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Xiao Y, Li W, Yang X, Xu P, Jin M, Yuan H, Zheng W, Soberón M, Bravo A, Wilson K, Wu K. Rapid spread of a densovirus in a major crop pest following wide-scale adoption of Bt-cotton in China. eLife 2021; 10:e66913. [PMID: 34263726 PMCID: PMC8324301 DOI: 10.7554/elife.66913] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 07/13/2021] [Indexed: 12/21/2022] Open
Abstract
Bacillus thuringiensis (Bt) crops have been widely planted and the effects of Bt-crops on populations of the target and non-target insect pests have been well studied. However, the effects of Bt-crops exposure on microorganisms that interact with crop pests have not previously been quantified. Here, we use laboratory and field data to show that infection of Helicoverpa armigera with a densovirus (HaDV2) is associated with its enhanced growth and tolerance to Bt-cotton. Moreover, field monitoring showed a much higher incidence of cotton bollworm infection with HaDV2 in regions cultivated with Bt-cotton than in regions without it, with the rate of densovirus infection increasing with increasing use of Bt-cotton. RNA-seq suggested tolerance to both baculovirus and Cry1Ac were enhanced via the immune-related pathways. These findings suggest that exposure to Bt-crops has selected for beneficial interactions between the target pest and a mutualistic microorganism that enhances its performance on Bt-crops under field conditions.
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Affiliation(s)
- Yutao Xiao
- The State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
| | - Wenjing Li
- The State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
- Institute of Plant Protection and Soil Fertility, Hubei Academy of Agricultural SciencesWuhanChina
| | - Xianming Yang
- The State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | - Pengjun Xu
- Tobacco Research Institute, Chinese Academy of Agricultural SciencesQingdaoChina
- Lancaster Environment Centre, Lancaster UniversityLancasterUnited Kingdom
| | - Minghui Jin
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
| | - He Yuan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
| | - Weigang Zheng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
| | - Mario Soberón
- Instituto de Biotecnología, Universidad Nacional Autónoma de MéxicoMorelosUnited States
| | - Alejandra Bravo
- Instituto de Biotecnología, Universidad Nacional Autónoma de MéxicoMorelosUnited States
| | - Kenneth Wilson
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
- Lancaster Environment Centre, Lancaster UniversityLancasterUnited Kingdom
| | - Kongming Wu
- The State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
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Liu Y, Ren G, Jiang L, Feng C, Liu D, Liu Y, Xu P. Sequencing and phylogenetic characterization of a novel RNA virus genome from Harmonia axyridis. Mol Biol Rep 2020; 47:4015-4019. [PMID: 32285328 DOI: 10.1007/s11033-020-05418-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 04/03/2020] [Indexed: 11/27/2022]
Abstract
As a natural predator of many insect pests on its native Asian range, Harmonia axyridis remains amongst the insects whose pathogenic or beneficial microorganisms are yet to be studied. The genome nucleotide (nt) and amino acid sequences of open reading frames (ORFs) of the novel RNA virus were identified. Neighbor-joining (NJ) were constructed using MEGA7 software packages with nt sequences and conserved amino acid sequences of predicted RNA-dependent RNA polymerase (RdRp).The complete genome of a novel virus named Harmonia axyridis virus 1 was determined by RNA-seq and rapid amplification of cDNA ends from H. axyridis, which had a single-stranded RNA genome of 8868 nts in length and contains two putative ORFs. ORF1 encodes a polypeptide of 2182 amino acids, which contained conserved domains for 2 picornavirus-like capsid proteins and one RNA helicase. ORF2 encodes a polypeptide of 655 amino acids, which contained 1 RdRp domain. Phylogenetic analysis of whole genome nt sequences and RdRp deduced amino acid sequences suggested that the virus clustered with several unclassified Hubei picorna-like virus. To our knowledge, this is the first full annotated genome of a novel member of the unclassified group of RNA viruses, infecting H. axyridis in natural field conditions.
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Affiliation(s)
- Yingjie Liu
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Guangwei Ren
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Lianqiang Jiang
- Liangshan Branch of Sichuan Provincial Tobacco Company, Technical Center, Xichang, 615000, China
| | - Changchun Feng
- Liangshan Branch of Sichuan Provincial Tobacco Company, Technical Center, Xichang, 615000, China
| | - Dongyang Liu
- Liangshan Branch of Sichuan Provincial Tobacco Company, Technical Center, Xichang, 615000, China
| | - Yongjie Liu
- College of Plant Protection, Shandong Agricultural University, Taian, 271018, China.
| | - Pengjun Xu
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
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Nigg JC, Falk BW. Diaphorina citri densovirus is a persistently infecting virus with a hybrid genome organization and unique transcription strategy. J Gen Virol 2019; 101:226-239. [PMID: 31855134 DOI: 10.1099/jgv.0.001371] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Diaphorina citri densovirus (DcDV) is an ambisense densovirus with a 5071 nt genome. Phylogenetic analysis places DcDV in an intermediate position between those in the Ambidensovirus and Iteradensovirus genera, a finding that is consistent with the observation that DcDV possesses an Iteradensoviris-like non-structural (NS) protein-gene cassette, but a capsid-protein (VP) gene cassette resembling those of other ambisense densoviruses. DcDV is maternally transmitted to 100 % of the progeny of infected female Diaphorina citri, and the progeny of infected females carry DcDV as a persistent infection without outward phenotypic effects. We were unable to infect naïve individuals by oral inoculation, however low levels of transient viral replication are detected following intrathoracic injection of DcDV virions into uninfected D. citri insects. Transcript mapping indicates that DcDV produces one transcript each from the NS and VP gene cassettes and that these transcripts are polyadenylated at internal sites to produce a ~2.2 kb transcript encoding the NS proteins and a ~2.4 kb transcript encoding the VP proteins. Additionally, we found that transcriptional readthrough leads to the production of longer non-canonical transcripts from both genomic strands.
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Affiliation(s)
- Jared C Nigg
- Department of Plant Pathology, University of California, Davis, CA, USA
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Gypsy moth genome provides insights into flight capability and virus-host interactions. Proc Natl Acad Sci U S A 2019; 116:1669-1678. [PMID: 30642971 DOI: 10.1073/pnas.1818283116] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Since its accidental introduction to Massachusetts in the late 1800s, the European gypsy moth (EGM; Lymantria dispar dispar) has become a major defoliator in North American forests. However, in part because females are flightless, the spread of the EGM across the United States and Canada has been relatively slow over the past 150 years. In contrast, females of the Asian gypsy moth (AGM; Lymantria dispar asiatica) subspecies have fully developed wings and can fly, thereby posing a serious economic threat if populations are established in North America. To explore the genetic determinants of these phenotypic differences, we sequenced and annotated a draft genome of L. dispar and used it to identify genetic variation between EGM and AGM populations. The 865-Mb gypsy moth genome is the largest Lepidoptera genome sequenced to date and encodes ∼13,300 proteins. Gene ontology analyses of EGM and AGM samples revealed divergence between these populations in genes enriched for several gene ontology categories related to muscle adaptation, chemosensory communication, detoxification of food plant foliage, and immunity. These genetic differences likely contribute to variations in flight ability, chemical sensing, and pathogen interactions among EGM and AGM populations. Finally, we use our new genomic and transcriptomic tools to provide insights into genome-wide gene-expression changes of the gypsy moth after viral infection. Characterizing the immunological response of gypsy moths to virus infection may aid in the improvement of virus-based bioinsecticides currently used to control larval populations.
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Dong Y, Chao J, Liu J, Rice A, Holdbrook R, Liu Y, Xu P. Characterization of a novel RNA virus from Nesidiocoris tenuis related to members of the genus Iflavirus. Arch Virol 2017; 163:571-574. [PMID: 29101538 DOI: 10.1007/s00705-017-3622-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 09/26/2017] [Indexed: 01/10/2023]
Abstract
The complete genome of a novel virus from Nesidiocoris tenuis was determined by RNA-seq and rapid amplification of cDNA ends. This virus has a single-stranded RNA genome of 10633 nucleotides (nt) in length, not including the poly(A) tail, and contains two putative open reading frames (ORFs). ORF1 encodes a polypeptide of 1320 amino acids (aa) with a predicted molecular mass of 147.92 kDa and theoretical isoelectric point (pI) of 6.96. ORF2 encodes a polypeptide of 1728 aa with a predicted molecular mass of 197.09 kDa and pI of 6.73. Phylogenetic analysis with the deduced aa sequences of the conserved RNA dependent RNA polymerase domain as well as whole genome nt sequences indicated that the virus clusters with viruses classified within the genus Iflavirus, with a high bootstrap value in the maximum-likelihood and neighbor-joining trees. However, this virus has a distinct genome structure with two ORFs, iflaviruses normally having one, suggesting the virus might be a prototype of a new genus. We named the virus isolate Nesidiocoris tenuis virus 1 (NtV-1). The prevalence of NtV-1 infection in wild samples of N. tenuis was at a low level (7.32%, 6 positive in 82 samples), suggesting a possible harmful effect to its host.
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Affiliation(s)
- Yonghao Dong
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, P.R. China.,College of Plant Protection, Shandong Agricultural University, Taian, P.R. China
| | - Jiangtao Chao
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, P.R. China
| | - Jinyan Liu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, P.R. China
| | - Annabel Rice
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Robert Holdbrook
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Yongjie Liu
- College of Plant Protection, Shandong Agricultural University, Taian, P.R. China
| | - Pengjun Xu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, P.R. China. .,Lancaster Environment Centre, Lancaster University, Lancaster, UK.
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