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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.


Distribution and classification of 3679 tomato lncRNAs. (A) Genome-wide distribution of tomato lncRNAs compared with that of protein-coding genes. Chromosomes 0–12 (SL2.50 genome) are shown with different colours and in a circular form as the outer thick track. The inner chromosome scale (Mb) is labelled on each chromosome. White circles show approximate centromere locations. On the second track (outer to inner), each vertical blue line reports the location of lncRNAs throughout the whole tomato genome. For the next two tracks, the abundance of lncRNAs and protein-coding genes in physical bins of 10Mb for each chromosome are shown by blue and red columns, respectively. (B) Classification of tomato lncRNAs according to its genomic position and overlap with protein-coding genes. Numbers of lncRNAs in the Watson or Crick strand for each of the four main classes were labelled on the columns (intergenic, intragenic, overlap, and antisense lncRNAs). The proportion of the four kinds of lncRNAs was calculated. A scheme of the position of the lncRNA (black box) relative to neighbouring genes (black empty box) is shown at the bottom.
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Figure 2: Distribution and classification of 3679 tomato lncRNAs. (A) Genome-wide distribution of tomato lncRNAs compared with that of protein-coding genes. Chromosomes 0–12 (SL2.50 genome) are shown with different colours and in a circular form as the outer thick track. The inner chromosome scale (Mb) is labelled on each chromosome. White circles show approximate centromere locations. On the second track (outer to inner), each vertical blue line reports the location of lncRNAs throughout the whole tomato genome. For the next two tracks, the abundance of lncRNAs and protein-coding genes in physical bins of 10Mb for each chromosome are shown by blue and red columns, respectively. (B) Classification of tomato lncRNAs according to its genomic position and overlap with protein-coding genes. Numbers of lncRNAs in the Watson or Crick strand for each of the four main classes were labelled on the columns (intergenic, intragenic, overlap, and antisense lncRNAs). The proportion of the four kinds of lncRNAs was calculated. A scheme of the position of the lncRNA (black box) relative to neighbouring genes (black empty box) is shown at the bottom.

Mentions: Next the lncRNAs were mapped onto the recently released tomato reference genome (Tomato Genome Consortium, 2012). A Circos plot clearly showed that tomato lncRNAs were not evenly distributed across chromosomes (Fig. 2A). Similar to protein-coding genes, lncRNAs have lower densities in the pericentromeric heterochromatin regions than in the euchromatin (Fig. 2A). This result suggested that lncRNAs may share similar features of transcription with the protein-coding genes. In addition, some lncRNAs were transcribed from loci much closer to the telomeres than protein-coding genes. For instance, some lncRNAs were generated from the ends of chromosomes #1 and 3 (Fig. 2A).


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)

Distribution and classification of 3679 tomato lncRNAs. (A) Genome-wide distribution of tomato lncRNAs compared with that of protein-coding genes. Chromosomes 0–12 (SL2.50 genome) are shown with different colours and in a circular form as the outer thick track. The inner chromosome scale (Mb) is labelled on each chromosome. White circles show approximate centromere locations. On the second track (outer to inner), each vertical blue line reports the location of lncRNAs throughout the whole tomato genome. For the next two tracks, the abundance of lncRNAs and protein-coding genes in physical bins of 10Mb for each chromosome are shown by blue and red columns, respectively. (B) Classification of tomato lncRNAs according to its genomic position and overlap with protein-coding genes. Numbers of lncRNAs in the Watson or Crick strand for each of the four main classes were labelled on the columns (intergenic, intragenic, overlap, and antisense lncRNAs). The proportion of the four kinds of lncRNAs was calculated. A scheme of the position of the lncRNA (black box) relative to neighbouring genes (black empty box) is shown at the bottom.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
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Figure 2: Distribution and classification of 3679 tomato lncRNAs. (A) Genome-wide distribution of tomato lncRNAs compared with that of protein-coding genes. Chromosomes 0–12 (SL2.50 genome) are shown with different colours and in a circular form as the outer thick track. The inner chromosome scale (Mb) is labelled on each chromosome. White circles show approximate centromere locations. On the second track (outer to inner), each vertical blue line reports the location of lncRNAs throughout the whole tomato genome. For the next two tracks, the abundance of lncRNAs and protein-coding genes in physical bins of 10Mb for each chromosome are shown by blue and red columns, respectively. (B) Classification of tomato lncRNAs according to its genomic position and overlap with protein-coding genes. Numbers of lncRNAs in the Watson or Crick strand for each of the four main classes were labelled on the columns (intergenic, intragenic, overlap, and antisense lncRNAs). The proportion of the four kinds of lncRNAs was calculated. A scheme of the position of the lncRNA (black box) relative to neighbouring genes (black empty box) is shown at the bottom.
Mentions: Next the lncRNAs were mapped onto the recently released tomato reference genome (Tomato Genome Consortium, 2012). A Circos plot clearly showed that tomato lncRNAs were not evenly distributed across chromosomes (Fig. 2A). Similar to protein-coding genes, lncRNAs have lower densities in the pericentromeric heterochromatin regions than in the euchromatin (Fig. 2A). This result suggested that lncRNAs may share similar features of transcription with the protein-coding genes. In addition, some lncRNAs were transcribed from loci much closer to the telomeres than protein-coding genes. For instance, some lncRNAs were generated from the ends of chromosomes #1 and 3 (Fig. 2A).

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.