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Haq IU, Muhammad M, Yuan H, Ali S, Abbasi A, Asad M, Ashraf HJ, Khurshid A, Zhang K, Zhang Q, Liu C. Satellitome Analysis and Transposable Elements Comparison in Geographically Distant Populations of Spodoptera frugiperda. Life (Basel) 2022; 12:521. [PMID: 35455012 PMCID: PMC9026859 DOI: 10.3390/life12040521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 11/29/2022] Open
Abstract
Spodoptera frugiperda (fall armyworm) is a member of the superfamily Noctuoidea that accounts for more than a third of all Lepidoptera and includes a considerable number of agricultural and forest pest species. Spodoptera frugiperda is a polyphagous species that is a significant agricultural pest worldwide, emphasizing its economic importance. Spodoptera frugiperda's genome size, assembly, phylogenetic classification, and transcriptome analysis have all been previously described. However, the different studies reported different compositions of repeated DNA sequences that occupied the whole assembled genome, and the Spodoptera frugiperda genome also lacks the comprehensive study of dynamic satellite DNA. We conducted a comparative analysis of repetitive DNA across geographically distant populations of Spodoptera frugiperda, particularly satellite DNA, using publicly accessible raw genome data from eight different geographical regions. Our results showed that most transposable elements (TEs) were commonly shared across all geographically distant samples, except for the Maverick and PIF/Harbinger elements, which have divergent repeat copies. The TEs age analysis revealed that most TEs families consist of young copies 1-15 million years old; however, PIF/Harbinger has some older/degenerated copies of 30-35 million years old. A total of seven satellite DNA families were discovered, accounting for approximately 0.65% of the entire genome of the Spodoptera frugiperda fall armyworm. The repeat profiling analysis of satellite DNA families revealed differential read depth coverage or copy numbers. The satellite DNA families range in size from the lowest 108 bp SfrSat06-108 families to the largest (1824 bp) SfrSat07-1824 family. We did not observe a statistically significant correlation between monomer length and K2P divergence, copy number, or abundance of each satellite family. Our findings suggest that the satellite DNA families identified in Spodoptera frugiperda account for a considerable proportion of the genome's repetitive fraction. The satellite DNA families' repeat profiling revealed a point mutation along the reference sequences. Limited TEs differentiation exists among geographically distant populations of Spodoptera frugiperda.
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Affiliation(s)
- Inzamam Ul Haq
- College of Plant Protection, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Lanzhou 730070, China; (I.U.H.); (A.K.); (K.Z.); (Q.Z.)
| | - Majid Muhammad
- College of Life Sciences, Shaanxi Normal University, Xi’an 710100, China; (M.M.); (H.Y.)
| | - Huang Yuan
- College of Life Sciences, Shaanxi Normal University, Xi’an 710100, China; (M.M.); (H.Y.)
| | - Shahbaz Ali
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan 64200, Pakistan;
| | - Asim Abbasi
- Department of Zoology, Bahawalpur Campus, University of Central Punjab, Bahawalpur 63100, Pakistan;
| | - Muhammad Asad
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Hafiza Javaria Ashraf
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Aroosa Khurshid
- College of Plant Protection, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Lanzhou 730070, China; (I.U.H.); (A.K.); (K.Z.); (Q.Z.)
| | - Kexin Zhang
- College of Plant Protection, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Lanzhou 730070, China; (I.U.H.); (A.K.); (K.Z.); (Q.Z.)
| | - Qiangyan Zhang
- College of Plant Protection, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Lanzhou 730070, China; (I.U.H.); (A.K.); (K.Z.); (Q.Z.)
| | - Changzhong Liu
- College of Plant Protection, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Lanzhou 730070, China; (I.U.H.); (A.K.); (K.Z.); (Q.Z.)
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Thrimawithana AH, Wu C, Christeller JT, Simpson RM, Hilario E, Tooman LK, Begum D, Jordan MD, Crowhurst R, Newcomb RD, Grapputo A. The Genomics and Population Genomics of the Light Brown Apple Moth, Epiphyas postvittana, an Invasive Tortricid Pest of Horticulture. INSECTS 2022; 13:insects13030264. [PMID: 35323562 PMCID: PMC8951345 DOI: 10.3390/insects13030264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/01/2022] [Accepted: 03/04/2022] [Indexed: 12/13/2022]
Abstract
Simple Summary In this study, we produced a genomic resource for the light brown apple moth, Epiphyas postvittana, to understand the biological basis of adaptation to a high number of hosts (polyphagy) and the invasive nature of this and other lepidopteran pests. The light brown apple moth is an invasive pest of horticultural plants, with over 500 recorded plant hosts. With origins in Australia, the pest has subsequently spread to New Zealand, Hawaii, California and Europe, causing significant economic losses for fruit producers. Comparative genomic analyses with other lepidopteran genomes indicate that a high proportion of the genome is made up of repetitive sequences, with the majority of the known elements being DNA transposable elements and retrotransposons. Twenty gene families show significant expansions, including some likely to have a role in its pest status. Finally, population genomics, investigated by a RAD-tag approach, indicated likely patterns of invasion and admixture, with Californian moths most probably being derived from Australia. Abstract The light brown apple moth, Epiphyas postvittana is an invasive, polyphagous pest of horticultural systems around the world. With origins in Australia, the pest has subsequently spread to New Zealand, Hawaii, California and Europe, where it has been found on over 500 plants, including many horticultural crops. We have produced a genomic resource, to understand the biological basis of the polyphagous and invasive nature of this and other lepidopteran pests. The assembled genome sequence encompassed 598 Mb and has an N50 of 301.17 kb, with a BUSCO completion rate of 97.9%. Epiphyas postvittana has 34% of its assembled genome represented as repetitive sequences, with the majority of the known elements made up of longer DNA transposable elements (14.07 Mb) and retrotransposons (LINE 17.83 Mb). Of the 31,389 predicted genes, 28,714 (91.5%) were assigned to 11,438 orthogroups across the Lepidoptera, of which 945 were specific to E. postvittana. Twenty gene families showed significant expansions in E. postvittana, including some likely to have a role in its pest status, such as cytochrome p450s, glutathione-S-transferases and UDP-glucuronosyltransferases. Finally, using a RAD-tag approach, we investigated the population genomics of this pest, looking at its likely patterns of invasion.
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Affiliation(s)
- Amali H. Thrimawithana
- The New Zealand Institute of Plant and Food Research Limited, Auckland 1025, New Zealand; (A.H.T.); (C.W.); (E.H.); (L.K.T.); (D.B.); (M.D.J.); (R.C.)
| | - Chen Wu
- The New Zealand Institute of Plant and Food Research Limited, Auckland 1025, New Zealand; (A.H.T.); (C.W.); (E.H.); (L.K.T.); (D.B.); (M.D.J.); (R.C.)
| | - John T. Christeller
- The New Zealand Institute of Plant and Food Research Limited, Palmerston North 4410, New Zealand; (J.T.C.); (R.M.S.)
| | - Robert M. Simpson
- The New Zealand Institute of Plant and Food Research Limited, Palmerston North 4410, New Zealand; (J.T.C.); (R.M.S.)
| | - Elena Hilario
- The New Zealand Institute of Plant and Food Research Limited, Auckland 1025, New Zealand; (A.H.T.); (C.W.); (E.H.); (L.K.T.); (D.B.); (M.D.J.); (R.C.)
| | - Leah K. Tooman
- The New Zealand Institute of Plant and Food Research Limited, Auckland 1025, New Zealand; (A.H.T.); (C.W.); (E.H.); (L.K.T.); (D.B.); (M.D.J.); (R.C.)
| | - Doreen Begum
- The New Zealand Institute of Plant and Food Research Limited, Auckland 1025, New Zealand; (A.H.T.); (C.W.); (E.H.); (L.K.T.); (D.B.); (M.D.J.); (R.C.)
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Melissa D. Jordan
- The New Zealand Institute of Plant and Food Research Limited, Auckland 1025, New Zealand; (A.H.T.); (C.W.); (E.H.); (L.K.T.); (D.B.); (M.D.J.); (R.C.)
| | - Ross Crowhurst
- The New Zealand Institute of Plant and Food Research Limited, Auckland 1025, New Zealand; (A.H.T.); (C.W.); (E.H.); (L.K.T.); (D.B.); (M.D.J.); (R.C.)
| | - Richard D. Newcomb
- The New Zealand Institute of Plant and Food Research Limited, Auckland 1025, New Zealand; (A.H.T.); (C.W.); (E.H.); (L.K.T.); (D.B.); (M.D.J.); (R.C.)
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
- Correspondence:
| | - Alessandro Grapputo
- Dipartimento di Biologia, Università degli Studi di Padova, 35131 Padova, Italy;
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Bird L, Miles M, Quade A, Spafford H. Insecticide resistance in Australian Spodoptera frugiperda (J.E. Smith) and development of testing procedures for resistance surveillance. PLoS One 2022; 17:e0263677. [PMID: 35143580 PMCID: PMC8830740 DOI: 10.1371/journal.pone.0263677] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 01/25/2022] [Indexed: 01/08/2023] Open
Abstract
Spodoptera frugiperda (J.E. Smith) is a highly invasive noctuid pest first reported in northern Australia during early 2020. To document current status of resistance in S. frugiperda in Australia, insecticide toxicity was tested in field populations collected during the first year of establishment, between March 2020 and March 2021. Dose-response was measured by larval bioassay in 11 populations of S. frugiperda and a susceptible laboratory strain of Helicoverpa armigera. Emamectin benzoate was the most efficacious insecticide (LC50 0.023μg/ml) followed by chlorantraniliprole (LC50 0.055μg/ml), spinetoram (LC50 0.098μg/ml), spinosad (LC50 0.526μg/ml), and methoxyfenozide (1.413μg/ml). Indoxacarb was the least toxic selective insecticide on S. frugiperda (LC50 3.789μg/ml). Emamectin benzoate, chlorantraniliprole and methoxyfenozide were 2- to 7-fold less toxic on S. frugiperda compared with H. armigera while spinosyns were equally toxic on both species. Indoxacarb was 28-fold less toxic on S. frugiperda compared with H. armigera. There was decreased sensitivity to Group 1 insecticides and synthetic pyrethroids in S. frugiperda compared with H. armigera: toxicity was reduced up to 11-fold for methomyl, 56 to 199-fold for cyhalothrin, and 44 to 132-fold for alpha cypermethrin. Synergism bioassays with metabolic inhibitors suggest involvement of mixed function oxidase in pyrethroid resistance. Recommended diagnostic doses for emamectin benzoate, chlorantraniliprole, spinetoram, spinosad, methoxyfenozide and indoxacarb are 0.19, 1.0, 0.75, 6, 12 and 48μg/μl, respectively.
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Affiliation(s)
- Lisa Bird
- NSW Department of Primary Industries, Tamworth Agricultural Institute, Calala, New South Wales, Australia
| | - Melina Miles
- Queensland Department of Agriculture and Fisheries, Toowoomba, Queensland, Australia
| | - Adam Quade
- Queensland Department of Agriculture and Fisheries, Toowoomba, Queensland, Australia
| | - Helen Spafford
- Department of Primary Industries and Regional Development, Frank Wise Institute of Tropical Agriculture, Kununurra, Western Australia, Australia
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Li Y, Gao H, Yu R, Zhang Y, Feng F, Tang J, Li B. Identification and characterization of G protein-coupled receptors in Spodoptera frugiperda (Insecta: Lepidoptera). Gen Comp Endocrinol 2022; 317:113976. [PMID: 35016911 DOI: 10.1016/j.ygcen.2022.113976] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/23/2021] [Accepted: 01/05/2022] [Indexed: 12/13/2022]
Abstract
Spodoptera frugiperda (Insecta: Lepidoptera) is a destructive invasive pest feeding on various plants and causing serious damage to several economically-important crops. G protein-coupled receptors (GPCRs) are cellular receptors that coordinate diverse signaling processes, associated with many physiological processes and disease states. However, less information about GPCRs had been reported in S. frugiperda, limiting the recognition of signaling system and in-depth studies of this pest. Here, a total of 167 GPCRs were identified in S. frugiperda. Compared with other insects, the GPCRs of S. frugiperda were significantly expanded. A large of tandem duplication and segmental duplication events were observed, which may be the key factor to increase the size of GPCR family. In detail, these expansion events mainly concentrate on biogenic amine receptors, neuropeptide and protein hormone receptors, which may be involved in feeding, reproduction, life span, and tolerance of S. frugiperda. Additionally, 17 Mth/Mthl members were identified in S. frugiperda, which may be similar to the evolutionary pattern of 16 Mth/Mthl members in Drosophila. Moreover, the expression patterns across different developmental stages of all GPCR genes were also analyzed. Among these, most of the GPCR genes are poorly expressed in S. frugiperda and some highly expressed GPCR genes help S. frugiperda adapt to the environment better, such as Rh6 and AkhR. In this study, all GPCRs in S. frugiperda were identified for the first time, which provided a basis for further revealing the role of these receptors in the physiological and behavioral regulation of this pest.
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Affiliation(s)
- Yanxiao Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Han Gao
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Runnan Yu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yonglei Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Fan Feng
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Jing Tang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Bin Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
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Xu L, Zhao J, Xu D, Xu G, Gu Z, Xiao Z, Dewer Y, Zhang Y. Application of transcriptomic analysis to unveil the toxicity mechanisms of fall armyworm response after exposure to sublethal chlorantraniliprole. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 230:113145. [PMID: 34979309 DOI: 10.1016/j.ecoenv.2021.113145] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/25/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
The anthranilic diamide insecticide chlorantraniliprole is highly effective against Lepidoptera pests, but the underlying mechanisms of toxic effects of chlorantraniliprole exposures for adapting to the chemical environment are poorly known in fall armyworm (FAW), Spodoptera frugiperda (J.E.Smith). FAW being one of the most pests of maize in Latin America, suddenly appeared in China in 2019 and spread rapidly. In this study, using bioassay and transcriptomic and biochemical analyses, we comprehensively investigated gene expression changes of third instar larvae in response to different sublethal concentrations (LC10 and LC30) of chlorantraniliprole in this insect. Exposure to LC10 chlorantraniliprole (0.73 mg/L) causes 1266 differentially expressed genes (DEGs), of which 578 are up-regulated and 688 down-regulated. Exposure to LC30 (2.49 mg/L) causes differential expression of 3637 DEGs (1545 up-, 2092 down-regulated). Interestingly, the LC30 treatment led to a significant increase in the number of DEGs compared to that of the LC10, indicating a concentration effect manner. Moreover, enrichment analysis identified important DEGs belonging to specific categories, such as amino acid, carbohydrate, lipid, energy, xenobiotics metabolisms, signal transduction, and posttranslational modification pathways, and enzymes activities in enriched pathways were significantly altered at the LC10 and LC30, which matched transcriptome analysis to mediate toxic mechanisms. The DEGs encoding detoxification-related genes were identified and validated by quantitative real-time PCR (qRT-PCR), which correlated with the RNA-sequencing (RNA-seq) data. To our knowledge, these findings provide the first toxicity mechanisms for a better understanding of chlorantraniliprole action and detoxification in FAW and other insect pests at molecular level.
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Affiliation(s)
- Lu Xu
- Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
| | - Jun Zhao
- Key Laboratory of Green Preservation and Control of Tobacco Diseases and Pests in the Huanghuai Growing Area, Institute of Tobacco Research, Henan Academy of Agricultural Sciences, Xuchang 461000, China
| | - Dejin Xu
- Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Guangchun Xu
- Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Zhongyan Gu
- Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Zheng Xiao
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, School of Landscape Architecture, Zhejiang A & F University, Hangzhou 311300, China
| | - Youssef Dewer
- Phytotoxicity Research Department, Central Agricultural Pesticide Laboratory, Agricultural Research Center, Dokki 12618, Giza, Egypt
| | - Yanan Zhang
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, Huaibei 235000, China.
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Breeschoten T, van der Linden CFH, Ros VID, Schranz ME, Simon S. Expanding the Menu: Are Polyphagy and Gene Family Expansions Linked across Lepidoptera? Genome Biol Evol 2022; 14:6482744. [PMID: 34951642 PMCID: PMC8725640 DOI: 10.1093/gbe/evab283] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2021] [Indexed: 12/31/2022] Open
Abstract
Evolutionary expansions and contractions of gene families are often correlated with key innovations and/or ecological characteristics. In butterflies and moths (Lepidoptera), expansions of gene families involved in detoxification of plant specialized metabolites are hypothesized to facilitate a polyphagous feeding style. However, analyses supporting this hypothesis are mostly based on a limited number of lepidopteran species. We applied a phylogenomics approach, using 37 lepidopteran genomes, to analyze if gene family evolution (gene gain and loss) is associated with the evolution of polyphagy. Specifically, we compared gene counts and evolutionary gene gain and loss rates of gene families involved in adaptations with plant feeding. We correlated gene evolution to host plant family range (phylogenetic diversity) and specialized metabolite content of plant families (functional metabolite diversity). We found a higher rate for gene loss than gene gain in Lepidoptera, a potential consequence of genomic rearrangements and deletions after (potentially small-scale) duplication events. Gene family expansions and contractions varied across lepidopteran families, and were associated to host plant use and specialization levels. Within the family Noctuidae, a higher expansion rate for gene families involved in detoxification can be related to the large number of polyphagous species. However, gene family expansions are observed in both polyphagous and monophagous lepidopteran species and thus seem to be species-specific in the taxa sampled. Nevertheless, a significant positive correlation of gene counts of the carboxyl- and choline esterase and glutathione-S-transferase detoxification gene families with the level of polyphagy was identified across Lepidoptera.
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Affiliation(s)
| | | | - Vera I D Ros
- Laboratory of Virology, Wageningen University & Research, The Netherlands
| | - M Eric Schranz
- Biosystematics Group, Wageningen University & Research, The Netherlands
| | - Sabrina Simon
- Biosystematics Group, Wageningen University & Research, The Netherlands
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Chen H, Xie M, Lin L, Zhong Y, Zhang F, Su W. Transcriptome Analysis of Detoxification-Related Genes in Spodoptera frugiperda (Lepidoptera: Noctuidae). JOURNAL OF INSECT SCIENCE (ONLINE) 2022; 22:11. [PMID: 35134188 PMCID: PMC8824446 DOI: 10.1093/jisesa/ieab108] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Indexed: 05/27/2023]
Abstract
Spodoptera frugiperda (J. E. Smith) (Lepidoptera: Noctuidae) is an important pest on maize, and it can cause large yield losses. As S. frugiperda has invaded many developing countries in Africa and Asia in recent years, it could impact food security. Pesticides remain the main method to control S. frugiperda in the field, and this pest has developed resistance to some pesticides. In this study, we used second-generation sequencing technology to detect the gene expression change of S. frugiperda after treatment by LC20 of three pesticides, lufenuron, spinetoram, and tetrachloroamide, which have different modes of actions. The sequence data were first assembled into a 60,236 unigenes database, and then the differential expression unigenes (DEUs) after pesticide treatment were identified. The DEU numbers, Gene Ontology catalog, and Kyoto Encyclopedia of Genes and Genomes pathway catalog were analyzed. Finally, 11 types of unigenes related to detoxification and DEUs after pesticide treatment were listed, and Cytochrome P450, Glutathione S-transferase, and ATP-binding cassette transporter were analyzed. This study provides a foundation for molecular research on S. frugiperda pesticide detoxification.
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Affiliation(s)
- Haoliang Chen
- Anhui-CABI Joint Laboratory for Agricultural Pest Control, Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Minghui Xie
- Anhui-CABI Joint Laboratory for Agricultural Pest Control, Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Lulu Lin
- Anhui-CABI Joint Laboratory for Agricultural Pest Control, Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Yongzhi Zhong
- Anhui-CABI Joint Laboratory for Agricultural Pest Control, Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Feng Zhang
- MARA-CABI Joint Laboratory for Bio-safety, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- CABI East & South-East Asia, Beijing 100081, China
| | - Weihua Su
- Anhui-CABI Joint Laboratory for Agricultural Pest Control, Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
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Xu H, Ye X, Yang Y, Yang Y, Sun YH, Mei Y, Xiong S, He K, Xu L, Fang Q, Li F, Ye G, Lu Z. Comparative Genomics Sheds Light on the Convergent Evolution of Miniaturized Wasps. Mol Biol Evol 2021; 38:5539-5554. [PMID: 34515790 PMCID: PMC8662594 DOI: 10.1093/molbev/msab273] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Miniaturization has occurred in many animal lineages, including insects and vertebrates, as a widespread trend during animal evolution. Among Hymenoptera, miniaturization has taken place in some parasitoid wasp lineages independently, and may have contributed to the diversity of species. However, the genomic basis of miniaturization is little understood. Diverged approximately 200 Ma, Telenomus wasps (Platygastroidea) and Trichogramma wasps (Chalcidoidea) have both evolved to a highly reduced body size independently, representing a paradigmatic example of convergent evolution. Here, we report a high-quality chromosomal genome of Telenomus remus, a promising candidate for controlling Spodoptera frugiperda, a notorious pest that has recently caused severe crop damage. The T. remus genome (129 Mb) is characterized by a low density of repetitive sequence and a reduction of intron length, resulting in the shrinkage of genome size. We show that hundreds of genes evolved faster in two miniaturized parasitoids Trichogramma pretiosum and T. remus. Among them, 38 genes exhibit extremely accelerated evolutionary rates in these miniaturized wasps, possessing diverse functions in eye and wing development as well as cell size control. These genes also highlight potential roles in body size regulation. In sum, our analyses uncover a set of genes with accelerated evolutionary rates in Tri. pretiosum and T. remus, which might be responsible for their convergent adaptations to miniaturization, and thus expand our understanding on the evolutionary basis of miniaturization. Additionally, the genome of T. remus represents the first genome resource of superfamily Platygastroidea, and will facilitate future studies of Hymenoptera evolution and pest control.
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Affiliation(s)
- Hongxing Xu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agroproducts, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xinhai Ye
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
- Shanghai Institute for Advanced Study, Zhejiang University, Shanghai, China
- Institute of Artificial Intelligence, College of Computer Science and Technology, Zhejiang University, Hangzhou, China
| | - Yajun Yang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agroproducts, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yi Yang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yu H Sun
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Yang Mei
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Shijiao Xiong
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Kang He
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Le Xu
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Qi Fang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Fei Li
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Gongyin Ye
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Zhongxian Lu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agroproducts, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Genomic and Transcriptomic Analysis Reveals Cuticular Protein Genes Responding to Different Insecticides in Fall Armyworm Spodoptera frugiperda. INSECTS 2021; 12:insects12110997. [PMID: 34821798 PMCID: PMC8622913 DOI: 10.3390/insects12110997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/29/2021] [Accepted: 11/03/2021] [Indexed: 11/16/2022]
Abstract
The fall armyworm (FAW), Spodoptera frugiperda, is a serious pest of crucial crops causing great threats to the food security of the world. It has evolved resistance to various insecticides, while the underlying molecular mechanisms remain largely unknown. Cuticular proteins (CPs), as primary components in cuticle, play an important role in insects' protection against environmental stresses. Few of them have been documented as participating in insecticide resistance in several insect species. In order to explore whether CP genes of the FAW exhibit a functional role in responding to insecticides stress, a total of 206 CPs, classified into eight families, were identified from the genome of the FAW through a homology-based approach coupled with manual efforts. The temporal expression profiles of all identified CP genes across developmental stages and their responses to 23 different insecticides were analyzed using the RNA-seq data. Expression profiling indicated that most of the CP genes displayed stage-specific expression patterns. It was found that the expression of 51 CP genes significantly changed after 48 h exposure to 17 different insecticides. The expression of eight CP genes responding to four insecticides were confirmed by RT-PCR analysis. The results showed that their overall expression profiles were consistent with RNA-seq analysis. The findings provide a basis for further functional investigation of CPs implied in insecticide stress in FAW.
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McComic SE, Rault LC, Anderson TD, Swale DR. Toxicological analysis of stilbenes against the fall armyworm, Spodoptera frugiperda. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2021; 179:104965. [PMID: 34802515 DOI: 10.1016/j.pestbp.2021.104965] [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: 06/09/2021] [Revised: 08/17/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
The fall armyworm (FAW), Spodoptera frugiperda, is a global pest of multiple economically important row crops and the development of resistance to commercially available insecticidal classes has inhibited FAW control. Thus, there is a need to identify chemical scaffolds that can provide inspiration for the development of novel insecticides for FAW management. This study aimed to assess the sensitivity of central neurons and susceptibility of FAW to chloride channel modulators to establish a platform for repurposing existing insecticides or designing new chemicals capable of controlling FAW. Potency of select chloride channel modulators were initially studied against FAW central neuron firing rate and rank order of potency was determined to be fipronil > lindane > Z-stilbene > DIDS > GABA > E-stilbene. Toxicity bioassays identified fipronil and lindane as the two most toxic modulators studied with topical LD50's of 41 and 75 ng/mg of caterpillar, respectively. Interestingly, Z-stilbene was toxic at 300 ng/mg of caterpillar, but no toxicity was observed with DIDS or E-stilbene. The significant shift in potency between stilbene isomers indicates structure-activity relationships between stilbene chemistry and the binding site in FAW may exist. The data presented in this study defines the potency of select chloride channel modulators to FAW neural activity and survivorship to establish a platform for development of novel chemical agents to control FAW populations. Although stilbenes may hold promise for insecticide development, the low toxicity of the scaffolds tested in this study dampen enthusiasm for their development into FAW specific insecticides.
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Affiliation(s)
- Sarah E McComic
- Louisiana State University AgCenter, Department of Entomology, Baton Rouge, LA 70803, United States of America
| | - Leslie C Rault
- University of Nebraska, Department of Entomology, 103 Entomology Hall, Lincoln, NE 68583, United States of America
| | - Troy D Anderson
- University of Nebraska, Department of Entomology, 103 Entomology Hall, Lincoln, NE 68583, United States of America
| | - Daniel R Swale
- Louisiana State University AgCenter, Department of Entomology, Baton Rouge, LA 70803, United States of America.
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Amezian D, Nauen R, Le Goff G. Comparative analysis of the detoxification gene inventory of four major Spodoptera pest species in response to xenobiotics. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2021; 138:103646. [PMID: 34469782 DOI: 10.1016/j.ibmb.2021.103646] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/09/2021] [Accepted: 08/25/2021] [Indexed: 05/21/2023]
Abstract
The genus Spodoptera (Lepidoptera: Noctuidae) comprises some of the most polyphagous and destructive agricultural pests worldwide. The success of many species of this genus is due to their striking abilities to adapt to a broad range of host plants. Superfamilies of detoxification genes play a crucial role in the adaption to overcome plant defense mechanisms mediated by numerous secondary metabolites and toxins. Over the past decade, a substantial amount of expression data in Spodoptera larvae was produced for those genes in response to xenobiotics such as plant secondary metabolites, but also insecticide exposure. However, this information is scattered throughout the literature and in most cases does not allow to clearly identify candidate genes involved in host-plant adaptation and insecticide resistance. In the present review, we analyzed and compiled information on close to 600 pairs of inducers (xenobiotics) and induced genes from four main Spodoptera species: S. exigua, S. frugiperda, S. littoralis and S. litura. The cytochrome P450 monooxygenases (P450s; encoded by CYP genes) were the most upregulated detoxification genes across the literature for all four species. Most of the data was provided from studies on S. litura, followed by S. exigua, S. frugiperda and S. littoralis. We examined whether these detoxification genes were reported for larval survival under xenobiotic challenge in forward and reverse genetic studies. We further analyzed whether biochemical assays were carried out showing the ability of corresponding enzymes and transporters to breakdown and excrete xenobiotics, respectively. This revealed a clear disparity between species and the lack of genetic and biochemical information in S. frugiperda. Finally, we discussed the biological importance of detoxification genes for this genus and propose a workflow to study the involvement of these enzymes in an ecological and agricultural context.
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Affiliation(s)
- Dries Amezian
- Université Côte d'Azur, INRAE, CNRS, ISA, F-06903, Sophia Antipolis, France
| | - Ralf Nauen
- Bayer AG, Crop Science Division, R&D, Alfred Nobel-Strasse 50, 40789, Monheim, Germany.
| | - Gaëlle Le Goff
- Université Côte d'Azur, INRAE, CNRS, ISA, F-06903, Sophia Antipolis, France.
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Simon S, Breeschoten T, Jansen HJ, Dirks RP, Schranz ME, Ros VID. Genome and transcriptome analysis of the beet armyworm Spodoptera exigua reveals targets for pest control. G3 (BETHESDA, MD.) 2021; 11:jkab311. [PMID: 34557910 PMCID: PMC8527508 DOI: 10.1093/g3journal/jkab311] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/19/2021] [Indexed: 12/13/2022]
Abstract
The genus Spodoptera (Lepidoptera: Noctuidae) includes some of the most infamous insect pests of cultivated plants including Spodoptera frugiperda, Spodoptera litura, and Spodoptera exigua. To effectively develop targeted pest control strategies for diverse Spodoptera species, genomic resources are highly desired. To this aim, we provide the genome assembly and developmental transcriptome comprising all major life stages of S. exigua, the beet armyworm. Spodoptera exigua is a polyphagous herbivore that can feed on > 130 host plants, including several economically important crops. The 419 Mb beet armyworm genome was sequenced from a female S. exigua pupa. Using a hybrid genome sequencing approach (Nanopore long-read data and Illumina short read), a high-quality genome assembly was achieved (N50 = 1.1 Mb). An official gene set (18,477 transcripts) was generated by automatic annotation and by using transcriptomic RNA-seq datasets of 18 S. exigua samples as supporting evidence. In-depth analyses of developmental stage-specific expression combined with gene tree analyses of identified homologous genes across Lepidoptera genomes revealed four potential genes of interest (three of them Spodoptera-specific) upregulated during first- and third-instar larval stages for targeted pest-outbreak management. The beet armyworm genome sequence and developmental transcriptome covering all major developmental stages provide critical insights into the biology of this devastating polyphagous insect pest species worldwide. In addition, comparative genomic analyses across Lepidoptera significantly advance our knowledge to further control other invasive Spodoptera species and reveals potential lineage-specific target genes for pest control strategies.
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Affiliation(s)
- Sabrina Simon
- Biosystematics Group, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Thijmen Breeschoten
- Biosystematics Group, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Hans J Jansen
- Future Genomics Technologies, Leiden, The Netherlands
| | - Ron P Dirks
- Future Genomics Technologies, Leiden, The Netherlands
| | - M Eric Schranz
- Biosystematics Group, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Vera I D Ros
- Laboratory of Virology, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
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Yang L, Xing B, Li F, Wang LK, Yuan L, Mbuji AL, Peng Z, Malhat F, Wu S. Full-length transcriptome analysis of Spodoptera frugiperda larval brain reveals detoxification genes. PeerJ 2021; 9:e12069. [PMID: 34513339 PMCID: PMC8395580 DOI: 10.7717/peerj.12069] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 08/05/2021] [Indexed: 11/20/2022] Open
Abstract
Background Spodoptera frugiperda (J. E. Smith), commonly known as fall armyworm (FAW), is one of the most destructive agricultural pests in the world and has posed a great threat to crops. The improper use of insecticides has led to rapid development of resistance. However, the genetic data available for uncovering the insecticide resistance mechanisms are scarce. Methods In this study, we used PacBio single-molecule real-time (SMRT) sequencing aimed at revealing the full-length transcriptome profiling of the FAW larval brain to obtain detoxification genes. Results A total of 18,642 high-quality transcripts were obtained with an average length of 2,371 bp, and 11,230 of which were successfully annotated in six public databases. Among these, 5,692 alternative splicing events were identified.
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Affiliation(s)
- Lei Yang
- Hainan University, Haikou, Hainan, China
| | | | - Fen Li
- Hainan University, Haikou, Hainan, China
| | | | | | - Amosi Leonard Mbuji
- Hainan University, Haikou, Hainan, China.,Department of Resources Utilization and Plant Protection, College of Resources and Environmental Science, China Agricultural University, Beijing, Beijing, China
| | - Zhengqiang Peng
- The Ministry of Agriculture and Rural Affairs Key Laboratory of Integrated Pest Management of Tropical Crops, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Farag Malhat
- Pesticide Residues and Environmental Pollution Department, Agricultural Research Center, Dokki, Giza, Egypt
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Garlet CG, Moreira RP, Gubiani PDS, Palharini RB, Farias JR, Bernardi O. Fitness Cost of Chlorpyrifos Resistance in Spodoptera frugiperda (Lepidoptera: Noctuidae) on Different Host Plants. ENVIRONMENTAL ENTOMOLOGY 2021; 50:898-908. [PMID: 34018549 DOI: 10.1093/ee/nvab046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Indexed: 06/12/2023]
Abstract
Spodoptera frugiperda (J. E. Smith, 1797) is a polyphagous pest of global relevance due to the damage it inflicts on agricultural crops. In South American countries, this species is one of the principal pests of maize and cotton. Currently, S. frugiperda is also emerging as an important pest of soybeans and winter cereals in Brazil. Chemical control is one of the main control tactics against S. frugiperda, even though resistance against numerous modes of action insecticides has been reported. To support insect resistance management programs, we evaluated the fitness costs of resistance of S. frugiperda to the acetylcholinesterase inhibitor chlorpyrifos. Fitness costs were quantified by comparing biological parameters of chlorpyrifos-resistant and -susceptible S. frugiperda and their F1 hybrids (heterozygotes) on non-Bt cotton, non-Bt maize, non-Bt soybean, and oats. The results revealed that the chlorpyrifos-resistant genotype showed lower pupa-to-adult and egg-to-adult survivorship and reduced larval weights on oats; longer neonate-to-pupa and egg-to-adult developmental periods, and lower pupal weights and fecundity on maize; lower pupal weights on soybean; and reduced fecundity on cotton compared with the chlorpyrifos-susceptible genotype. Fitness costs also affected fertility life table parameters of the resistant genotype, increasing the mean length of a generation on cotton and maize and reducing the potential for population growth on all hosts. These findings suggest fitness costs at the individual and population levels of chlorpyrifos resistance in S. frugiperda, indicating that removal of the selective agent from the environment would result in reduced resistance and opportunities for the restoration of susceptibility.
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Affiliation(s)
- Cínthia G Garlet
- Department of Plant Protection, Federal University of Santa Maria (UFSM), Roraima avenue 1000, Santa Maria, Rio Grande do Sul 97105-900, Brazil
| | - Rafaella P Moreira
- Department of Plant Protection, Federal University of Santa Maria (UFSM), Roraima avenue 1000, Santa Maria, Rio Grande do Sul 97105-900, Brazil
| | - Patricia da S Gubiani
- Department of Plant Protection, Federal University of Santa Maria (UFSM), Roraima avenue 1000, Santa Maria, Rio Grande do Sul 97105-900, Brazil
| | - Ramon B Palharini
- Department of Plant Protection, Federal University of Santa Maria (UFSM), Roraima avenue 1000, Santa Maria, Rio Grande do Sul 97105-900, Brazil
| | - Juliano R Farias
- Department of Crop Protection, Regional Integrated University of Alto Uruguay (URI), Santo Ângelo, Rio Grande do Sul 98902-470, Brazil
| | - Oderlei Bernardi
- Department of Plant Protection, Federal University of Santa Maria (UFSM), Roraima avenue 1000, Santa Maria, Rio Grande do Sul 97105-900, Brazil
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Jiang F, Chang G, Li Z, Abouzaid M, Du X, Hull JJ, Ma W, Lin Y. The HSP/co-chaperone network in environmental cold adaptation of Chilo suppressalis. Int J Biol Macromol 2021; 187:780-788. [PMID: 34358598 DOI: 10.1016/j.ijbiomac.2021.07.113] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/16/2021] [Indexed: 01/07/2023]
Abstract
Winter cold is one of the major environmental stresses for ectotherm species. Chilo suppressalis, a notorious lepidopteran pest of rice, has a wide geographic region that includes temperate zones with severe environmental conditions. Although C. suppressalis exhibits remarkable cold tolerance, its cold-adaptation mechanisms remain unclear. Here, we used bioinformatics approaches to evaluate transcript levels of genes comprising the C. suppressalis heat shock protein (HSP)/co-chaperone network in response to cold-induced stress. Using all such genes identified in the C. suppressalis genome, we experimentally examined the corresponding transcript levels under cold-acclimation or intermittent cold-shock stresses in diapause and non-diapausing larvae. In total, we identified 19 HSPs and 8 HSP co-chaperones in the C. suppressalis genome. Nine (hsp90, hsp75, hsp70, hsp40, small hsp, activator of 90 kDa heat shock protein ATPase-like, heat shock factor, heat shock factor binding protein 1-like and HSPB1-associated protein 1) were highly cold-inducible and likely comprise the principal cold-response HSP/co-chaperone network in C. suppressalis. We also found that transcriptional regulation of the HSP/co-chaperone networks response differs between cold-acclimation and short-term cold-shock. Moreover, activation of the HSP/co-chaperone network depends on the diapause state of overwintering larvae and cold acclimation may further increase larval cold tolerance. These results provide key new insights in the cold-adaptation mechanisms in C. suppressalis.
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Affiliation(s)
- Fan Jiang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Wuhan, Hubei, China; College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Guofeng Chang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Wuhan, Hubei, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhenzhen Li
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Mostafa Abouzaid
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xiaoyong Du
- College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, China
| | - J Joe Hull
- U.S. Arid Land Agricultural Research Center, U.S. Agricultural Research Service, Department of Agriculture, Maricopa, AZ, USA
| | - Weihua Ma
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Wuhan, Hubei, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China.
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Wuhan, Hubei, China.
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Zuo Y, Shi Y, Zhang F, Guan F, Zhang J, Feyereisen R, Fabrick JA, Yang Y, Wu Y. Genome mapping coupled with CRISPR gene editing reveals a P450 gene confers avermectin resistance in the beet armyworm. PLoS Genet 2021; 17:e1009680. [PMID: 34252082 PMCID: PMC8297932 DOI: 10.1371/journal.pgen.1009680] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/22/2021] [Accepted: 06/23/2021] [Indexed: 01/08/2023] Open
Abstract
The evolution of insecticide resistance represents a global constraint to agricultural production. Because of the extreme genetic diversity found in insects and the large numbers of genes involved in insecticide detoxification, better tools are needed to quickly identify and validate the involvement of putative resistance genes for improved monitoring, management, and countering of field-evolved insecticide resistance. The avermectins, emamectin benzoate (EB) and abamectin are relatively new pesticides with reduced environmental risk that target a wide number of insect pests, including the beet armyworm, Spodoptera exigua, an important global pest of many crops. Unfortunately, field resistance to avermectins recently evolved in the beet armyworm, threatening the sustainable use of this class of insecticides. Here, we report a high-quality chromosome-level assembly of the beet armyworm genome and use bulked segregant analysis (BSA) to identify the locus of avermectin resistance, which mapped on 15-16 Mbp of chromosome 17. Knockout of the CYP9A186 gene that maps within this region by CRISPR/Cas9 gene editing fully restored EB susceptibility, implicating this gene in avermectin resistance. Heterologous expression and in vitro functional assays further confirm that a natural substitution (F116V) found in the substrate recognition site 1 (SRS1) of the CYP9A186 protein results in enhanced metabolism of EB and abamectin. Hence, the combined approach of coupling gene editing with BSA allows for the rapid identification of metabolic resistance genes responsible for insecticide resistance, which is critical for effective monitoring and adaptive management of insecticide resistance.
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Affiliation(s)
- Yayun Zuo
- The Key Laboratory of Plant Immunity and College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Institute of Pesticide Science, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Yu Shi
- The Key Laboratory of Plant Immunity and College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Feng Zhang
- The Key Laboratory of Plant Immunity and College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Fang Guan
- The Key Laboratory of Plant Immunity and College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Jianpeng Zhang
- The Key Laboratory of Plant Immunity and College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - René Feyereisen
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jeffrey A. Fabrick
- USDA ARS, U.S. Arid Land Agricultural Research Center, Maricopa, Arizona, United States of America
| | - Yihua Yang
- The Key Laboratory of Plant Immunity and College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- * E-mail: (YY); (YW)
| | - Yidong Wu
- The Key Laboratory of Plant Immunity and College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- * E-mail: (YY); (YW)
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Garcia AG, Malaquias JB, Ferreira CP, Tomé MP, Weber ID, Godoy WAC. Ecological Modelling of Insect Movement in Cropping Systems. NEOTROPICAL ENTOMOLOGY 2021; 50:321-334. [PMID: 33900576 DOI: 10.1007/s13744-021-00869-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
Abstract
The spatio-temporal dynamics of insect pests in agricultural landscapes involves the potential of species to move, invade, colonise, and establish in different areas. This study revised the dispersal of the important crop pests Diabrotica speciosa Germar and Spodoptera frugiperda (J.E. Smith) by using computational modelling to represent the movement of these polyphagous pests in agricultural mosaics. The findings raise significant questions regarding the dispersal of pests through crops and refuge areas, indicating that understanding pest movement is essential for developing strategies to predict critical infestation levels to assist in pest-management decisions. In addition, our modelling approach can be adapted for other insect species and other cropping systems despite discussing two specific species in the current manuscript. We present an overview of studies, combining experimentation and ecological modelling, discussing the methods used and the importance of studying insect movement as well as the implications for agricultural landscapes in Brazil.
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Affiliation(s)
- Adriano Gomes Garcia
- Dept of Entomology and Acarology, Luiz de Queiroz College of Agriculture, Univ of São Paulo, Piracicaba, São Paulo, Brazil
| | | | | | - Maysa Pereira Tomé
- Dept of Entomology and Acarology, Luiz de Queiroz College of Agriculture, Univ of São Paulo, Piracicaba, São Paulo, Brazil
| | - Igor Daniel Weber
- Dept of Entomology and Acarology, Luiz de Queiroz College of Agriculture, Univ of São Paulo, Piracicaba, São Paulo, Brazil
| | - Wesley Augusto Conde Godoy
- Dept of Entomology and Acarology, Luiz de Queiroz College of Agriculture, Univ of São Paulo, Piracicaba, São Paulo, Brazil.
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Yang P, Wang D, Guo W, Kang L. FAWMine: An integrated database and analysis platform for fall armyworm genomics. INSECT SCIENCE 2021; 28:590-601. [PMID: 33511767 DOI: 10.1111/1744-7917.12903] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/14/2020] [Accepted: 12/31/2020] [Indexed: 06/12/2023]
Abstract
Fall armyworm (Spodoptera frugiperda), a native insect species in the Americas, is rapidly becoming a major agricultural pest worldwide and is causing great damage to corn, rice, soybeans, and other crops. To control this pest, scientists have accumulated a great deal of high-throughput data of fall armyworm, and nine versions of its genomes and transcriptomes have been published. However, easily accessing and performing integrated analysis of these omics data sets is challenging. Here, we developed the Fall Armyworm Genome Database (FAWMine, http://159.226.67.243:8080/fawmine/) to maintain genome sequences, structural and functional annotations, transcriptomes, co-expression, protein interactions, homologs, pathways, and single-nucleotide variations. FAWMine provides a powerful framework that helps users to perform flexible and customized searching, present integrated data sets using diverse visualization methods, output results tables in a range of file formats, analyze candidate gene lists using multiple widgets, and query data available in other InterMine systems. Additionally, stand-alone JBrowse and BLAST services are also established, allowing the users to visualize RNA-Seq data and search genome and annotated gene sequences. Altogether, FAWMine is a useful tool for querying, visualizing, and analyzing compiled data sets rapidly and efficiently. FAWMine will be continually updated to function as a community resource for fall armyworm genomics and pest control research.
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Affiliation(s)
- Pengcheng Yang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Depin Wang
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Wei Guo
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Le Kang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
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Geographic Monitoring of Insecticide Resistance Mutations in Native and Invasive Populations of the Fall Armyworm. INSECTS 2021; 12:insects12050468. [PMID: 34070167 PMCID: PMC8158505 DOI: 10.3390/insects12050468] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 12/18/2022]
Abstract
Simple Summary The moth fall armyworm (Spodoptera frugiperda) is a major agricultural pest insect damaging a wide range of crops, especially corn. Field evolved resistance against Bacillus thuringiensis (Bt) toxins and synthetic insecticides has been repeatedly reported. While the fall armyworm is native to the Americas, its biological invasion was first reported from West Africa in 2016. Since then, this pest has been detected across sub-Saharan and North Africa, Asia, and Oceania. Here, we examine the geographical distribution of mutations causing resistance against Bt or synthetic insecticides to test if the invasion was accompanied by the spread of resistance mutations using 177 individuals collected from 12 geographic populations including North and South America, West and East Africa, India, and China. We observed that Bt resistance mutations generated in Puerto Rico or Brazil were found only from their native populations, while invasive populations had higher copy numbers of cytochrome P450 genes and higher proportions of resistance mutations at AChE, which are known to cause resistance against synthetic insecticides. This result explains the susceptibility to Bt insecticides and the resistance against synthetic insecticides in invasive Chinese populations. This information will be helpful in investigating the cause and consequence associated with insecticide resistance. Abstract Field evolved resistance to insecticides is one of the main challenges in pest control. The fall armyworm (FAW) is a lepidopteran pest species causing severe crop losses, especially corn. While native to the Americas, the presence of FAW was confirmed in West Africa in 2016. Since then, the FAW has been detected in over 70 countries covering sub-Saharan Africa, the Middle East, North Africa, South Asia, Southeast Asia, and Oceania. In this study, we tested whether this invasion was accompanied by the spread of resistance mutations from native to invasive areas. We observed that mutations causing Bt resistance at ABCC2 genes were observed only in native populations where the mutations were initially reported. Invasive populations were found to have higher gene numbers of cytochrome P450 genes than native populations and a higher proportion of multiple resistance mutations at acetylcholinesterase genes, supporting strong selective pressure for resistance against synthetic insecticides. This result explains the susceptibility to Bt insecticides and resistance to various synthetic insecticides in Chinese populations. These results highlight the necessity of regular and standardized monitoring of insecticide resistance in invasive populations using both genomic approaches and bioassay experiments.
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Lazarte JN, Valacco MP, Moreno S, Salerno GL, Berón CM. Molecular characterization of a Bacillus thuringiensis strain from Argentina, toxic against Lepidoptera and Coleoptera, based on its whole-genome and Cry protein analysis. J Invertebr Pathol 2021; 183:107563. [PMID: 33639153 DOI: 10.1016/j.jip.2021.107563] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 02/20/2021] [Accepted: 02/21/2021] [Indexed: 10/22/2022]
Abstract
The insecticidal proteins of Bacillus thuringiensis are used in formulations of spore-crystal complexes and their genes have been incorporated into several crops, providing a model for genetic engineering in agriculture. Despite the variability of the Cry proteins described so far, it is still necessary to look for toxins with a broad spectrum of action, since a significant number of pests are not controlled with the available Cry proteins. It is also important to provide alternatives to address the problem of insect resistance, which has already appeared with the use of formulations and with transgenic plants that express cry genes that code for insecticidal proteins. The FCC 7 strain was characterized by the ultrastructural parasporal body under optical and electronic microscopy, and for the detection of Cry8-type proteins by genomic and proteomic approaches. The identity of the strain and the presence of putative toxin encoding genes, and virulence factors analyzed by Illumina Miseq 1500 platform genomic sequencing, was confirmed. The identity of the two Cry8 proteins that make up the parasporal body was confirmed by MALDI-TOF/TOF. To expand knowledge about the insecticidal activity of this strain, we conducted preliminary tests against the cotton boll weevil, Anthonomus grandis. Here we report the characterization of a novel B. thuringiensis isolate native to Argentina (FCC 7) toxic against A. grandis. The strain shows a rounded parasporal body harboring mainly a protein of about 140 kDa and two different types of Cry8 proteins. Through whole-genome sequencing, we identified the presence of two cry8-like crystal protein genes, one vpa-like and two vpb-like genes, and multiple virulence factors, deepening the knowledge of a strain that had already been described as toxic against some lepidopterans and coleopterans, including Spodoptera frugiperda, Anticarsia gemmatalis, Tenebrio molitor and Diabrotica speciosa.
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Affiliation(s)
- J Nicolás Lazarte
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC) - CONICET and Fundación para Investigaciones Biológicas Aplicadas (FIBA), Vieytes 3103, Mar del Plata, Buenos Aires Province 7600, Argentina
| | - María Pía Valacco
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Facultad de Ciencias Exactas y Naturales, 1428 Ciudad Autónoma de Buenos Aires, Argentina
| | - Silvia Moreno
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Facultad de Ciencias Exactas y Naturales, 1428 Ciudad Autónoma de Buenos Aires, Argentina
| | - Graciela L Salerno
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC) - CONICET and Fundación para Investigaciones Biológicas Aplicadas (FIBA), Vieytes 3103, Mar del Plata, Buenos Aires Province 7600, Argentina
| | - Corina M Berón
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC) - CONICET and Fundación para Investigaciones Biológicas Aplicadas (FIBA), Vieytes 3103, Mar del Plata, Buenos Aires Province 7600, Argentina.
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71
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Chen XI, Mei Y, Chen M, Jing D, He Y, Liu F, He K, Li F. InSexBase: an annotated genomic resource of sex chromosomes and sex-biased genes in insects. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2021:6122465. [PMID: 33507270 PMCID: PMC7904046 DOI: 10.1093/database/baab001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/09/2020] [Accepted: 01/06/2021] [Indexed: 11/13/2022]
Abstract
Sex determination and the regulation of sexual dimorphism are among the most fascinating topics in modern biology. As the most species-rich group of sexually reproducing organisms on Earth, insects have multiple sex determination systems. Though sex chromosomes and sex-biased genes are well-studied in dozens of insects, their gene sequences are scattered in various databases. Moreover, a shortage of annotation hinders the deep mining of these data. Here, we collected the chromosome-level sex chromosome data of 49 insect species, including 34 X chromosomes, 15 Z chromosomes, 5 W chromosomes and 2 Y chromosomes. We also obtained Y-linked contigs of four insects species—Anopheles gambiae, Drosophila innubila, Drosophila yakuba and Tribolium castaneum. The unannotated chromosome-level sex chromosomes were annotated using a standard pipeline, yielding a total of 123 030 protein-coding genes, 2 159 427 repeat sequences, 894 miRNAs, 1574 rRNAs, 5105 tRNAs, 395 snoRNAs (small nucleolar RNA), 54 snRNAs (small nuclear RNA) and 5959 other ncRNAs (non-coding RNA). In addition, 36 781 sex-biased genes were identified by analyzing 62 RNA-seq (RNA sequencing) datasets. Together with 5707 sex-biased genes from the Drosophila genus collected from the Sex-Associated Gene Database, we obtained a total of 42 488 sex-biased genes from 13 insect species. All these data were deposited into InSexBase, a new user-friendly database of insect sex chromosomes and sex-biased genes. Database URL:http://www.insect-genome.com/Sexdb/.
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Affiliation(s)
- X I Chen
- Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China
| | - Yang Mei
- Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China
| | - Mengyao Chen
- Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China
| | - Dong Jing
- Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China
| | - Yumin He
- Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China
| | - Feiling Liu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China
| | - Kang He
- Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China
| | - Fei Li
- Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China
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72
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Shi Y, Li J, Li L, Lin G, Bilal AM, Smagghe G, Liu TX. Genomics, transcriptomics, and peptidomics of Spodoptera frugiperda (Lepidoptera, Noctuidae) neuropeptides. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2021; 106:e21740. [PMID: 33020953 DOI: 10.1002/arch.21740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 08/24/2020] [Accepted: 08/27/2020] [Indexed: 06/11/2023]
Abstract
Neuropeptides control many physiological and behavioral processes, and so they are functionally important classes of cell-to-cell signaling molecules. Nowadays, the fall armyworm, Spodoptera frugiperda, is one of the most destructive agricultural pests in the world. In this study, we mined the publicly accessible genome assembly data for S. frugiperda, and the transcriptomic and proteomic data of the larval central nervous system (CNS) for putative neuropeptide-encoding, and subsequently we used these to anticipate a peptidome for this species. In essence, we could identify 57 orthologs of insect neuropeptides, including Allatotropin, CCHamide, Corazonin, pheromone biosynthesis activating neuropeptide, short neuropeptide F, Trissin, and Natalisin. Interesting features for S. frugiperda were the absence of genes coding for CNMamide, Elevein, and the differential evolution of ancestral neuropeptide genes such as adipokinetic corazonin-related peptide, adipokinetic hormone, Tachykinin, and Natalisin. In conclusion, our study provides the most complete neuropeptide description for the important pest S. frugiperda as a foundation to study the factors regulating insect growth, reproduction, and behavior. Second, we confirm that a comprehensive multi-omics analysis is necessary for the identification of neuropeptides. Finally, our data provide a reliable reference for other comparative studies in other insects beyond the supermodel insect of Drosophila melanogaster and the finding of potential candidates as selective for pests versus beneficial insects.
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Affiliation(s)
- Yan Shi
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - JiangJie Li
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - LinYu Li
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - GanLin Lin
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Amir M Bilal
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Guy Smagghe
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Tong-Xian Liu
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
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73
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Cao LJ, Song W, Yue L, Guo SK, Chen JC, Gong YJ, Hoffmann AA, Wei SJ. Chromosome-level genome of the peach fruit moth Carposina sasakii (Lepidoptera: Carposinidae) provides a resource for evolutionary studies on moths. Mol Ecol Resour 2020; 21:834-848. [PMID: 33098233 DOI: 10.1111/1755-0998.13288] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/05/2020] [Accepted: 10/16/2020] [Indexed: 01/22/2023]
Abstract
The peach fruit moth (PFM), Carposina sasakii Matsumura, is a major phytophagous orchard pest widely distributed across Northeast Asia. Here, we report the chromosome-level genome for the PFM, representing the first genome for the family Carposinidae, from the lepidopteran superfamily Copromorphoidea. The genome was assembled into 404.83 Mb sequences using PacBio long-read and Illumina short-read sequences, including 275 contigs, with a contig N50 length of 2.62 Mb. All contigs were assembled into 31 linkage groups assisted by the Hi-C technique, including 30 autosomes and a Z chromosome. BUSCO analysis showed that 98.3% of genes were complete and 0.4% of genes were fragmented, while 1.3% of genes were missing in the assembled genome. In total, 21,697 protein-coding genes were predicted, of which 84.80% were functionally annotated. Because of the importance of diapause triggered by photoperiod in PFM, five circadian genes in the PFM as well as in the other related species were annotated, and potential genes related to diapause and photoperiodic reaction were also identified from transcriptome sequencing. In addition, manual annotation of detoxification gene families was undertaken and showed a higher number of glutathione S-transferase (GST) gene in PFM than in most other lepidopterans, in contrast to a lower number of uridine diphosphate (UDP)-glycosyltransferase (UGT) gene, carboxyl/cholinesterases (CCE) gene and cytochrome P450 monooxygenase (P450) gene, suggesting different detoxication pathways in this moth. The high-quality genome provides a resource for comparative evolutionary studies of this moth and its relatives within the context of radiations across Lepidoptera.
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Affiliation(s)
- Li-Jun Cao
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Wei Song
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Lei Yue
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Shao-Kun Guo
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jin-Cui Chen
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ya-Jun Gong
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ary Anthony Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Vic, Australia
| | - Shu-Jun Wei
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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74
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Zhao X, Xu H, He K, Shi Z, Chen X, Ye X, Mei Y, Yang Y, Li M, Gao L, Xu L, Xiao H, Liu Y, Lu Z, Li F. A chromosome-level genome assembly of rice leaffolder, Cnaphalocrocis medinalis. Mol Ecol Resour 2020; 21:561-572. [PMID: 33051980 DOI: 10.1111/1755-0998.13274] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/21/2020] [Accepted: 10/01/2020] [Indexed: 12/01/2022]
Abstract
The rice leaffolder, Cnaphalocrocis medinalis Guenée (Crambidae, Lepidoptera), is an important agricultural pest that causes serious losses to rice production in rice-growing regions with high humidity and temperature. However, a lack of genomic resources limits in-depth understanding of its biological characteristics and ecological adaptation. Here, we sequenced the genome of rice leaffolder using the Illumina and PacBio platforms, yielding a genome assembly of 528.3 Mb with a contig N50 of 524.6 kb. A high percentage (96.4%) of Benchmarking Universal Single-Copy Orthologs (BUSCOs) were successfully detected, suggesting high-level completeness of the genome assembly. In total, 39.5% of the genome consists of repeat sequences and 15,045 protein-coding genes were annotated. Comparative phylogenomic analysis showed that some gene families associated with hormone biosynthesis expanded in rice leaffolder. Next, we used the Hi-C technique to produce a chromosome-level genome assembly with a scaffold N50 of 16.1 Mb by anchoring 3,248 scaffolds to 31 chromosomes. The rice leaffolder genome showed high chromosomal synteny with the genome of four other lepidopteran insects. By comparing coverage ratios from the genome resequencing of male and female pupae, we identified near intact Z and W chromosomes. The W chromosome is estimated as 20.75 Mb, which is the most complete known W chromosome in Lepidoptera. The protein-coding genes on the W chromosome were significantly enriched in metabolic pathways. In all, the high-quality genome assembly and the near-intact W chromosome of rice leaffolder should be a useful resource for the fields of insect migration, chromosome evolution and pest control.
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Affiliation(s)
- Xianxin Zhao
- 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, China
| | - Hongxing Xu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agroproducts, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Kang He
- 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, China
| | - Zhenmin Shi
- 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, China
| | - Xi Chen
- 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, China
| | - Xinhai Ye
- 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, China
| | - Yang Mei
- 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, China
| | - Yajun Yang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agroproducts, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Meizhen Li
- 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, China
| | - Libin Gao
- 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, China
| | - Le Xu
- 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, China
| | - Huamei Xiao
- 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, China.,College of Life Sciences and Resource Environment, Key Laboratory of Crop Growth and Development Regulation of Jiangxi Province, Yichun University, Yichun, China
| | - Ying Liu
- Agriculture Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Zhongxian Lu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agroproducts, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Fei Li
- 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, China
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75
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Gui F, Lan T, Zhao Y, Guo W, Dong Y, Fang D, Liu H, Li H, Wang H, Hao R, Cheng X, Li Y, Yang P, Sahu SK, Chen Y, Cheng L, He S, Liu P, Fan G, Lu H, Hu G, Dong W, Chen B, Jiang Y, Zhang Y, Xu H, Lin F, Slippers B, Postma A, Jackson M, Abate BA, Tesfaye K, Demie AL, Bayeleygne MD, Degefu DT, Chen F, Kuria PK, Kinyua ZM, Liu TX, Yang H, Huang F, Liu X, Sheng J, Kang L. Genomic and transcriptomic analysis unveils population evolution and development of pesticide resistance in fall armyworm Spodoptera frugiperda. Protein Cell 2020; 13:513-531. [PMID: 33108584 PMCID: PMC9226219 DOI: 10.1007/s13238-020-00795-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 09/15/2020] [Indexed: 11/24/2022] Open
Abstract
The fall armyworm (FAW), Spodoptera frugiperda, is a destructive pest native to America and has recently become an invasive insect pest in China. Because of its rapid spread and great risks in China, understanding of FAW genetic background and pesticide resistance is urgent and essential to develop effective management strategies. Here, we assembled a chromosome-level genome of a male FAW (SFynMstLFR) and compared re-sequencing results of the populations from America, Africa, and China. Strain identification of 163 individuals collected from America, Africa and China showed that both C and R strains were found in the American populations, while only C strain was found in the Chinese and African populations. Moreover, population genomics analysis showed that populations from Africa and China have close relationship with significantly genetic differentiation from American populations. Taken together, FAWs invaded into China were most likely originated from Africa. Comparative genomics analysis displayed that the cytochrome p450 gene family is extremely expanded to 425 members in FAW, of which 283 genes are specific to FAW. Treatments of Chinese populations with twenty-three pesticides showed the variant patterns of transcriptome profiles, and several detoxification genes such as AOX, UGT and GST specially responded to the pesticides. These findings will be useful in developing effective strategies for management of FAW in China and other invaded areas.
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Affiliation(s)
- Furong Gui
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China.,Yunnan Plateau Characteristic Agriculture Industry Research Institute, Kunming, 650201, China
| | - Tianming Lan
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Yue Zhao
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
| | - Wei Guo
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Yang Dong
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China.,Yunnan Plateau Characteristic Agriculture Industry Research Institute, Kunming, 650201, China
| | - Dongming Fang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Haimeng Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Hongli Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Ruoshi Hao
- Yunnan Plateau Characteristic Agriculture Industry Research Institute, Kunming, 650201, China
| | | | - Yahong Li
- Yunnan Plant Protection and Quarantine Station, Kunming, 650034, China
| | - Pengcheng Yang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yaping Chen
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
| | - Le Cheng
- BGI-Yunnan, No. 389 Haiyuan Road, High-tech Development Zone, Kunming, 650106, China
| | - Shuqi He
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
| | - Ping Liu
- MGI, BGI-Shenzhen, Shenzhen, 518083, China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Haorong Lu
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen, 518120, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, China
| | - Guohai Hu
- China National GeneBank, Jinsha Road, Dapeng New District, Shenzhen, 518120, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, China
| | - Wei Dong
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Bin Chen
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
| | - Yuan Jiang
- BGI-Americas, One Broadway, 14th Floor, Cambridge, MA, 02142, USA
| | - Yongwei Zhang
- BGI-Americas, One Broadway, 14th Floor, Cambridge, MA, 02142, USA
| | - Hanhong Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Fei Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Bernard Slippers
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Alisa Postma
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Matthew Jackson
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | | | - Kassahun Tesfaye
- Ethiopian Biotechnology Institute, Addis Ababa, Ethiopia.,College of Natural Science, Addis Ababa University, Addis Ababa, Ethiopia
| | | | | | - Dawit Tesfaye Degefu
- Melkassa Agricultural Research Center, Ethiopian Institute of Agricultural Research, Melkassa, Addis Ababa, Ethiopia
| | - Feng Chen
- MGI, BGI-Shenzhen, Shenzhen, 518083, China
| | - Paul K Kuria
- Kenya Agricultural and Livestock Research Organization, P.O. Box 57811, Nairobi, 00800, Kenya
| | - Zachary M Kinyua
- Kenya Agricultural and Livestock Research Organization, P.O. Box 57811, Nairobi, 00800, Kenya
| | - Tong-Xian Liu
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Huanming Yang
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, China.,Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen, 518120, China
| | - Fangneng Huang
- Department of Entomology, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA.
| | - Xin Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China. .,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, China.
| | - Jun Sheng
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China. .,Yunnan Plateau Characteristic Agriculture Industry Research Institute, Kunming, 650201, China.
| | - Le Kang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China. .,Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China. .,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100101, China.
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76
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Deng Z, Zhang Y, Zhang M, Huang J, Li C, Ni X, Li X. Characterization of the First W-Specific Protein-Coding Gene for Sex Identification in Helicoverpa armigera. Front Genet 2020; 11:649. [PMID: 32636875 PMCID: PMC7317607 DOI: 10.3389/fgene.2020.00649] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 05/28/2020] [Indexed: 12/11/2022] Open
Abstract
Helicoverpa armigera is a globally-important crop pest with a WZ (female)/ZZ (male) sex chromosome system. The absence of discernible sexual dimorphism in its egg and larval stages makes it impossible to address any sex-related theoretical and applied questions before pupation unless a W-specific sequence marker is available for sex diagnosis. To this end, we used one pair of morphologically pre-sexed pupae to PCR-screen 17 non-transposon transcripts selected from 4855 W-linked candidate reads identified by mapping a publicly available egg transcriptome of both sexes to the male genome of this species and detected the read SRR1015458.67499 only in the female pupa. Subsequent PCR screenings of this read and the previously reported female-specific RAPD (random amplified polymorphic DNA) marker AF18 with ten more pairs of pre-sexed pupae and different annealing positions and/or temperatures as well as its co-occurrence with the female-specific transcript splicing isoforms of doublesex gene of H. armigera (Hadsx) and amplification and sequencing of their 5′ unknown flanking sequences in three additional pairs of pre-sexed pupae verified that SRR1015458.67499 is a single copy protein-coding gene unique to W chromosome (named GUW1) while AF18 is a multicopy MITE transposon located on various chromosomes. Test application of GUW1 as a marker to sex 30 neonates of H. armigera yielded a female/male ratio of 1.14: 1.00. Both GUW1 and Hadsx splicing isoforms assays revealed that the H. armigera embryo cell line QB-Ha-E-1 is a male cell line. Taken together, GUW1 is not only a reliable DNA marker for sexing all stages of H. armigera and its cell lines, but also represents the first W-specific protein-coding gene in lepidopterans.
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Affiliation(s)
- Zhongyuan Deng
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China.,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yakun Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Min Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Jinyong Huang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Changyou Li
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Xinzhi Ni
- Agricultural Research Service, U.S. Department of Agriculture, Crop Genetics and Breeding Research Unit, University of Georgia - Tifton Campus, Tifton, GA, United States
| | - Xianchun Li
- Department of Entomology and BIO5 Institute, University of Arizona, Tucson, AZ, United States
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