of transcripts that di not pass the filter is shown.

Mentions: Paired-end ssRNA-Seq has become a powerful tool for the discovery of lncRNA (Ilott and Ponting, 2013), but also facilitates identification of transcript orientation. To identify lncRNAs in tomato fruits, paired-end ssRNA-Seq of transcripts from AC and rin fruits at the BR stage was performed in two biological replicates. A total of ~28 million clean reads was obtained (Table 1; Fig.1). A total of 38 159 unique transcripts were assembled from high-throughput RNA-Seq data from AC and rin fruits (Fig. 1).


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)

Detailed schematic diagram of the informatics pipeline for identification of tomato lncRNAs. Paired-end strand-specific RNA-Seq was performed for AC and rin fruits at the BR stage. Clean reads were mapped and assembled according to the known tomato genome using TopHat and Cufflinks. Transcripts were filtered with the six criteria for identification of putative lncRNAs. (i) Not tomato coding genes; (2) length >200 nucleotides and ORF <100 amino acids; (iii) not encoding known protein domains; (iv) little coding potential; (v) not housekeeping ncRNAs; and (vi) not miRNA precursors. At each step, a green arrow indicates those transcripts which were passed by the filter; a red arrow, those that were excluded. The number of transcripts that di not pass the filter is shown.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 1: Detailed schematic diagram of the informatics pipeline for identification of tomato lncRNAs. Paired-end strand-specific RNA-Seq was performed for AC and rin fruits at the BR stage. Clean reads were mapped and assembled according to the known tomato genome using TopHat and Cufflinks. Transcripts were filtered with the six criteria for identification of putative lncRNAs. (i) Not tomato coding genes; (2) length >200 nucleotides and ORF <100 amino acids; (iii) not encoding known protein domains; (iv) little coding potential; (v) not housekeeping ncRNAs; and (vi) not miRNA precursors. At each step, a green arrow indicates those transcripts which were passed by the filter; a red arrow, those that were excluded. The number of transcripts that di not pass the filter is shown.
Mentions: Paired-end ssRNA-Seq has become a powerful tool for the discovery of lncRNA (Ilott and Ponting, 2013), but also facilitates identification of transcript orientation. To identify lncRNAs in tomato fruits, paired-end ssRNA-Seq of transcripts from AC and rin fruits at the BR stage was performed in two biological replicates. A total of ~28 million clean reads was obtained (Table 1; Fig.1). A total of 38 159 unique transcripts were assembled from high-throughput RNA-Seq data from AC and rin fruits (Fig. 1).

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.


Related in: MedlinePlus