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Identification and the potential roles of long non-coding RNAs in cotton leaves damaged by Aphis gossypii

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Abstract

Long non-coding RNAs (lncRNAs) belong to a family of regulatory RNAs of non-coding RNAs (ncRNAs). They play essential roles in plant various developmental processes and stress responses. However, lncRNA functions in cotton are rarely known under attack of cotton aphids (Aphis gossypii Glover). Herein, we performed whole-transcriptome RNA sequencing for cotton four-leaf-stage leaves (Gossypium hirsutum, ZM-03199) damaged by cotton aphids at different time stages (6, 12, 24, 48, and 72 h) and without cotton aphid damage (0 h). We identified 8414 lncRNAs in 6 RNA-Seq data, including 6516 intergenic lncRNAs (77%), 759 anti-sense lncRNAs (7%), 334 intronic lncRNAs (4%) and 805 (10%) sense lncRNAs. Furthermore, 1331 lncRNAs showed differential expressions, and the gene ontology (Go) and KEGG analysis discovered that many target protein-coding genes of lncRNAs were enriched in stress-related categories. In addition, a total of 55 lncRNAs among 8414 lncRNAs were predicted as target mimics of cotton 285 miRNAs. Real-time quantitative PCR (qPCR) confirmed that all selected lncRNAs were relative to aphid damage. These results laid a solid foundation for the study of cotton lncRNA functions under the damage of cotton aphids.

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Acknowledgements

This work was supported by grants from the National Natural Science Foundation of China (Grant No. 31471783).

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  1. Jianmin Zhang and Zhen Yang contributed equally to this work and should be considered as co-first authors.

Authors and Affiliations

  1. Institute of Entomology, College of Agriculture, Yangtze University, Jingzhou, 434025, China

    Jianmin Zhang, Zhen Yang, Pei Feng, Xiao Zhong, Qiqi Ma, Qi Su, Xiangping Wang & Chuanren Li

  2. College of Life Sciences, Yangtze University, Jingzhou, 434025, China

    Chuanren Li & Yazhen Yang

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  1. Jianmin Zhang
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ZJM and YYZ designed the research. YZ, MQQ, FP, ZX, SQ carried out the experiments, ZJM and WXP analyzed the experimental data and wrote the manuscript.

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Correspondence to Yazhen Yang.

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Zhang, J., Yang, Z., Feng, P. et al. Identification and the potential roles of long non-coding RNAs in cotton leaves damaged by Aphis gossypii. Plant Growth Regul 88, 215–225 (2019). https://doi.org/10.1007/s10725-019-00500-7

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