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Int. J. Mol. Sci. 2018, 19(1), 71; https://doi.org/10.3390/ijms19010071

Transcriptome-Wide Identification and Characterization of Potato Circular RNAs in Response to Pectobacterium carotovorum Subspecies brasiliense Infection

1
College of Agriculture/College of Horticulture and Gardening/Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, Yangtze University, Jingzhou 434025, China
2
College of Agronomy, Shandong Agricultural University, Tai’an 271018, China
3
College of Plant Protection, Northwest A&F University, Yangling 712100, China
These authors contributed equally to this work.
*
Authors to whom correspondence should be addressed.
Received: 11 November 2017 / Revised: 5 December 2017 / Accepted: 13 December 2017 / Published: 27 December 2017
(This article belongs to the Special Issue Host-Microbe Interaction 2018)
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Abstract

Little information about the roles of circular RNAs (circRNAs) during potato-Pectobacterium carotovorum subsp. brasiliense (Pcb) interaction is currently available. In this study, we conducted the systematic identification of circRNAs from time series samples of potato cultivars Valor (susceptible) and BP1 (disease tolerant) infected by Pcb. A total of 2098 circRNAs were detected and about half (931, 44.38%) were intergenic circRNAs. And differential expression analysis detected 429 significantly regulated circRNAs. circRNAs play roles by regulating parental genes and sponging miRNAs. Gene Ontology (GO) enrichment of parental genes and miRNAs targeted mRNAs revealed that these differentially expressed (DE) circRNAs were involved in defense response (GO:0006952), cell wall (GO:0005199), ADP binding (GO:0043531), phosphorylation (GO:0016310), and kinase activity (GO:0016301), suggesting the roles of circRNAs in regulating potato immune response. Furthermore, weighted gene co-expression network analysis (WGCNA) found that circRNAs were closely related with coding-genes and long intergenic noncoding RNAs (lincRNAs). And together they were cultivar-specifically regulated to strengthen immune response of potato to Pcb infection, implying the roles of circRNAs in reprogramming disease responsive transcriptome. Our results will provide new insights into the potato-Pcb interaction and may lead to novel disease control strategy in the future. View Full-Text
Keywords: potato circRNAs; Pectobacterium carotovorum; parental genes; miRNA sponges; GO enrichment; WGCNA potato circRNAs; Pectobacterium carotovorum; parental genes; miRNA sponges; GO enrichment; WGCNA
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

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Zhou, R.; Zhu, Y.; Zhao, J.; Fang, Z.; Wang, S.; Yin, J.; Chu, Z.; Ma, D. Transcriptome-Wide Identification and Characterization of Potato Circular RNAs in Response to Pectobacterium carotovorum Subspecies brasiliense Infection. Int. J. Mol. Sci. 2018, 19, 71.

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