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Int. J. Mol. Sci. 2018, 19(7), 2001; https://doi.org/10.3390/ijms19072001

Analysis of the Coding and Non-Coding RNA Transcriptomes in Response to Bell Pepper Chilling

1,2,3,4,5,* , 6
,
7
,
7
,
1,2,3,4,* and 1,2,3,4,*
1
Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
2
Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
3
Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
4
Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
5
Boyce Thompson Institute for Plant Research, Cornell University Campus, Ithaca, NY 14853, USA
6
Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100093, China
7
Laboratory of Postharvest Molecular Biology of Fruits and vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
*
Authors to whom correspondence should be addressed.
Received: 21 May 2018 / Revised: 25 June 2018 / Accepted: 27 June 2018 / Published: 9 July 2018
(This article belongs to the Special Issue Plant Genomics)
Full-Text   |   PDF [3402 KB, uploaded 9 July 2018]   |  

Abstract

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. View Full-Text
Keywords: analysis; non-coding RNA; transcriptomes; bell pepper; chilling injury analysis; non-coding RNA; transcriptomes; bell pepper; chilling injury
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Zuo, J.; Wang, Y.; Zhu, B.; Luo, Y.; Wang, Q.; Gao, L. Analysis of the Coding and Non-Coding RNA Transcriptomes in Response to Bell Pepper Chilling. Int. J. Mol. Sci. 2018, 19, 2001.

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