ATAC-seq and RNA-seq reveal the role of AGL18 in regulating fruit ripening via ethylene-auxin crosstalk in papaya

Cai, Jiahui; Wu, Ziling; Song, Zunyang; Abbas, Farhat; Chen, Weixin; Li, Xueping; Zhu, Xiaoyang

doi:10.1016/j.postharvbio.2022.111984

Cited by 17 publications

(7 citation statements)

References 53 publications

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“…OsNAC10, OsERF48, OsSGL, SNAC1 and OsbZIP23. Integrating ATAC-seq and RNA-seq analyses showed that a TF gene CpAGL18 plays a key role in fruit softening and ripening in papaya by activating the promoters of CpACS1 and CpSAUR32 (Cai et al, 2022).…”

Section: Discussionmentioning

confidence: 99%

“…( 2020 ) used ATAC‐seq to show that OsNMCP1 ‐overexpression altered chromatin accessibility in hundreds of genes related to drought resistance and root growth, including OsNAC10 , OsERF48 , OsSGL , SNAC1 and OsbZIP23 . Integrating ATAC‐seq and RNA‐seq analyses showed that a TF gene CpAGL18 plays a key role in fruit softening and ripening in papaya by activating the promoters of CpACS1 and CpSAUR32 (Cai et al., 2022 ). In this study, we identified a total of 34 TFs (Tables S6 and S7 ) by a search of upstream motifs (Table S11 ) in the DEG data (Tables S4 and S5 ).…”

Section: Discussionmentioning

confidence: 99%

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Integrated ATAC‐seq and RNA‐seq data analysis identifies transcription factors related to rice stripe virus infection in Oryza sativa

Li,

Zhang

et al. 2024

Molecular Plant Pathology

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Animal studies have shown that virus infection causes changes in host chromatin accessibility, but little is known about changes in chromatin accessibility of plants infected by viruses and its potential impact. Here, rice infected by rice stripe virus (RSV) was used to investigate virus‐induced changes in chromatin accessibility. Our analysis identified a total of 6462 open‐ and 3587 closed‐differentially accessible chromatin regions (DACRs) in rice under RSV infection by ATAC‐seq. Additionally, by integrating ATAC‐seq and RNA‐seq, 349 up‐regulated genes in open‐DACRs and 126 down‐regulated genes in closed‐DACRs were identified, of which 34 transcription factors (TFs) were further identified by search of upstream motifs. Transcription levels of eight of these TFs were validated by reverse transcription‐PCR. Importantly, four of these TFs (OsWRKY77, OsWRKY28, OsZFP12 and OsERF91) interacted with RSV proteins and are therefore predicted to play important roles in RSV infection. This is the first application of ATAC‐seq and RNA‐seq techniques to analyse changes in rice chromatin accessibility caused by RSV infection. Integrating ATAC‐seq and RNA‐seq provides a new approach to select candidate TFs in response to virus infection.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Integrated ATAC‐seq and RNA‐seq data analysis identifies transcription factors related to rice stripe virus infection in Oryza sativa

Li,

Zhang

et al. 2024

Molecular Plant Pathology

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“…PCR mixtures included the purified DNA, and PCR was subsequently performed. The final DNA libraries were run on an Illumina platform after the DNA was purified ( Cai et al., 2022 ).…”

Section: Methodsmentioning

confidence: 99%

“…Fruit softening results from cell wall disruption caused by structural changes, hydration of cell wall polymers and dozens of cell wall-related enzymes involved in the biological processes ( Saladie et al., 2007 ). Some enzymes have been identified specific functions involving in altering cell wall structure, limiting the expression of a single gene does not necessarily affect softening ( Zhang et al., 2017 ; Cai et al., 2022 ). The most studied cell wall modification-related enzyme is polygalacturonase (PG).…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic, metabolomic, and ATAC-seq analysis reveal the regulatory mechanism of senescence of post-harvest tomato fruit

Guo

Zheng

et al. 2023

Front. Plant Sci.

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Several physiological changes occur during fruit storage, which include the regulation of genes, metabolisms and transcription factors. In this study, we compared ‘JF308’ (a normal tomato cultivar) and ‘YS006’ (a storable tomato cultivar) to determine the difference in accumulated metabolites, gene expression, and accessible chromatin regions through metabolome, transcriptome, and ATAC-seq analysis. A total of 1006 metabolites were identified in two cultivars. During storage time, sugars, alcohols and flavonoids were found to be more abundant in ‘YS006’ compared to ‘JF308’ on day 7, 14, and 21, respectively. Differentially expressed genes, which involved in starch and sucrose biosynthesis were observed higher in ‘YS006’. ‘YS006’ had lower expression levels of CesA (cellulose synthase), PL (pectate lyase), EXPA (expansin) and XTH (xyglucan endoglutransglucosylase/hydrolase) than ‘JF308’. The results showed that phenylpropanoid pathway, carbohydrate metabolism and cell wall metabolism play important roles in prolonging the shelf life of tomato (Solanum lycopersicum) fruit. The ATAC-seq analysis revealed that the most significantly up-regulated transcription factors during storage were TCP 2,3,4,5, and 24 in ‘YS006’ compared to ‘JF308’ on day 21. This information on the molecular regulatory mechanisms and metabolic pathways of post-harvest quality changes in tomato fruit provides a theoretical foundation for slowing post-harvest decay and loss, and has theoretical importance and application value in breeding for longer shelf life cultivars.

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“…The results of these studies showed that high light and high temperature accelerated the ripening rate of fruits. There are many studies on chemical ripening techniques, such as those exploring the effects of organic and chemical synthetic solvents on fenugreek, the effect of 1‐MCP on the ripening of papaya, and studies on the ripening effect of ethylene glycol on bananas and kiwis (Cai et al, 2022; Orisa & Usoroh, 2021; Ruwali et al, 2022; Verde et al, 2023). The results of these studies showed that the ripening effect of samples treated with ethylene‐releasing chemicals was better.…”

Section: Introductionmentioning

confidence: 99%

Consumer‐oriented intelligent ripening control system for post‐ripening fruit

Li,

Huang,

et al. 2023

J Food Process Engineering

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To address the issues commonly encountered in traditional fruit ripening processes, which include reliance on manual experience, low efficiency, single control parameter, and significant fluctuations, a new intelligent fruit ripening control system has been designed. This system is based on a mathematical modeling algorithm, which allows for more effective and precise control over the ripening process. To ensure that the ripe fruits are transported to the fruit processing center in a low ripeness state, the proposed system adopts a strategy of precise control of temperature and ethylene, as well as range control of other environmental parameters. The RSSA‐PID model is used for ethylene and temperature control, which has high smoothness, fast response time, and high stability. Compared with the traditional PID model, the RSSA‐PID model has better dynamic performance and stability. Finally, the proposed system is applied to the ripening process of post‐ripening fruits, and the results show that the system achieves intelligent ripening, precise control, and low power consumption. The temperature and ethylene concentration are controlled within a variation of no more than 0.5%, and the humidity, oxygen, and carbon dioxide are maintained within reasonable thresholds. Overall, this paper provides a promising solution for the ripening process of post‐ripening fruits, which can benefit the fruit industry by improving the efficiency and quality of the supply chain.Practical ApplicationThe ripening chamber environment is a dynamic equilibrium environment with non‐linear characteristics because the fruits in the ripening chamber are constantly exchanging substances and energy with the environment through respiration and transpiration. An intelligent ripening control system (IRCS) for post‐ripening fruits is proposed in this paper (Figure 1). The whole ripening process runs automatically, which significantly reduces the ripening time and saves a lot of post‐processing time. The shorter ripening time combined with the latest intelligent software and hardware means that only as much energy as is actually needed is consumed. If the sales market changes, the fruit can be stored under air conditioning (CA) until the scheduled delivery date without significant further ripening and losses and complaints can be minimized.

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ATAC-seq and RNA-seq reveal the role of AGL18 in regulating fruit ripening via ethylene-auxin crosstalk in papaya

Cited by 17 publications

References 53 publications

Integrated ATAC‐seq and RNA‐seq data analysis identifies transcription factors related to rice stripe virus infection in Oryza sativa

Integrated ATAC‐seq and RNA‐seq data analysis identifies transcription factors related to rice stripe virus infection in Oryza sativa

Transcriptomic, metabolomic, and ATAC-seq analysis reveal the regulatory mechanism of senescence of post-harvest tomato fruit

Consumer‐oriented intelligent ripening control system for post‐ripening fruit

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