Analysis of the Coding and Non-Coding RNA Transcriptomes in Response to Bell Pepper Chilling
Increasing evidence suggests that long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs) have roles during biotic and abiotic stress, though their exact contributions remain unclear. To explore their biological functions in response to chilling in bell pepper, we examined t...
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MDPI AG
2018-07-01
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| Series: | International Journal of Molecular Sciences |
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| author | Jinhua Zuo Yunxiang Wang Benzhong Zhu Yunbo Luo Qing Wang Lipu Gao |
| author_facet | Jinhua Zuo Yunxiang Wang Benzhong Zhu Yunbo Luo Qing Wang Lipu Gao |
| author_sort | Jinhua Zuo |
| collection | DOAJ |
| description | Increasing evidence suggests that long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs) have roles during biotic and abiotic stress, though their exact contributions remain unclear. To explore their biological functions in response to chilling in bell pepper, we examined their accumulation profiles by deep sequencing and identified 380 lncRNAs, 36 circRNAs, 18 miRNAs, and 4128 differentially expressed mRNAs in the chilled versus the non-chilled fruit. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed differentially expressed genes and putative ncRNA targets, including transcription factors of multiple classes, such as myeloblastosis (MYB), basic helix-loop-helix (bHLH), and ethylene response factor (ERF) transcription factors (TFs), enzymes involved in bio-oxidation and oxidative phosphorylation (serine/threonine-protein kinase, polyphenol oxidase, catalase, peroxidase, lipoxygenase, and ATPase), and cell wall metabolism-related enzymes (beta-galactosidase, pectate lyase, pectinesterase, and polygalacturonase). On the basis of the accumulation profiles, a network of putatively interacting RNAs associated with bell pepper chilling was developed, which pointed to ncRNAs that could provide the foundation for further developing a more refined understanding of the molecular response to chilling injury. |
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| id | doaj.art-4905f9b7eae549bdbab9137e91abd8c9 |
| institution | Directory Open Access Journal |
| issn | 1422-0067 |
| language | English |
| last_indexed | 2024-04-12T17:52:32Z |
| publishDate | 2018-07-01 |
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| spelling | doaj.art-4905f9b7eae549bdbab9137e91abd8c92022-12-22T03:22:27ZengMDPI AGInternational Journal of Molecular Sciences1422-00672018-07-01197200110.3390/ijms19072001ijms19072001Analysis of the Coding and Non-Coding RNA Transcriptomes in Response to Bell Pepper ChillingJinhua Zuo0Yunxiang Wang1Benzhong Zhu2Yunbo Luo3Qing Wang4Lipu Gao5Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, ChinaBeijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100093, ChinaLaboratory of Postharvest Molecular Biology of Fruits and vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, ChinaLaboratory of Postharvest Molecular Biology of Fruits and vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, ChinaKey Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, ChinaKey Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, ChinaIncreasing evidence suggests that long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs) have roles during biotic and abiotic stress, though their exact contributions remain unclear. To explore their biological functions in response to chilling in bell pepper, we examined their accumulation profiles by deep sequencing and identified 380 lncRNAs, 36 circRNAs, 18 miRNAs, and 4128 differentially expressed mRNAs in the chilled versus the non-chilled fruit. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed differentially expressed genes and putative ncRNA targets, including transcription factors of multiple classes, such as myeloblastosis (MYB), basic helix-loop-helix (bHLH), and ethylene response factor (ERF) transcription factors (TFs), enzymes involved in bio-oxidation and oxidative phosphorylation (serine/threonine-protein kinase, polyphenol oxidase, catalase, peroxidase, lipoxygenase, and ATPase), and cell wall metabolism-related enzymes (beta-galactosidase, pectate lyase, pectinesterase, and polygalacturonase). On the basis of the accumulation profiles, a network of putatively interacting RNAs associated with bell pepper chilling was developed, which pointed to ncRNAs that could provide the foundation for further developing a more refined understanding of the molecular response to chilling injury.http://www.mdpi.com/1422-0067/19/7/2001analysisnon-coding RNAtranscriptomesbell pepperchilling injury |
| spellingShingle | Jinhua Zuo Yunxiang Wang Benzhong Zhu Yunbo Luo Qing Wang Lipu Gao Analysis of the Coding and Non-Coding RNA Transcriptomes in Response to Bell Pepper Chilling International Journal of Molecular Sciences analysis non-coding RNA transcriptomes bell pepper chilling injury |
| title | Analysis of the Coding and Non-Coding RNA Transcriptomes in Response to Bell Pepper Chilling |
| title_full | Analysis of the Coding and Non-Coding RNA Transcriptomes in Response to Bell Pepper Chilling |
| title_fullStr | Analysis of the Coding and Non-Coding RNA Transcriptomes in Response to Bell Pepper Chilling |
| title_full_unstemmed | Analysis of the Coding and Non-Coding RNA Transcriptomes in Response to Bell Pepper Chilling |
| title_short | Analysis of the Coding and Non-Coding RNA Transcriptomes in Response to Bell Pepper Chilling |
| title_sort | analysis of the coding and non coding rna transcriptomes in response to bell pepper chilling |
| topic | analysis non-coding RNA transcriptomes bell pepper chilling injury |
| url | http://www.mdpi.com/1422-0067/19/7/2001 |
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