A survey on the off-target effects of insecticidal double-stranded RNA targeting the Hvβ´COPI gene in the crop pest Henosepilachna vigintioctopunctata through RNA-seq
The specificity of the double-stranded RNA (dsRNA) used in the RNA interference (RNAi) technique is crucial for the success of sequence-specific gene silencing. Currently, RNAi-mediated insect control is a trending research topic. However, the off-target effects of the dsRNA in RNAi are a major conc...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-01-01
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| Series: | Journal of Integrative Agriculture |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2095311922000247 |
| _version_ | 1828358300965535744 |
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| author | Jing LÜ Satyabrata NANDA Shi-min CHEN Yang MEI Kang HE Bao-li QIU You-jun ZHANG Fei LI Hui-peng PAN |
| author_facet | Jing LÜ Satyabrata NANDA Shi-min CHEN Yang MEI Kang HE Bao-li QIU You-jun ZHANG Fei LI Hui-peng PAN |
| author_sort | Jing LÜ |
| collection | DOAJ |
| description | The specificity of the double-stranded RNA (dsRNA) used in the RNA interference (RNAi) technique is crucial for the success of sequence-specific gene silencing. Currently, RNAi-mediated insect control is a trending research topic. However, the off-target effects of the dsRNA in RNAi are a major concern. In this study, the dsHvβ´COPI (coat protein complex I, β´ subunit)-treated and untreated transcriptomes of the 28-spotted potato lady beetle (Henosepilachna vigintioctopunctata) were compared to understand its off-target gene silencing effects. The RNA-seq results revealed that 63 and 44 differentially expressed genes (DEGs) were upregulated and downregulated, respectively, in the dsHvβ´COPI treated group as compared with the control. Validation of the differential expressions of some selected DEGs via reverse transcription-quantitative PCR (RT-qPCR) analysis confirmed the reliability of the transcriptome analysis results. Further downstream analysis revealed that there were no genes homologous with Hvβ´COPI in H. vigintioctopunctata. Additionally, no genes with a >11 bp continuous match with dsHvβ´COPI were found in the H. vigintioctopunctata transcriptome. Six genes (Hvcitron, Hvhelicase, Hvtransposase, Hvserine, Hvdynein, and HvE3 ubiquitin) were selected to examine the off-target activity of dsHvβ´COPI based on their potential involvement in various H. vigintioctopunctata metabolic pathways. The severity of silencing these six off-target genes was evaluated by employing RNAi. The RNAi results confirmed the downregulation of the expression of all six genes, although there was no significant lethality. The findings of this study will be helpful in the risk analysis of future RNAi-mediated pest control experiments. |
| first_indexed | 2024-04-14T03:27:44Z |
| format | Article |
| id | doaj.art-eed3b1c3a4a7408db4380804d1b8c133 |
| institution | Directory Open Access Journal |
| issn | 2095-3119 |
| language | English |
| last_indexed | 2024-04-14T03:27:44Z |
| publishDate | 2022-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Integrative Agriculture |
| spelling | doaj.art-eed3b1c3a4a7408db4380804d1b8c1332022-12-22T02:15:07ZengElsevierJournal of Integrative Agriculture2095-31192022-01-0121926652674A survey on the off-target effects of insecticidal double-stranded RNA targeting the Hvβ´COPI gene in the crop pest Henosepilachna vigintioctopunctata through RNA-seqJing LÜ0Satyabrata NANDA1Shi-min CHEN2Yang MEI3Kang HE4Bao-li QIU5You-jun ZHANG6Fei LI7Hui-peng PAN8Key Laboratory of Bio-pesticide Innovation and Application of Guangdong Province, South China Agricultural University, Guangzhou 510642, P.R.ChinaMS Swaminathan School of Agriculture, Centurion University of Technology and Management, Paralakhemundi 761211, IndiaKey Laboratory of Bio-pesticide Innovation and Application of Guangdong Province, South China Agricultural University, Guangzhou 510642, P.R.ChinaInstitute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, P.R.ChinaInstitute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, P.R.ChinaKey Laboratory of Bio-pesticide Innovation and Application of Guangdong Province, South China Agricultural University, Guangzhou 510642, P.R.ChinaDepartment of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.ChinaInstitute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, P.R.China; Correspondence LI FeiKey Laboratory of Bio-pesticide Innovation and Application of Guangdong Province, South China Agricultural University, Guangzhou 510642, P.R.China; Correspondence PAN Hui-pengThe specificity of the double-stranded RNA (dsRNA) used in the RNA interference (RNAi) technique is crucial for the success of sequence-specific gene silencing. Currently, RNAi-mediated insect control is a trending research topic. However, the off-target effects of the dsRNA in RNAi are a major concern. In this study, the dsHvβ´COPI (coat protein complex I, β´ subunit)-treated and untreated transcriptomes of the 28-spotted potato lady beetle (Henosepilachna vigintioctopunctata) were compared to understand its off-target gene silencing effects. The RNA-seq results revealed that 63 and 44 differentially expressed genes (DEGs) were upregulated and downregulated, respectively, in the dsHvβ´COPI treated group as compared with the control. Validation of the differential expressions of some selected DEGs via reverse transcription-quantitative PCR (RT-qPCR) analysis confirmed the reliability of the transcriptome analysis results. Further downstream analysis revealed that there were no genes homologous with Hvβ´COPI in H. vigintioctopunctata. Additionally, no genes with a >11 bp continuous match with dsHvβ´COPI were found in the H. vigintioctopunctata transcriptome. Six genes (Hvcitron, Hvhelicase, Hvtransposase, Hvserine, Hvdynein, and HvE3 ubiquitin) were selected to examine the off-target activity of dsHvβ´COPI based on their potential involvement in various H. vigintioctopunctata metabolic pathways. The severity of silencing these six off-target genes was evaluated by employing RNAi. The RNAi results confirmed the downregulation of the expression of all six genes, although there was no significant lethality. The findings of this study will be helpful in the risk analysis of future RNAi-mediated pest control experiments.http://www.sciencedirect.com/science/article/pii/S2095311922000247RNAidsRNAoff-target effectsRNA-seqtranscriptome analysis |
| spellingShingle | Jing LÜ Satyabrata NANDA Shi-min CHEN Yang MEI Kang HE Bao-li QIU You-jun ZHANG Fei LI Hui-peng PAN A survey on the off-target effects of insecticidal double-stranded RNA targeting the Hvβ´COPI gene in the crop pest Henosepilachna vigintioctopunctata through RNA-seq Journal of Integrative Agriculture RNAi dsRNA off-target effects RNA-seq transcriptome analysis |
| title | A survey on the off-target effects of insecticidal double-stranded RNA targeting the Hvβ´COPI gene in the crop pest Henosepilachna vigintioctopunctata through RNA-seq |
| title_full | A survey on the off-target effects of insecticidal double-stranded RNA targeting the Hvβ´COPI gene in the crop pest Henosepilachna vigintioctopunctata through RNA-seq |
| title_fullStr | A survey on the off-target effects of insecticidal double-stranded RNA targeting the Hvβ´COPI gene in the crop pest Henosepilachna vigintioctopunctata through RNA-seq |
| title_full_unstemmed | A survey on the off-target effects of insecticidal double-stranded RNA targeting the Hvβ´COPI gene in the crop pest Henosepilachna vigintioctopunctata through RNA-seq |
| title_short | A survey on the off-target effects of insecticidal double-stranded RNA targeting the Hvβ´COPI gene in the crop pest Henosepilachna vigintioctopunctata through RNA-seq |
| title_sort | survey on the off target effects of insecticidal double stranded rna targeting the hvβ´copi gene in the crop pest henosepilachna vigintioctopunctata through rna seq |
| topic | RNAi dsRNA off-target effects RNA-seq transcriptome analysis |
| url | http://www.sciencedirect.com/science/article/pii/S2095311922000247 |
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