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Wang Z, Hao W, Wang H, Deng P, Li T, Wang C, Zhao J, Chen C, Ji W, Liu X. Genome-Wide Comparative Analysis of the Cytochrome P450 Monooxygenase Family in 19 Aphid Species and Their Expression Analysis in 4 Cereal Crop Aphids. Int J Mol Sci 2024; 25:6668. [PMID: 38928374 PMCID: PMC11203792 DOI: 10.3390/ijms25126668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 05/30/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
Cytochrome P450 monooxygenases (CYP450s) play a variety of physiological roles, including pesticide resistance, plant allelochemical detoxification, and hormone metabolism catalysis. However, limited information is available on the classification and expression profiles of the CYP450 gene family in aphid species. This is the first study to identify the cytochrome P450 gene family in 19 aphid species at the whole genome level. A total of 1100 CYP450 genes were identified in 19 aphid species. Three hundred CYP450 genes belonged to six cereal crop aphid species, which were further classified into four subfamilies according to the phylogenetic relationship. The conserved motifs, exon-intron structures, and genomic organization of the same subfamilies were similar. Predictions of subcellular localization revealed that the endoplasmic reticulum harbored the majority of CYP450 proteins. In Sitobion avenae and Rhopalosiphum maidis, the increase in the CYP450 gene was primarily caused by segmental duplication events. However, only tandem duplication occurred in the CYP450 gene family of Diuraphis noxia, Rhopalosiphum padi, Schizaphis graminum, and Sitobion miscanthi. Synteny analysis found three continuous colinear CYP450 gene pairs among six cereal crop aphid species. Furthermore, we obtained the expression profiles of four cereal crop aphids, including R. padi, D. noxia, S. graminum, and S. avenae. Differential expression analysis provided growth stage specificity genes, tissue specificity genes, organ specificity genes and some detoxification metabolic genes among these four cereal crop aphids. Meanwhile, their expression patterns were showed. The related functions and pathways of CYP450s were revealed by GO and KEGG enrichment analysis. Above all, we picked the differentially expressed CYP450 genes from all of the differentially expressed genes (DEGs). These differentially expressed CYP450 genes provided some new potential candidates for aphid control and management. This work establishes the foundation for further investigations into the regulatory functions of the CYP450 gene family in aphid species and beyond.
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Affiliation(s)
- Zhenyu Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Xianyang 712100, China; (Z.W.); (W.H.); (H.W.); (P.D.); (T.L.); (C.W.); (J.Z.); (C.C.)
| | - Weixi Hao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Xianyang 712100, China; (Z.W.); (W.H.); (H.W.); (P.D.); (T.L.); (C.W.); (J.Z.); (C.C.)
| | - Hao Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Xianyang 712100, China; (Z.W.); (W.H.); (H.W.); (P.D.); (T.L.); (C.W.); (J.Z.); (C.C.)
| | - Pingchuan Deng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Xianyang 712100, China; (Z.W.); (W.H.); (H.W.); (P.D.); (T.L.); (C.W.); (J.Z.); (C.C.)
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, Xianyang 712100, China
| | - Tingdong Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Xianyang 712100, China; (Z.W.); (W.H.); (H.W.); (P.D.); (T.L.); (C.W.); (J.Z.); (C.C.)
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, Xianyang 712100, China
| | - Changyou Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Xianyang 712100, China; (Z.W.); (W.H.); (H.W.); (P.D.); (T.L.); (C.W.); (J.Z.); (C.C.)
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, Xianyang 712100, China
| | - Jixin Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Xianyang 712100, China; (Z.W.); (W.H.); (H.W.); (P.D.); (T.L.); (C.W.); (J.Z.); (C.C.)
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, Xianyang 712100, China
| | - Chunhuan Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Xianyang 712100, China; (Z.W.); (W.H.); (H.W.); (P.D.); (T.L.); (C.W.); (J.Z.); (C.C.)
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, Xianyang 712100, China
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Xianyang 712100, China; (Z.W.); (W.H.); (H.W.); (P.D.); (T.L.); (C.W.); (J.Z.); (C.C.)
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, Xianyang 712100, China
| | - Xinlun Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Xianyang 712100, China; (Z.W.); (W.H.); (H.W.); (P.D.); (T.L.); (C.W.); (J.Z.); (C.C.)
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, Xianyang 712100, China
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Sandal S, Singh S, Bansal G, Kaur R, Mogilicherla K, Pandher S, Roy A, Kaur G, Rathore P, Kalia A. Nanoparticle-Shielded dsRNA Delivery for Enhancing RNAi Efficiency in Cotton Spotted Bollworm Earias vittella (Lepidoptera: Nolidae). Int J Mol Sci 2023; 24:ijms24119161. [PMID: 37298113 DOI: 10.3390/ijms24119161] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 06/12/2023] Open
Abstract
The spotted bollworm Earias vittella (Lepidoptera: Nolidae) is a polyphagous pest with enormous economic significance, primarily affecting cotton and okra. However, the lack of gene sequence information on this pest has a significant constraint on molecular investigations and the formulation of superior pest management strategies. An RNA-seq-based transcriptome study was conducted to alleviate such limitations, and de novo assembly was performed to obtain transcript sequences of this pest. Reference gene identification across E. vittella developmental stages and RNAi treatments were conducted using its sequence information, which resulted in identifying transcription elongation factor (TEF), V-type proton ATPase (V-ATPase), and Glyceraldehyde -3-phosphate dehydrogenase (GAPDH) as the most suitable reference genes for normalization in RT-qPCR-based gene expression studies. The present study also identified important developmental, RNAi pathway, and RNAi target genes and performed life-stage developmental expression analysis using RT-qPCR to select the optimal targets for RNAi. We found that naked dsRNA degradation in the E. vittella hemolymph is the primary reason for poor RNAi. A total of six genes including Juvenile hormone methyl transferase (JHAMT), Chitin synthase (CHS), Aminopeptidase (AMN), Cadherin (CAD), Alpha-amylase (AMY), and V-type proton ATPase (V-ATPase) were selected and knocked down significantly with three different nanoparticles encapsulated dsRNA conjugates, i.e., Chitosan-dsRNA, carbon quantum dots-dsRNA (CQD-dsRNA), and Lipofectamine-dsRNA conjugate. These results demonstrate that feeding nanoparticle-shielded dsRNA silences target genes and suggests that nanoparticle-based RNAi can efficiently manage this pest.
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Affiliation(s)
- Shelja Sandal
- Regional Research Station, Punjab Agricultural University, Faridkot 151203, Punjab, India
- Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala 140072, Punjab, India
| | - Satnam Singh
- Regional Research Station, Punjab Agricultural University, Faridkot 151203, Punjab, India
| | - Gulshan Bansal
- Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala 140072, Punjab, India
| | - Ramandeep Kaur
- Regional Research Station, Punjab Agricultural University, Faridkot 151203, Punjab, India
| | - Kanakachari Mogilicherla
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 21 Praha, Czech Republic
| | - Suneet Pandher
- Regional Research Station, Punjab Agricultural University, Faridkot 151203, Punjab, India
| | - Amit Roy
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 21 Praha, Czech Republic
| | - Gurmeet Kaur
- Regional Research Station, Punjab Agricultural University, Faridkot 151203, Punjab, India
| | - Pankaj Rathore
- Regional Research Station, Punjab Agricultural University, Faridkot 151203, Punjab, India
| | - Anu Kalia
- Electron Microscopy and Nanoscience Laboratory, Punjab Agricultural University, Ludhiana 141004, Punjab, India
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Gao L, Wang Y, Abbas M, Zhang T, Ma E, Merzendorfer H, Zhu KY, Zhang J. Both LmDicer-1 and two LmDicer-2s participate in siRNA-mediated RNAi pathway and contribute to high gene silencing efficiency in Locusta migratoria. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2022; 151:103865. [PMID: 36336194 DOI: 10.1016/j.ibmb.2022.103865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/29/2022] [Accepted: 10/29/2022] [Indexed: 06/16/2023]
Abstract
Dicers belong to a class of large RNase III multidomain ribonucleases and are central components of the RNA interference (RNAi) pathways. In insects, Dicer-2 has been known to cleave long double-stranded RNA (dsRNA) in small interfering RNA (siRNA)-mediated-RNAi pathway. However, Dicer-1 is responsible for cleaving precursor microRNAs (pre28 miRNAs) in miRNA-mediated RNAi pathway. In this study, we identified one LmDicer-1 and two LmDicer-2 (LmDicer-2a and LmDicer-2b) genes in Locusta migratoria. The RNAi of RNAi assay showed that knockdown of each of the Dicer genes reduced RNAi efficiency against a target gene (Lmβ-Tubulin), suggesting that all these genes participated in the siRNA-mediated RNAi pathway. Sequence analyses of the siRNAs generated from dsLmβ-Tubulin after silencing each LmDicer gene showed no significant difference in the pattern of siRNAs mapped to dsLmβ-Tubulin. This result indicated that all the three LmDicers are capable of generating siRNAs from the dsRNA. We then generated recombinant proteins consisting of different domains using Escherichia coli expression system and incubated each recombinant protein with dsLmβ-Tubulin. We found that the recombinant Dicer proteins successfully cleaved dsLmβ-Tubulin. However, LmDicer-2a-R lacking dsRBD domain lost activity, suggesting that dsRBD domain is critical for Dicer function. Furthermore, overexpression of these proteins in Drosophila S2 cells improved RNAi efficiency. Our siRNA affinity chromatography and LC-MS/MS analysis identified LmDicer-2a, LmDicer-2b, LmR2D2, LmAgo2a, LmAgo1, LmStaufen and LmTARBP2 as constituents of RNA-induced silencing complex. Taken together, these data show that both LmDicer-1 and two LmDicer-2s all participate in siRNA-mediated RNAi pathway and likely contribute to high RNAi efficiency in L. migratoria.
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Affiliation(s)
- Lu Gao
- Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, 030006, China; College of Life Science, Shanxi University, Taiyuan, China
| | - Yanli Wang
- Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, 030006, China
| | - Mureed Abbas
- Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, 030006, China
| | - Tingting Zhang
- Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, 030006, China
| | - Enbo Ma
- Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, 030006, China
| | | | - Kun Yan Zhu
- Department of Entomology, 123 Waters Hall, Kansas State University, Manhattan, KS, 66506, USA.
| | - Jianzhen Zhang
- Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, 030006, China.
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