Identification of circularRNAs and their targets in Gossypium under Verticillium wilt stress based on RNA-seq
Circular RNAs (circRNAs), a class of recently discovered non-coding RNAs, play a role in biological and developmental processes. A recent study showed that circRNAs exist in plants and play a role in their environmental stress responses. However, cotton circRNAs and their role in Verticillium wilt r...
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PeerJ Inc.
2018-03-01
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| Online Access: | https://peerj.com/articles/4500.pdf |
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| author | Liuxin Xiang Chaowei Cai Jieru Cheng Lu Wang Chaofeng Wu Yuzhen Shi Jingzhi Luo Lin He Yushan Deng Xiao Zhang Youlu Yuan Yingfan Cai |
| author_facet | Liuxin Xiang Chaowei Cai Jieru Cheng Lu Wang Chaofeng Wu Yuzhen Shi Jingzhi Luo Lin He Yushan Deng Xiao Zhang Youlu Yuan Yingfan Cai |
| author_sort | Liuxin Xiang |
| collection | DOAJ |
| description | Circular RNAs (circRNAs), a class of recently discovered non-coding RNAs, play a role in biological and developmental processes. A recent study showed that circRNAs exist in plants and play a role in their environmental stress responses. However, cotton circRNAs and their role in Verticillium wilt response have not been identified up to now. In this study, two CSSLs (chromosome segment substitution lines) of G.barbadense introgressed into G. hirsutum, CSSL-1 and CSSL-4 (a resistant line and a susceptible line to Verticillium wilt, respectively), were inoculated with V. dahliae for RNA-seq library construction and circRNA analysis. A total of 686 novel circRNAs were identified. CSSL-1 and CSSL-4 had similar numbers of circRNAs and shared many circRNAs in common. However, CSSL-4 differentially expressed approximately twice as many circRNAs as CSSL-1, and the differential expression levels of the common circRNAs were generally higher in CSSL-1 than in CSSL-4. Moreover, two C-RRI comparisons, C-RRI-vs-C-RRM and C-RRI-vs-C-RSI, possessed a large proportion (approximately 50%) of the commonly and differentially expressed circRNAs. These results indicate that the differentially expressed circRNAs may play roles in the Verticillium wilt response in cotton. A total of 280 differentially expressed circRNAs were identified. A Gene Ontology analysis showed that most of the ‘stimulus response’ term source genes were NBS family genes, of which most were the source genes from the differentially expressed circRNAs, indicating that NBS genes may play a role in Verticillium wilt resistance and might be regulated by circRNAs in the disease-resistance process in cotton. |
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| last_indexed | 2024-03-09T06:39:39Z |
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| spelling | doaj.art-d9703a943f154856b7ecbf7bf146df332023-12-03T10:54:02ZengPeerJ Inc.PeerJ2167-83592018-03-016e450010.7717/peerj.4500Identification of circularRNAs and their targets in Gossypium under Verticillium wilt stress based on RNA-seqLiuxin Xiang0Chaowei Cai1Jieru Cheng2Lu Wang3Chaofeng Wu4Yuzhen Shi5Jingzhi Luo6Lin He7Yushan Deng8Xiao Zhang9Youlu Yuan10Yingfan Cai11State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, School of Computer and Information Engineering, Henan University, Kaifeng, Henan, ChinaState Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, School of Computer and Information Engineering, Henan University, Kaifeng, Henan, ChinaState Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, School of Computer and Information Engineering, Henan University, Kaifeng, Henan, ChinaSchool of Bioinformatics, School of Software Engineering, Chongqing University of Posts and Telecommunications, Chongqing, ChinaSchool of Bioinformatics, School of Software Engineering, Chongqing University of Posts and Telecommunications, Chongqing, ChinaState Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, Henan, ChinaSchool of Bioinformatics, School of Software Engineering, Chongqing University of Posts and Telecommunications, Chongqing, ChinaSchool of Bioinformatics, School of Software Engineering, Chongqing University of Posts and Telecommunications, Chongqing, ChinaSchool of Bioinformatics, School of Software Engineering, Chongqing University of Posts and Telecommunications, Chongqing, ChinaState Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, School of Computer and Information Engineering, Henan University, Kaifeng, Henan, ChinaState Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, Henan, ChinaState Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, School of Computer and Information Engineering, Henan University, Kaifeng, Henan, ChinaCircular RNAs (circRNAs), a class of recently discovered non-coding RNAs, play a role in biological and developmental processes. A recent study showed that circRNAs exist in plants and play a role in their environmental stress responses. However, cotton circRNAs and their role in Verticillium wilt response have not been identified up to now. In this study, two CSSLs (chromosome segment substitution lines) of G.barbadense introgressed into G. hirsutum, CSSL-1 and CSSL-4 (a resistant line and a susceptible line to Verticillium wilt, respectively), were inoculated with V. dahliae for RNA-seq library construction and circRNA analysis. A total of 686 novel circRNAs were identified. CSSL-1 and CSSL-4 had similar numbers of circRNAs and shared many circRNAs in common. However, CSSL-4 differentially expressed approximately twice as many circRNAs as CSSL-1, and the differential expression levels of the common circRNAs were generally higher in CSSL-1 than in CSSL-4. Moreover, two C-RRI comparisons, C-RRI-vs-C-RRM and C-RRI-vs-C-RSI, possessed a large proportion (approximately 50%) of the commonly and differentially expressed circRNAs. These results indicate that the differentially expressed circRNAs may play roles in the Verticillium wilt response in cotton. A total of 280 differentially expressed circRNAs were identified. A Gene Ontology analysis showed that most of the ‘stimulus response’ term source genes were NBS family genes, of which most were the source genes from the differentially expressed circRNAs, indicating that NBS genes may play a role in Verticillium wilt resistance and might be regulated by circRNAs in the disease-resistance process in cotton.https://peerj.com/articles/4500.pdfCircular RNADifferential expressionVerticillium wiltCotton chromosome segment substitution linesNBS family genes |
| spellingShingle | Liuxin Xiang Chaowei Cai Jieru Cheng Lu Wang Chaofeng Wu Yuzhen Shi Jingzhi Luo Lin He Yushan Deng Xiao Zhang Youlu Yuan Yingfan Cai Identification of circularRNAs and their targets in Gossypium under Verticillium wilt stress based on RNA-seq PeerJ Circular RNA Differential expression Verticillium wilt Cotton chromosome segment substitution lines NBS family genes |
| title | Identification of circularRNAs and their targets in Gossypium under Verticillium wilt stress based on RNA-seq |
| title_full | Identification of circularRNAs and their targets in Gossypium under Verticillium wilt stress based on RNA-seq |
| title_fullStr | Identification of circularRNAs and their targets in Gossypium under Verticillium wilt stress based on RNA-seq |
| title_full_unstemmed | Identification of circularRNAs and their targets in Gossypium under Verticillium wilt stress based on RNA-seq |
| title_short | Identification of circularRNAs and their targets in Gossypium under Verticillium wilt stress based on RNA-seq |
| title_sort | identification of circularrnas and their targets in gossypium under verticillium wilt stress based on rna seq |
| topic | Circular RNA Differential expression Verticillium wilt Cotton chromosome segment substitution lines NBS family genes |
| url | https://peerj.com/articles/4500.pdf |
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