Complementary iTRAQ-based proteomic and RNA sequencing-based transcriptomic analyses reveal a complex network regulating pomegranate (Punica granatum L.) fruit peel colour

Luo, Xiang; Cao, Da; Li, Haoxian; Zhao, Dan; Xue, Hui; Niu, Juan; Chen, Lina; Zhang, Fuhong; Cao, Shangyin

doi:10.1038/s41598-018-30088-3

Cited by 38 publications

(28 citation statements)

References 45 publications

(51 reference statements)

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“…Moreover, correlation analyses showed negative correlations between the proteome and transcriptome, indicating a discordance between the transcript levels and protein abundance. These results were similar to those observed in previous reports, suggesting that post-transcriptional and post-translational regulation, reversible phosphorylation, splicing events in cells, and translation efficiency play key roles in the regulation of fruit ripening [40,41]. Thus, gene translation and post-translation processes could be important regulatory methods in fruit ripening and cracking.…”

Section: Translational and Post-translational Regulation Of A Trifolsupporting

confidence: 91%

Integrative transcriptome and proteome analyses provide new insights into different stages of Akebia trifoliata fruit cracking during ripening

Niu

Shi

Huang

et al. 2020

Biotechnol Biofuels

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Background: Akebia trifoliata (Thunb.) Koidz may have applications as a new potential source of biofuels owing to its high seed count, seed oil content, and in-field yields. However, the pericarp of A. trifoliata cracks longitudinally during fruit ripening, which increases the incidence of pests and diseases and can lead to fruit decay and deterioration, resulting in significant losses in yield. Few studies have evaluated the mechanisms underlying A. trifoliata fruit cracking. Results: In this study, by observing the cell wall structure of the pericarp, we found that the cell wall became thinner and looser and showed substantial breakdown in the pericarp of cracking fruit compared with that in non-cracking fruit. Moreover, integrative analyses of transcriptome and proteome profiles at different stages of fruit ripening demonstrated changes in the expression of various genes and proteins after cracking. Furthermore, the mRNA levels of 20 differentially expressed genes were analyzed, and parallel reaction monitoring analysis of 20 differentially expressed proteins involved in cell wall metabolism was conducted. Among the molecular targets, pectate lyases and pectinesterase, which are involved in pentose and glucuronate interconversion, and β-galactosidase 2, which is involved in galactose metabolism, were significantly upregulated in cracking fruits than in non-cracking fruits. This suggested that they might play crucial roles in A. trifoliata fruit cracking. Conclusions: Our findings provided new insights into potential genes influencing the fruit cracking trait in A. trifoliata and established a basis for further research on the breeding of cracking-resistant varieties to increase seed yields for biorefineries.

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Section: Translational and Post-translational Regulation Of A Trifolsupporting

confidence: 91%

Integrative transcriptome and proteome analyses provide new insights into different stages of Akebia trifoliata fruit cracking during ripening

Niu

Shi

Huang

et al. 2020

Biotechnol Biofuels

Self Cite

View full text Add to dashboard Cite

show abstract

“…Moreover, correlation analyses showed negative correlations between the proteome and transcriptome, indicating a discordance between the transcript levels and protein abundance. These results were similar to those observed in previous reports, suggesting that post-transcriptional and post-translational regulation, reversible phosphorylation, splicing events in cells, and translation e ciency play key roles in the regulation of fruit ripening [40][41]. Thus, gene translation and post-translation processes could be important regulatory methods in fruit ripening and cracking.…”

Section: General Features Of the Transcriptomes And Proteomes Of Diffsupporting

confidence: 90%

Integrative transcriptome and proteome analyses provide new insights into different stages of Akebia trifoliata fruit cracking during ripening

Niu

Shi

Huang

et al. 2020

Preprint

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Background: Akebia trifoliata (Thunb.) Koid may have applications as a new source of biofuels owing to its high seed count, seed oil content, and in-field yields. However, the pericarp of A. trifoliata cracks longitudinally during fruit ripening, which increases the incidence of pests and diseases and can lead to fruit decay and deterioration, resulting in significant losses in yield. Few studies have evaluated the mechanisms underlying A. trifoliata fruit cracking. Results: In this study, by observing the cell wall structure of the pericarp, we found that the cell wall became thinner and looser and showed substantial breakdown in the pericarp of cracking fruit compared with that in non-cracking fruit. Moreover, integrative analyses of transcriptome and proteome profiles at different stages of fruit ripening demonstrated changes in the expression of various genes and proteins after cracking. Furthermore, the mRNA levels of 20 differentially expressed genes were analyzed, and parallel reaction monitoring analysis of 20 differentially expressed proteins involved in cell wall metabolism was conducted. Among the molecular targets, pectate lyases and pectinesterase, which are involved in pentose and glucuronate interconversion, and β-galactosidase 2, which is involved in galactose metabolism, were significantly upregulated in cracking fruits than in non-cracking fruits. This suggested that they might play crucial roles in A. trifoliata fruit cracking. Conclusions: Our findings provided new insights into potential genes influencing the fruit cracking trait in A. trifoliata and established a basis for further research on the breeding of cracking-resistant varieties to increase seed yields for biorefineries.

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“…The correlation coefficients of the overall differentially expressed genes (DEGs) [27] and DEP data indicated a positive but very weak correlation between the two light treatments (Figure 8), implying that some post-transcriptional and post-translational modifications or splicing events might occur in the related RNA and protein expression level processes [36], which is consistent with several previous studies [37][38][39][40]. A possible explanation for the poor correlation between transcript levels and protein abundance is that the transcription level can fluctuate more quickly than protein translation and modification processes.…”

Section: Overview the Rna-seq And Itraq Datasupporting

confidence: 90%

iTRAQ-Based Protein Profiling Provides Insights into the Mechanism of Light-Induced Anthocyanin Biosynthesis in Chrysanthemum (Chrysanthemum × morifolium)

Hong

Dai

2019

Genes

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The generation of chrysanthemum (Chrysanthemum × morifolium) flower color is mainly attributed to the accumulation of anthocyanins. Light is one of the key environmental factors that affect the anthocyanin biosynthesis, but the deep molecular mechanism remains elusive. In our previous study, a series of light-induced structural and regulatory genes involved in the anthocyanin biosynthetic pathway in the chrysanthemum were identified using RNA sequencing. In the present study, differentially expressed proteins that are in response to light with the capitulum development of the chrysanthemum ‘Purple Reagan’ were further identified using isobaric tags for relative and absolute quantification (iTRAQ) technique, and correlation between the proteomic and the transcriptomic libraries was analyzed. In general, 5106 raw proteins were assembled based on six proteomic libraries (three capitulum developmental stages × two light treatments). As many as 160 proteins were differentially expressed between the light and the dark libraries with 45 upregulated and 115 downregulated proteins in response to shading. Comparative analysis between the pathway enrichment and the gene expression patterns indicated that most of the proteins involved in the anthocyanin biosynthetic pathway were downregulated after shading, which was consistent with the expression patterns of corresponding encoding genes; while five light-harvesting chlorophyll a/b-binding proteins were initially downregulated after shading, and their expressions were enhanced with the capitulum development thereafter. As revealed by correlation analysis between the proteomic and the transcriptomic libraries, GDSL esterase APG might also play an important role in light signal transduction. Finally, a putative mechanism of light-induced anthocyanin biosynthesis in the chrysanthemum was proposed. This study will help us to clearly identify light-induced proteins associated with flower color in the chrysanthemum and to enrich the complex mechanism of anthocyanin biosynthesis for use in cultivar breeding.

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Complementary iTRAQ-based proteomic and RNA sequencing-based transcriptomic analyses reveal a complex network regulating pomegranate (Punica granatum L.) fruit peel colour

Cited by 38 publications

References 45 publications

Integrative transcriptome and proteome analyses provide new insights into different stages of Akebia trifoliata fruit cracking during ripening

Integrative transcriptome and proteome analyses provide new insights into different stages of Akebia trifoliata fruit cracking during ripening

Integrative transcriptome and proteome analyses provide new insights into different stages of Akebia trifoliata fruit cracking during ripening

iTRAQ-Based Protein Profiling Provides Insights into the Mechanism of Light-Induced Anthocyanin Biosynthesis in Chrysanthemum (Chrysanthemum × morifolium)

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