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| Using transcriptome Shannon entropy to evaluate the off-target effects and safety of insecticidal siRNAs |
| MA Wei-hua1, WU Tong1, 2, ZHANG Zan3, LI Hang3, SITU Gong-ming3, YIN Chuan-lin2, YE Xin-hai2, CHEN Meng-yao2, ZHAO Xian-xin2, HE Kang2, LI Fei2 |
1 College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, P.R.China
2 State Key Laboratory of Rice Biology/Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests/Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, P.R.China
3 College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, P.R.China
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摘要
RNAi介导的有害生物防控策略是农业生物技术领域的最新突破之一。但是，目前对RNAi防控策略可能产生的脱靶效应仍未完全了解。本文中，我们研究了两种昆虫致死基因siRNA在靶标和非标靶昆虫中的脱靶效应。结果表明，致死基因siRNA的脱靶效应广泛存在于靶标昆虫和非靶标昆虫中。我们根据基因的同源性、相关KEGG途径以及与siRNA序列的连续匹配度，对所有表达量受影响的基因进行了分类。出人意料的是，非靶标基因表达量受影响的程度与序列的连续匹配度并不一直。而少部分同源基因和KEGG相关基因的表达量正如预期的一样发生了显著变化。通过计算转录组熵值，结果表明尽管在siRNA处理后数百个基因的表达受到影响，但转录组的熵值保持不变，这表明转录组的表达模式在整体上是平衡的。本文的结果表明，siRNA与非靶标生物中的单个基因发生交叉反应，但在基因组水平上对靶标和非靶标生物中转录组完整性并没有显着影响。同时，本文提出了一种评估昆虫致死基因siRNA脱靶效应的体系，将有助于评估RNAi害虫防控策略的安全性。
Abstract A recent breakthrough in agricultural biotechnology is the introduction of RNAi-mediated strategies in pest control. However, the off-target effects of RNAi pest control are still not fully understood. Here, we studied the off-target effects of two insecticidal siRNAs in both target and non-target insects. The results revealed that off-target effects of insecticidal siRNAs occur widely in both target and non-target insects. We classified the expression-changed genes according to their homology to the siRNA-targeted gene, related KEGG pathways with the siRNA-targeted gene and continuous matches with siRNAs. Surprisingly, the unintended significant changes in gene expression levels did not strictly match with the number of contiguous nucleotides in the siRNAs. As expected, the expression of small portions of the homologous and KEGG-related genes were significantly changed. We calculated the Shannon entropy of the transcriptome profile of the insects after injecting them with insecticidal siRNAs. Though hundreds of genes were affected in their expression levels post siRNA-treatment, the Shannon entropy of the transcriptome remained unchanged, suggesting that the transcriptome expression was balanced. Our results provide evidence that siRNAs cross-reacted with individual genes in non-target species, but did not have significant effects on the integrity of the transcriptome profiles in either target or non-target species on a genomic scale. The metric we proposed can be used to estimate the off-target effects of insecticidal siRNAs, which might be useful for evaluating the safety of RNAi in pest control.
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Received: 12 June 2020
Accepted: 08 August 2020
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| Fund: This work was funded by grants from the National Science and Technology Major Project of China (2016ZX08011002). We also thank the DBMediting Company for professional English language editing services. |
| About author: MA Wei-hua, E-mail: weihuama@mail.hzau.edu.cn; Correspondence LI Fei, E-mail: lifei18@zju.edu.cn |
Cite this article:
MA Wei-hua, WU Tong, ZHANG Zan, LI Hang, SITU Gong-ming, YIN Chuan-lin, YE Xin-hai, CHEN Meng-yao, ZHAO Xian-xin, HE Kang, LI Fei .
2022.
Using transcriptome Shannon entropy to evaluate the off-target effects and safety of insecticidal siRNAs. Journal of Integrative Agriculture, 21(1): 170-177.
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