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Transcriptome analysis of ripe and unripe fruit tissue of banana identifies major metabolic networks involved in fruit ripening process.

Asif MH, Lakhwani D, Pathak S, Gupta P, Bag SK, Nath P, Trivedi PK - BMC Plant Biol. (2014)

Bottom Line: Many of these are associated with cell wall degradation and synthesis of aromatic volatiles.A large number of differentially expressed genes did not align with any of the databases and might be novel genes in banana.The datasets developed in this study will help in developing strategies to manipulate banana fruit ripening and reduce post harvest losses.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Banana is one of the most important crop plants grown in the tropics and sub-tropics. It is a climacteric fruit and undergoes ethylene dependent ripening. Once ripening is initiated, it proceeds at a fast rate making postharvest life short, which can result in heavy economic losses. During the fruit ripening process a number of physiological and biochemical changes take place and thousands of genes from various metabolic pathways are recruited to produce a ripe and edible fruit. To better understand the underlying mechanism of ripening, we undertook a study to evaluate global changes in the transcriptome of the fruit during the ripening process.

Results: We sequenced the transcriptomes of the unripe and ripe stages of banana (Musa accuminata; Dwarf Cavendish) fruit. The transcriptomes were sequenced using a 454 GSFLX-Titanium platform that resulted in more than 7,00,000 high quality (HQ) reads. The assembly of the reads resulted in 19,410 contigs and 92,823 singletons. A large number of the differentially expressed genes identified were linked to ripening dependent processes including ethylene biosynthesis, perception and signalling, cell wall degradation and production of aromatic volatiles. In the banana fruit transcriptomes, we found transcripts included in 120 pathways described in the KEGG database for rice. The members of the expansin and xyloglucan transglycosylase/hydrolase (XTH) gene families were highly up-regulated during ripening, which suggests that they might play important roles in the softening of the fruit. Several genes involved in the synthesis of aromatic volatiles and members of transcription factor families previously reported to be involved in ripening were also identified.

Conclusions: A large number of differentially regulated genes were identified during banana fruit ripening. Many of these are associated with cell wall degradation and synthesis of aromatic volatiles. A large number of differentially expressed genes did not align with any of the databases and might be novel genes in banana. These genes can be good candidates for future studies to establish their role in banana fruit ripening. The datasets developed in this study will help in developing strategies to manipulate banana fruit ripening and reduce post harvest losses.

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The expression profiles for selected members of gene families associated with (A) Ethylene perception and signaling (B) cell wall modification and (C) aroma formation. Quantitative real time PCR of the gene families was carried out using total RNA isolated from fruit tissues. 0 to 8 represent the days post ethylene treatment in the banana fruits. The relative transcript abundance was normalised using banana actin gene.
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Fig4: The expression profiles for selected members of gene families associated with (A) Ethylene perception and signaling (B) cell wall modification and (C) aroma formation. Quantitative real time PCR of the gene families was carried out using total RNA isolated from fruit tissues. 0 to 8 represent the days post ethylene treatment in the banana fruits. The relative transcript abundance was normalised using banana actin gene.

Mentions: The differential expression of a few selected genes was confirmed by RT-qPCR. These genes were randomly selected from three categories including genes related to the ethylene signalling, aroma and softening. The expressions for each gene was examined in unripe fruit (0) and 2, 4, 6 and 8 days post ethylene treatment (Figure 4). In regard to genes related to ethylene signalling, of the ethylene receptor genes examined, expression of an ERS1-like gene and an EIN4-like gene increased markedly (>10-fold) during ripening. The CTR1 gene, which is downstream from the ethylene-receptors, initially showed a reduction in expression in the early stages of ripening, but had a significant increase in expression at 6 days post ethylene exposure (Figure 4). Similarly, the ETR1 gene showed a reduction in expression at day 2, which later increased at 6 days post ethylene exposure. Out of all the genes selected for analysis, one of the ERS1 genes did not show significant change in expression and the EIN4 gene showed a down-regulation during ripening process. The differential expression of these genes as analysed through quantitative real time PCR was similar to that observed in the comparative transcriptome analysis. The aroma related GTs and MTs showed a significant increase in expression as the ripening progressed, and this increase in expression generally began at day 4 and reached a maximum at day 6 of ripening. Expression of the aroma genes appears to correlated with the stage when the fruit emits a characteristic aroma and after this senescence and over-ripening sets in resulting in a less palitable fruit. The aroma volatiles are no longer needed and hence the expression of these genes starts to decrease.Figure 4


Transcriptome analysis of ripe and unripe fruit tissue of banana identifies major metabolic networks involved in fruit ripening process.

Asif MH, Lakhwani D, Pathak S, Gupta P, Bag SK, Nath P, Trivedi PK - BMC Plant Biol. (2014)

The expression profiles for selected members of gene families associated with (A) Ethylene perception and signaling (B) cell wall modification and (C) aroma formation. Quantitative real time PCR of the gene families was carried out using total RNA isolated from fruit tissues. 0 to 8 represent the days post ethylene treatment in the banana fruits. The relative transcript abundance was normalised using banana actin gene.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4263013&req=5

Fig4: The expression profiles for selected members of gene families associated with (A) Ethylene perception and signaling (B) cell wall modification and (C) aroma formation. Quantitative real time PCR of the gene families was carried out using total RNA isolated from fruit tissues. 0 to 8 represent the days post ethylene treatment in the banana fruits. The relative transcript abundance was normalised using banana actin gene.
Mentions: The differential expression of a few selected genes was confirmed by RT-qPCR. These genes were randomly selected from three categories including genes related to the ethylene signalling, aroma and softening. The expressions for each gene was examined in unripe fruit (0) and 2, 4, 6 and 8 days post ethylene treatment (Figure 4). In regard to genes related to ethylene signalling, of the ethylene receptor genes examined, expression of an ERS1-like gene and an EIN4-like gene increased markedly (>10-fold) during ripening. The CTR1 gene, which is downstream from the ethylene-receptors, initially showed a reduction in expression in the early stages of ripening, but had a significant increase in expression at 6 days post ethylene exposure (Figure 4). Similarly, the ETR1 gene showed a reduction in expression at day 2, which later increased at 6 days post ethylene exposure. Out of all the genes selected for analysis, one of the ERS1 genes did not show significant change in expression and the EIN4 gene showed a down-regulation during ripening process. The differential expression of these genes as analysed through quantitative real time PCR was similar to that observed in the comparative transcriptome analysis. The aroma related GTs and MTs showed a significant increase in expression as the ripening progressed, and this increase in expression generally began at day 4 and reached a maximum at day 6 of ripening. Expression of the aroma genes appears to correlated with the stage when the fruit emits a characteristic aroma and after this senescence and over-ripening sets in resulting in a less palitable fruit. The aroma volatiles are no longer needed and hence the expression of these genes starts to decrease.Figure 4

Bottom Line: Many of these are associated with cell wall degradation and synthesis of aromatic volatiles.A large number of differentially expressed genes did not align with any of the databases and might be novel genes in banana.The datasets developed in this study will help in developing strategies to manipulate banana fruit ripening and reduce post harvest losses.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Banana is one of the most important crop plants grown in the tropics and sub-tropics. It is a climacteric fruit and undergoes ethylene dependent ripening. Once ripening is initiated, it proceeds at a fast rate making postharvest life short, which can result in heavy economic losses. During the fruit ripening process a number of physiological and biochemical changes take place and thousands of genes from various metabolic pathways are recruited to produce a ripe and edible fruit. To better understand the underlying mechanism of ripening, we undertook a study to evaluate global changes in the transcriptome of the fruit during the ripening process.

Results: We sequenced the transcriptomes of the unripe and ripe stages of banana (Musa accuminata; Dwarf Cavendish) fruit. The transcriptomes were sequenced using a 454 GSFLX-Titanium platform that resulted in more than 7,00,000 high quality (HQ) reads. The assembly of the reads resulted in 19,410 contigs and 92,823 singletons. A large number of the differentially expressed genes identified were linked to ripening dependent processes including ethylene biosynthesis, perception and signalling, cell wall degradation and production of aromatic volatiles. In the banana fruit transcriptomes, we found transcripts included in 120 pathways described in the KEGG database for rice. The members of the expansin and xyloglucan transglycosylase/hydrolase (XTH) gene families were highly up-regulated during ripening, which suggests that they might play important roles in the softening of the fruit. Several genes involved in the synthesis of aromatic volatiles and members of transcription factor families previously reported to be involved in ripening were also identified.

Conclusions: A large number of differentially regulated genes were identified during banana fruit ripening. Many of these are associated with cell wall degradation and synthesis of aromatic volatiles. A large number of differentially expressed genes did not align with any of the databases and might be novel genes in banana. These genes can be good candidates for future studies to establish their role in banana fruit ripening. The datasets developed in this study will help in developing strategies to manipulate banana fruit ripening and reduce post harvest losses.

Show MeSH
Related in: MedlinePlus