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Nian X, Wu S, He J, Holford P, Beattie GAC, Wang D, Cen Y, He Y, Zhang S. The conserved role of miR-2 and novel miR-109 in the increase in fecundity of Diaphorina citri induced by symbiotic bacteria and pathogenic fungi. mBio 2024:e0154124. [PMID: 39373536 DOI: 10.1128/mbio.01541-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 08/15/2024] [Indexed: 10/08/2024] Open
Abstract
Infection with pathogens can increase the fecundity and other fitness-related traits of insect vectors for their own advantage. Our previous research has reported the pivotal role of DcKr-h1 in the fecundity improvement of Diaphorina citri induced by the bacterium, "Candidatus Liberibacter asiaticus" (CLas), and the fungus, Cordyceps fumosorosea (Cf). However, the posttranscriptional regulation of this process remains poorly understood. Given the significance of miRNAs in gene regulation, we delved into their roles in shaping phenotypes and their underlying molecular mechanisms. Our results indicated that two miRNAs, miR-2 and novel-miR-109, jointly inhibited DcKr-h1 expression by binding to its 3' untranslated region (UTR). In the D. citri-CLas interaction, the expression levels of miR-2 and novel-miR-109 in the ovaries of CLas-positive psyllids were lower compared to CLas-negative individuals. Overexpression of miR-2 or novel-miR-109 significantly decreased fecundity and CLas titer in ovaries and caused reproductive defects reminiscent of DcKr-h1 knockdown. Similarly, in the D. citri-Cf interaction, the levels of miR-2 and novel-miR-109 markedly decreased in the ovaries. Upregulation of miR-2 or novel-miR-109 also resulted in reduced fecundity and ovary defects similar to those caused by DcKr-h1 silencing. Moreover, feeding antagomir-2 or antagomir-109 partially rescued the defective phenotypes caused by DcKr-h1 silencing in both model systems, and miR-2 and novel-miR-109 were repressed by juvenile hormone (JH) and regulated the genes associated with egg development. This study shows a conserved regulatory mechanism, whereby JH suppresses the expression of miR-2 and novel-miR-109 which, together with JH-induced transcription of DcKr-h1, increases female fecundity induced by both symbiotic bacteria and pathogenic fungi. IMPORTANCE Infection with pathogens can increase the fecundity and other fitness-related traits of insect vectors for their own advantage. Our previous research has reported that DcKr-h1 plays a critical role in the increase in fecundity of Diaphorina citri induced by the bacterium, "Candidatus Liberibacter asiaticus" (CLas) and the fungus, Cordyceps fumosorosea (Cf). However, the posttranscriptional regulation of this process remains poorly understood. Given the significance of miRNAs in gene regulation, we delved into their roles in shaping phenotypes and their underlying molecular mechanisms. Our results indicated that two miRNAs, miR-2 and novel-miR-109, jointly inhibited DcKr-h1 expression by binding to its 3' untranslated region (UTR). In both D. citri-CLas and D. citri-Cf interactions, the increased juvenile hormone (JH) titer and reduced abundance of miR-2 and novel-miR-109 ensure high levels of DcKr-h1 expression, consequently stimulating ovarian development and enhancing fecundity. These observations provide evidence that miR-2 and miR-109 are crucial players in the JH-dependent increase in fecundity in psyllids induced by infection with different pathogens.
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Affiliation(s)
- Xiaoge Nian
- National Key Laboratory of Green Pesticide, Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou, China
- School of Biology and Agriculture, Shaoguan University, Shaoguan, China
| | - Shujie Wu
- National Key Laboratory of Green Pesticide, Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Jielan He
- National Key Laboratory of Green Pesticide, Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Paul Holford
- School of Science, Western Sydney University, Penrith, Australia
| | | | - Desen Wang
- National Key Laboratory of Green Pesticide, Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Yijing Cen
- National Key Laboratory of Green Pesticide, Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Yurong He
- National Key Laboratory of Green Pesticide, Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Songdou Zhang
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
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Mbewe W, Mukasa S, Ochwo-Ssemakula M, Sseruwagi P, Tairo F, Ndunguru J, Duffy S. Cassava brown streak virus evolves with a nucleotide-substitution rate that is typical for the family Potyviridae. Virus Res 2024; 346:199397. [PMID: 38750679 PMCID: PMC11145536 DOI: 10.1016/j.virusres.2024.199397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 05/08/2024] [Accepted: 05/12/2024] [Indexed: 05/25/2024]
Abstract
The ipomoviruses (family Potyviridae) that cause cassava brown streak disease (cassava brown streak virus [CBSV] and Uganda cassava brown streak virus [UCBSV]) are damaging plant pathogens that affect the sustainability of cassava production in East and Central Africa. However, little is known about the rate at which the viruses evolve and when they emerged in Africa - which inform how easily these viruses can host shift and resist RNAi approaches for control. We present here the rates of evolution determined from the coat protein gene (CP) of CBSV (Temporal signal in a UCBSV dataset was not sufficient for comparable analysis). Our BEAST analysis estimated the CBSV CP evolves at a mean rate of 1.43 × 10-3 nucleotide substitutions per site per year, with the most recent common ancestor of sampled CBSV isolates existing in 1944 (95% HPD, between years 1922 - 1963). We compared the published measured and estimated rates of evolution of CPs from ten families of plant viruses and showed that CBSV is an average-evolving potyvirid, but that members of Potyviridae evolve more quickly than members of Virgaviridae and the single representatives of Betaflexiviridae, Bunyaviridae, Caulimoviridae and Closteroviridae.
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Affiliation(s)
- Willard Mbewe
- Department of Biological Sciences, Malawi University of Science and Technology, P. O. Box 5196, Limbe, Malawi.
| | - Settumba Mukasa
- School of Agriculture and Environmental Science, Department of Agricultural Production, P. O. Box 7062, Makerere University, Kampala, Uganda
| | - Mildred Ochwo-Ssemakula
- School of Agriculture and Environmental Science, Department of Agricultural Production, P. O. Box 7062, Makerere University, Kampala, Uganda
| | - Peter Sseruwagi
- Mikocheni Agricultural Research Institute, P.O. Box 6226, Dar es Slaam, Tanzania
| | - Fred Tairo
- Mikocheni Agricultural Research Institute, P.O. Box 6226, Dar es Slaam, Tanzania
| | - Joseph Ndunguru
- Mikocheni Agricultural Research Institute, P.O. Box 6226, Dar es Slaam, Tanzania
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ 08901, United States.
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Nian X, Luo Y, He X, Wu S, Li J, Wang D, Holford P, Beattie GAC, Cen Y, Zhang S, He Y. Infection with 'Candidatus Liberibacter asiaticus' improves the fecundity of Diaphorina citri aiding its proliferation: A win-win strategy. Mol Ecol 2024; 33:e17214. [PMID: 38018658 DOI: 10.1111/mec.17214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 10/21/2023] [Accepted: 10/30/2023] [Indexed: 11/30/2023]
Abstract
The evolution of insect vector-pathogen relationships has long been of interest in the field of molecular ecology. One system of special relevance, due to its economic impacts, is that between Diaphorina citri and 'Candidatus Liberibacter asiaticus' (CLas), the cause of the severe Asian form of huanglongbing. CLas-positive D. citri are more fecund than their CLas-negative counterparts, boosting opportunities for pathogens to acquire new vector hosts. The molecular mechanism behind this life-history shift remains unclear. Here, we found that CLas promoted ovarian development and increased the expression of the vitellogenin receptor (DcVgR) in ovaries. DcVgR RNAi significantly decreased fecundity and CLas titer in ovaries, extended the preoviposition period, shortened the oviposition period and blocked ovarian development. Given their importance in gene regulation, we explored the role of miRNAs in shaping these phenotypes and their molecular triggers. Our results showed that one miRNA, miR-275, suppressed DcVgR expression by binding to its 3' UTR. Overexpression of miR-275 knocked down DcVgR expression and CLas titer in ovaries, causing reproductive defects that mimicked DcVgR knockdown phenotypes. We focused, further, on roles of the Juvenile Hormone (JH) pathway in shaping the observed fecundity phenotype, given its known impacts on ovarian development. After CLas infection, this pathway was upregulated, thereby increasing DcVgR expression. From these combined results, we conclude that CLas hijacks the JH signalling pathway and miR-275, thereby targeting DcVgR to increase D. citri fecundity. These changes simultaneously increase CLas replication, suggesting a pathogen-vector host mutualism, or a seemingly helpful, but cryptically costly life-history manipulation.
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Affiliation(s)
- Xiaoge Nian
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou, China
- Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan, China
| | - Yaru Luo
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Xinyu He
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Shujie Wu
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Jiayun Li
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Desen Wang
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Paul Holford
- School of Science, Western Sydney University, Penrith, New South Wales, Australia
| | | | - Yijing Cen
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Songdou Zhang
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Yurong He
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou, China
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Wang K, Fu S, Wu L, Wu J, Wang Y, Xu Y, Zhou X. Rice stripe virus nonstructural protein 3 suppresses plant defence responses mediated by the MEL-SHMT1 module. MOLECULAR PLANT PATHOLOGY 2023; 24:1359-1369. [PMID: 37404045 PMCID: PMC10576177 DOI: 10.1111/mpp.13373] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/15/2023] [Accepted: 06/19/2023] [Indexed: 07/06/2023]
Abstract
Our previous study identified an evolutionarily conserved C4HC3-type E3 ligase, named microtubule-associated E3 ligase (MEL), that regulates broad-spectrum plant resistance against viral, fungal and bacterial pathogens in multiple plant species by mediating serine hydroxymethyltransferase (SHMT1) degradation via the 26S proteasome pathway. In the present study, we found that NS3 protein encoded by rice stripe virus could competitively bind to the MEL substrate recognition site, thereby inhibiting MEL interacting with and ubiquitinating SHMT1. This, in turn, leads to the accumulation of SHMT1 and the repression of downstream plant defence responses, including reactive oxygen species accumulation, mitogen-activated protein kinase pathway activation, and the up-regulation of disease-related gene expression. Our findings shed light on the ongoing arms race between pathogens and demonstrate how a plant virus can counteract the plant defence response.
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Affiliation(s)
- Kun Wang
- State Key Laboratory of Rice Biology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Shuai Fu
- State Key Laboratory of Rice Biology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | - Liang Wu
- State Key Laboratory of Rice Biology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Jianxiang Wu
- State Key Laboratory of Rice Biology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Yaqin Wang
- State Key Laboratory of Rice Biology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Yi Xu
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
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5
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Li S, Guo W, Wang C, Tang Y, Li L, Zhang H, Li Y, Wei Z, Chen J, Sun Z. Alternative splicing impacts the rice stripe virus response transcriptome. Virology 2023; 587:109870. [PMID: 37669612 DOI: 10.1016/j.virol.2023.109870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/12/2023] [Accepted: 08/16/2023] [Indexed: 09/07/2023]
Abstract
Alternative splicing (AS) is an important form of post transcriptional modification present in both animals and plants. However, little information was obtained about AS events in response to plant virus infection. In this study, we conducted a genome-wide transcriptome analysis on AS change in rice infected by a devastating virus, Rice stripe virus (RSV). KEGG analysis was performed on the differentially expressed (DE) genes and differentially alternative spliced (DAS) genes. The results showed that DE genes were significantly enriched in the pathway of interaction with plant pathogens. The DAS genes were mainly enriched in basal metabolism and RNA splicing pathways. The heat map clustering showed that DEGs clusters were mainly enriched in regulation of transcription and defense response while differential transcript usage (DTU) clusters were strongly enriched in mRNA splicing and calcium binding. Overall, our results provide a fundamental basis for gene-wide AS changes in rice after RSV infection.
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Affiliation(s)
- Shanshan Li
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Wenbin Guo
- Information and Computational Sciences, James Hutton Institute, Dundee, DD2 5DA, Scotland, UK
| | - Chen Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Yao Tang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Lulu Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Hehong Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Yanjun Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Zhongyan Wei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Jianping Chen
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
| | - Zongtao Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
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6
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Lu C, Miu Q, Jin D, Li A, Cheng Z, Zhou Y, Wang Y, Li S. Genetic variability of rice stripe virus after its pandemic in Jiangsu. Mol Biol Rep 2023; 50:7263-7274. [PMID: 37422539 DOI: 10.1007/s11033-023-08652-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 06/28/2023] [Indexed: 07/10/2023]
Abstract
BACKGROUND Rice stripe virus (RSV) caused a serious disease pandemic in rice in East China between 2001 and 2010. The continuous integrated managements reduced virus epidemic year by year until it was non-epidemic. As an RNA virus, its genetic variability after undergoing a long-term non-epidemic period was meaningful to study. While in 2019, the sudden occurrence of RSV in Jiangsu provided an opportunity for the study. METHODS AND RESULTS The complete genome of JY2019, an RSV isolate from Jiangyan, was determined. A genotype profile of 22 isolates from China, Japan and Korea indicated that the isolates from Yunnan formed the subtype II, and other isolates clustered the subtype I. RNA 1-3 of JY2019 isolate well-clustered in the subtype I clade, and RNA 4 was also in subtype I, but it had a slight separation from other intra-group isolates. After phylogenetic analyses, it was considered NSvc4 gene contributed to the tendency, because it exhibited an obvious trend towards the subtype II (Yunnan) group. High sequence identity (100%) of NSvc4 between JY2019 and barnyardgrass isolate from different regions demonstrated genetic variation of NSvc4 was consistent in RSV natural populations in Jiangsu in the non-epidemic period. In the phylogenetic tree of all 74 NSvc4 genes, JY2019 belonged to a minor subtype Ib, suggesting the subtype Ib isolates might have existed in natural populations before the non-epidemic period, but not a dominant population. CONCLUSIONS Our results suggested that NSvc4 gene was susceptible to selection pressure, and the subtype Ib might be more adaptable for the interaction between RSV and hosts in the non-epidemic ecological conditions.
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Affiliation(s)
- Chengye Lu
- Institute of Plant Protection, Jiangsu Key Laboratory for Food Quality and Safety, State Key Laboratory Cultivation Base, Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Ministry of Education Key Laboratory of Agriculture Biodiversity for Plant Disease Management, Yunnan Agricultural University, Kunming, 650201, China
| | - Qian Miu
- Institute of Plant Protection, Jiangsu Key Laboratory for Food Quality and Safety, State Key Laboratory Cultivation Base, Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Daoran Jin
- Institute of Plant Protection, Jiangsu Key Laboratory for Food Quality and Safety, State Key Laboratory Cultivation Base, Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Aiguo Li
- Plant Protection and Quarantine Station, Agricultural Technology Extension Center of Jiangyan, Taizhou, 225500, China
| | - Zhaobang Cheng
- Institute of Plant Protection, Jiangsu Key Laboratory for Food Quality and Safety, State Key Laboratory Cultivation Base, Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Yijun Zhou
- Institute of Plant Protection, Jiangsu Key Laboratory for Food Quality and Safety, State Key Laboratory Cultivation Base, Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Yunyue Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Ministry of Education Key Laboratory of Agriculture Biodiversity for Plant Disease Management, Yunnan Agricultural University, Kunming, 650201, China
| | - Shuo Li
- Institute of Plant Protection, Jiangsu Key Laboratory for Food Quality and Safety, State Key Laboratory Cultivation Base, Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
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7
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Wang L, Zhao H, Wang Z, Ding S, Qin L, Jiang R, Deng X, He Z, Li L. An Evolutionary Perspective of Codon Usage Pattern, Dinucleotide Composition and Codon Pair Bias in Prunus Necrotic Ringspot Virus. Genes (Basel) 2023; 14:1712. [PMID: 37761852 PMCID: PMC10530913 DOI: 10.3390/genes14091712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Prunus necrotic ringspot virus (PNRSV) is a significant virus of ornamental plants and fruit trees. It is essential to study this virus due to its impact on the horticultural industry. Several studies on PNRSV diversity and phytosanitary detection technology were reported, but the content on the codon usage bias (CUB), dinucleotide preference and codon pair bias (CPB) of PNRSV is still uncertain. We performed comprehensive analyses on a dataset consisting of 359 coat protein (CP) gene sequences in PNRSV to examine the characteristics of CUB, dinucleotide composition, and CPB. The CUB analysis of PNRSV CP sequences showed that it was not only affected by natural selection, but also affected by mutations, and natural selection played a more significant role compared to mutations as the driving force. The dinucleotide composition analysis showed an over-expression of the CpC/GpA dinucleotides and an under-expression of the UpA/GpC dinucleotides. The dinucleotide composition of the PNRSV CP gene showed a weak association with the viral lineages and hosts, but a strong association with viral codon positions. Furthermore, the CPB of PNRSV CP gene is low and is related to dinucleotide preference and codon usage patterns. This research provides reference for future research on PNRSV genetic diversity and gene evolution mechanism.
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Affiliation(s)
- Lingqi Wang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China;
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
| | - Haiting Zhao
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
| | - Zhilei Wang
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
| | - Shiwen Ding
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
| | - Lang Qin
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
| | - Runzhou Jiang
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
| | - Xiaolong Deng
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
| | - Zhen He
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Liangjun Li
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China;
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
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8
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Qin L, Ding S, He Z. Compositional biases and evolution of the largest plant RNA virus order Patatavirales. Int J Biol Macromol 2023; 240:124403. [PMID: 37076075 DOI: 10.1016/j.ijbiomac.2023.124403] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 03/13/2023] [Accepted: 03/25/2023] [Indexed: 04/21/2023]
Abstract
Patatavirales is the largest order of plant RNA viruses and exclusively contains the family Potyviridae, accounting for 30 % of all known plant viruses. The composition bias of animal RNA viruses and several plant RNA viruses has been determined. However, the comprehensive nucleic acid composition, codon pair usage patterns, dinucleotide preference and codon pair preference of plant RNA viruses have not been investigated to date. In this study, integrated analysis and discussion of the nucleic acid composition, codon usage patterns, dinucleotide composition and codon pair bias of potyvirids were performed using 3732 complete genome coding sequences. The nucleic acid composition of potyvirids was significantly enriched in A/U. Interestingly, the A/U-rich nucleotide composition of Patatavirales is essential for determining the preferred A-ended and U-ended codons and the overexpression of UpG and CpA dinucleotides. The codon usage patterns and codon pair bias of potyvirids were significantly correlated with their nucleic acid composition. Additionally, the codon usage pattern, dinucleotide composition and codon-pair bias of potyvirids are more dependent on the classification of the virus compared with their hosts. Our analysis provides a better understanding of future research on the origin and evolution patterns of the order Patatavirales.
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Affiliation(s)
- Lang Qin
- College of Plant Protection, Yangzhou University, Wenhui East Road No.48, Yangzhou 225009, Jiangsu Province, PR China
| | - Shiwen Ding
- College of Plant Protection, Yangzhou University, Wenhui East Road No.48, Yangzhou 225009, Jiangsu Province, PR China
| | - Zhen He
- College of Plant Protection, Yangzhou University, Wenhui East Road No.48, Yangzhou 225009, Jiangsu Province, PR China.
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9
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He M, He CQ, Ding NZ. Evolution of cucurbit-infecting tobamoviruses: Recombination and codon usage bias. Virus Res 2023; 323:198970. [PMID: 36273733 PMCID: PMC10194277 DOI: 10.1016/j.virusres.2022.198970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 11/09/2022]
Abstract
Currently, there are seven cucurbit-infecting tobamoviruses comprising cucumber green mottle mosaic virus (CGMMV), Kyuri green mottle mosaic virus (KGMMV), cucumber fruit mottle mosaic virus (CFMMV), zucchini green mottle mosaic virus (ZGMMV), cucumber mottle virus (CMoV), watermelon green mottle mosaic virus (WGMMV), and Trichosanthes mottle mosaic virus (TrMMV). To gain more insights into their evolution, recombination analyses were conducted. Four CGMMV isolates and one KGMMV isolate were suggested to be recombinants. And there was an interspecies recombination event between CGMMV and ZGMMV. Phylogenetic incongruence was also observed for CGMMV and KGMMV. A probable ancestral pattern was inferred for the gene junction region between RdRp and MP. Codon usage bias analysis revealed that the viral genes had additional influence independent of compositional constraint. In codon preference, the seven viruses were both similar to and different from the host cucumber (Cucumis sativus). Moreover, the viruses were not deficient in CpG and UpA dinucleotides.
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Affiliation(s)
- Mei He
- Dongying Institute, Shandong Normal University, Dongying 257000, China; College of Life Science, Shandong Normal University, Jinan 250014, China
| | - Cheng-Qiang He
- Dongying Institute, Shandong Normal University, Dongying 257000, China; College of Life Science, Shandong Normal University, Jinan 250014, China.
| | - Nai-Zheng Ding
- Dongying Institute, Shandong Normal University, Dongying 257000, China; College of Life Science, Shandong Normal University, Jinan 250014, China.
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10
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Wu K, Yang Y, Zhang W, Jiang X, Zhuang W, Gao F, Du Z. Bayesian Phylogeographic Inference Suggests Japan as the Center for the Origin and Dissemination of Rice Stripe Virus. Viruses 2022; 14:v14112547. [PMID: 36423156 PMCID: PMC9698939 DOI: 10.3390/v14112547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/11/2022] [Accepted: 11/16/2022] [Indexed: 11/19/2022] Open
Abstract
Rice stripe virus (RSV) is one of the most important viral pathogens of rice in East Asia. The origin and dispersal of RSV remain poorly understood, but an emerging hypothesis suggests that: (i) RSV originates from Yunnan, a southwest province of China; and (ii) some places of eastern China have acted as a center for the international dissemination of RSV. This hypothesis, however, has never been tested rigorously. Using a data set comprising more than 200 time-stamped coat protein gene sequences of RSV from Japan, China and South Korea, we reconstructed the phylogeographic history of RSV with Bayesian phylogeographic inference. Unexpectedly, the results did not support the abovementioned hypothesis. Instead, they suggested that RSV originates from Japan and Japan has been the major center for the dissemination of RSV in the past decades. Based on these data and the temporal dynamics of RSV reported recently by another group, we proposed a new hypothesis to explain the origin and dispersal of RSV. This new hypothesis may be valuable for further studies aiming to clarify the epidemiology of RSV. It may also be useful in designing management strategies against this devastating virus.
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Affiliation(s)
- Kangcheng Wu
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yunyue Yang
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wenwen Zhang
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaofeng Jiang
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Weijian Zhuang
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Fangluan Gao
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (F.G.); (Z.D.)
| | - Zhenguo Du
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (F.G.); (Z.D.)
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11
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Qin L, Ding S, Wang Z, Jiang R, He Z. Host Plants Shape the Codon Usage Pattern of Turnip Mosaic Virus. Viruses 2022; 14:v14102267. [PMID: 36298822 PMCID: PMC9607058 DOI: 10.3390/v14102267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 01/25/2023] Open
Abstract
Turnip mosaic virus (TuMV), an important pathogen that causes mosaic diseases in vegetable crops worldwide, belongs to the genus Potyvirus of the family Potyviridae. Previously, the areas of genetic variation, population structure, timescale, and migration of TuMV have been well studied. However, the codon usage pattern and host adaptation analysis of TuMV is unclear. Here, compositional bias and codon usage of TuMV were performed using 184 non-recombinant sequences. We found a relatively stable change existed in genomic composition and a slightly lower codon usage choice displayed in TuMV protein-coding sequences. Statistical analysis presented that the codon usage patterns of TuMV protein-coding sequences were mainly affected by natural selection and mutation pressure, and natural selection was the key influencing factor. The codon adaptation index (CAI) and relative codon deoptimization index (RCDI) revealed that TuMV genes were strongly adapted to Brassica oleracea from the present data. Similarity index (SiD) analysis also indicated that B. oleracea is potentially the preferred host of TuMV. Our study provides the first insights for assessing the codon usage bias of TuMV based on complete genomes and will provide better advice for future research on TuMV origins and evolution patterns.
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Affiliation(s)
- Lang Qin
- College of Plant Protection, Yangzhou University, Wenhui East Road No.48, Yangzhou 225009, China
| | - Shiwen Ding
- College of Plant Protection, Yangzhou University, Wenhui East Road No.48, Yangzhou 225009, China
| | - Zhilei Wang
- College of Plant Protection, Yangzhou University, Wenhui East Road No.48, Yangzhou 225009, China
| | - Runzhou Jiang
- College of Plant Protection, Yangzhou University, Wenhui East Road No.48, Yangzhou 225009, China
| | - Zhen He
- College of Plant Protection, Yangzhou University, Wenhui East Road No.48, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Correspondence:
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12
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Determinants of Virus Variation, Evolution, and Host Adaptation. Pathogens 2022; 11:pathogens11091039. [PMID: 36145471 PMCID: PMC9501407 DOI: 10.3390/pathogens11091039] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/06/2022] [Accepted: 09/09/2022] [Indexed: 11/17/2022] Open
Abstract
Virus evolution is the change in the genetic structure of a viral population over time and results in the emergence of new viral variants, strains, and species with novel biological properties, including adaptation to new hosts. There are host, vector, environmental, and viral factors that contribute to virus evolution. To achieve or fine tune compatibility and successfully establish infection, viruses adapt to a particular host species or to a group of species. However, some viruses are better able to adapt to diverse hosts, vectors, and environments. Viruses generate genetic diversity through mutation, reassortment, and recombination. Plant viruses are exposed to genetic drift and selection pressures by host and vector factors, and random variants or those with a competitive advantage are fixed in the population and mediate the emergence of new viral strains or species with novel biological properties. This process creates a footprint in the virus genome evident as the preferential accumulation of substitutions, insertions, or deletions in areas of the genome that function as determinants of host adaptation. Here, with respect to plant viruses, we review the current understanding of the sources of variation, the effect of selection, and its role in virus evolution and host adaptation.
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13
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Guo W, Du L, Li C, Ma S, Wang Z, Lan Y, Lin F, Zhou Y, Wang Y, Zhou T. Rice Stripe Virus Modulates the Feeding Preference of Small Brown Planthopper from the Stems to Leaves of Rice Plants to Promote Virus Infection. PHYTOPATHOLOGY 2022; 112:2022-2027. [PMID: 35297646 DOI: 10.1094/phyto-01-22-0040-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Research on plant-virus-vector interactions has revealed that viruses can enhance their spread to new host plants by attracting nonviruliferous vectors to infected plants or driving viruliferous vectors to noninfected plants. However, whether viruses can also modulate the feeding preference of viruliferous vectors for different plant parts remains largely unknown. Here, by using rice stripe virus (RSV) and its vector, the small brown planthopper (SBPH), as a model, the effect of the virus on the feeding preference of its vector was studied by calculating the number of nonviruliferous and viruliferous SBPHs settling on different parts of rice plants. The results showed that the RSV-free SBPHs significantly preferred feeding on the stems of rice plants, whereas RSV-carrying SBPHs fed more on rice leaves. Moreover, the rice plants inoculated with RSV on the leaves showed more severe symptoms, with enhanced disease incidence and virus accumulation compared with rice plants inoculated at the top and bottom of stems, suggesting that the leaves are more susceptible to RSV than the stems of rice plants. These results demonstrate that RSV modulates the feeding preference of its transmitting vector SBPH from the stems to leaves of rice plants to promote virus infection. Interestingly, we also found that the leaves were more susceptible than the stems to rice black-streaked dwarf virus. This study proves that the feeding preference of insect vectors can be modulated by plant viruses to facilitate virus transmission.
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Affiliation(s)
- Wei Guo
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Ministry of Education Key Laboratory of Agriculture Biodiversity for Plant Disease Management, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China
| | - Linlin Du
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Chenyang Li
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Shuhui Ma
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhaoyun Wang
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Ying Lan
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Feng Lin
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Yijun Zhou
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Yunyue Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Ministry of Education Key Laboratory of Agriculture Biodiversity for Plant Disease Management, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China
| | - Tong Zhou
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- International Rice Research Institute and Jiangsu Academy of Agricultural Sciences Joint Laboratory, Nanjing 210014, China
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14
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He Z, Qin L, Xu X, Ding S. Evolution and host adaptability of plant RNA viruses: Research insights on compositional biases. Comput Struct Biotechnol J 2022; 20:2600-2610. [PMID: 35685354 PMCID: PMC9160401 DOI: 10.1016/j.csbj.2022.05.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 01/23/2023] Open
Abstract
During recent decades, many new emerging or re-emerging RNA viruses have been found in plants through the development of deep-sequencing technology and big data analysis. These findings largely changed our understanding of the origin, evolution and host range of plant RNA viruses. There is evidence that their genetic composition originates from viruses, and host populations play a key role in the evolution and host adaptability of plant RNA viruses. In this mini-review, we describe the state of our understanding of the evolution of plant RNA viruses in view of compositional biases and explore how they adapt to the host. It appears that adenine rich (A-rich) coding sequences, low CpG and UpA dinucleotide frequencies and lower codon usage patterns were found in the vast majority of plant RNA viruses. The codon usage pattern of plant RNA viruses was influenced by both natural selection and mutation pressure, and natural selection mostly from hosts was the dominant factor. The codon adaptation analyses support that plant RNA viruses probably evolved a dynamic balance between codon adaptation and deoptimization to maintain efficient replication cycles in multiple hosts with various codon usage patterns. In the future, additional combinations of computational and experimental analyses of the nucleotide composition and codon usage of plant RNA viruses should be addressed.
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Affiliation(s)
- Zhen He
- School of Horticulture and Plant Protection, Yangzhou University, Wenhui East Road No. 48, Yangzhou 225009, Jiangsu Province, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Wenhui East Road No. 48, Yangzhou 225009, Jiangsu Province, PR China
- Corresponding author.
| | - Lang Qin
- School of Horticulture and Plant Protection, Yangzhou University, Wenhui East Road No. 48, Yangzhou 225009, Jiangsu Province, PR China
| | - Xiaowei Xu
- School of Horticulture and Plant Protection, Yangzhou University, Wenhui East Road No. 48, Yangzhou 225009, Jiangsu Province, PR China
| | - Shiwen Ding
- School of Horticulture and Plant Protection, Yangzhou University, Wenhui East Road No. 48, Yangzhou 225009, Jiangsu Province, PR China
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15
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He Z, Ding S, Guo J, Qin L, Xu X. Synonymous Codon Usage Analysis of Three Narcissus Potyviruses. Viruses 2022; 14:v14050846. [PMID: 35632588 PMCID: PMC9143068 DOI: 10.3390/v14050846] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/13/2022] [Accepted: 04/18/2022] [Indexed: 02/04/2023] Open
Abstract
Narcissus degeneration virus (NDV), narcissus late season yellows virus (NLSYV) and narcissus yellow stripe virus (NYSV), which belong to the genus Potyvirus of the family Potyviridae, cause significant losses in the ornamental value and quality of narcissus. Several previous studies have explored the genetic diversity and evolution rate of narcissus viruses, but the analysis of the synonymous codons of the narcissus viruses is still unclear. Herein, the coat protein (CP) of three viruses is used to analyze the viruses’ phylogeny and codon usage pattern. Phylogenetic analysis showed that NYSV, NDV and NLSYV isolates were divided into five, three and five clusters, respectively, and these clusters seemed to reflect the geographic distribution. The effective number of codon (ENC) values indicated a weak codon usage bias in the CP coding region of the three narcissus viruses. ENC-plot and neutrality analysis showed that the codon usage bias of the three narcissus viruses is all mainly influenced by natural selection compared with the mutation pressure. The three narcissus viruses shared the same best optimal codon (CCA) and the synonymous codon prefers to use codons ending with A/U, compared to C/G. Our study shows the codon analysis of different viruses on the same host for the first time, which indicates the importance of the evolutionary-based design to control these viruses.
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Affiliation(s)
- Zhen He
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (S.D.); (L.Q.); (X.X.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Correspondence: or
| | - Shiwen Ding
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (S.D.); (L.Q.); (X.X.)
| | - Jiyuan Guo
- Department of Resources and Environment, Moutai Institute, Zunyi 564507, China;
| | - Lang Qin
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (S.D.); (L.Q.); (X.X.)
| | - Xiaowei Xu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (S.D.); (L.Q.); (X.X.)
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16
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Transgenic Rice Plants Expressing Artificial miRNA Targeting the Rice Stripe Virus MP Gene Are Highly Resistant to the Virus. BIOLOGY 2022; 11:biology11020332. [PMID: 35205198 PMCID: PMC8869529 DOI: 10.3390/biology11020332] [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: 12/24/2021] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 11/29/2022]
Abstract
Simple Summary Rice stripe virus is a disastrous viral disease that causes significant yield losses in rice production in South, Southeast, and East Asian countries. To decrease the use of chemical insecticides, genetic engineering has become a pivotal strategy to combat the virus. In this study, we constructed a dimeric artificial microRNA precursor expression vector that targets the viral MP gene based on the structure of the rice osa-MIR528 precursor. Marker-free transgenic plants successfully expressing the MP amiRNAs were obtained and were highly resistant to RSV infection. The novel rice germplasms generated are promising for RSV control. Abstract Rice stripe virus (RSV) causes one of the most serious viral diseases of rice. RNA interference is one of the most efficient ways to control viral disease. In this study, we constructed an amiRNA targeting the RSV MP gene (amiR MP) based on the backbone sequence of the osa-MIR528 precursor, and obtained marker-free transgenic rice plants constitutively expressing amiR MP by Agrobacterium tumefaciens-mediated transformation. A transient expression assay demonstrated that dimeric amiR MP could be effectively recognized and cleaved at the target MP gene in plants. Northern blot of miRNA indicated that amiR MP-mediated viral resistance could be stably inherited. The transgenic rice plants were highly resistant to RSV (73–90%). Our research provides novel rice germplasm for RSV control.
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17
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PAM-free loop-mediated isothermal amplification coupled with CRISPR/Cas12a cleavage (Cas-PfLAMP) for rapid detection of rice pathogens. Biosens Bioelectron 2022; 204:114076. [DOI: 10.1016/j.bios.2022.114076] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/24/2022] [Accepted: 02/03/2022] [Indexed: 12/26/2022]
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18
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Guo W, Li C, Zeng B, Li J, Wang Z, Ma S, Du L, Lan Y, Sun F, Lu C, Li S, Zhou Y, Wang Y, Zhou T. Analyses on the Infection Process of Rice Virus and the Spatiotemporal Expression Pattern of Host Defense Genes Based on a Determined-Part Inoculation Approach. Pathogens 2022; 11:pathogens11020144. [PMID: 35215088 PMCID: PMC8880328 DOI: 10.3390/pathogens11020144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/13/2022] [Accepted: 01/21/2022] [Indexed: 02/05/2023] Open
Abstract
Rice viral diseases adversely affect crop yield and quality. Most rice viruses are transmitted through insect vectors. However, the traditional whole-plant inoculation method cannot control the initial inoculation site in rice plants because the insect feeding sites in plants are random. To solve this problem, we established a determined-part inoculation approach in this study that restricted the insect feeding sites to specific parts of the rice plant. Rice stripe virus (RSV) was used as the model virus and was inoculated at the bottom of the stem using our method. Quantitative real-time PCR and Western blot analyses detected RSV only present at the bottom of the Nipponbare (NPB) stem at 1 day post-inoculation (dpi), indicating that our method successfully controlled the inoculation site. With time, RSV gradually moved from the bottom of the stem to the leaf in NPB rice plants, indicating that systemic viral spread can also be monitored using this method. In addition, a cultivar resistant to RSV, Zhendao 88 (ZD88), was inoculated using this method. We found that RSV accumulation in ZD88 was significantly lower than in NPB. Additionally, the expression level of the resistant gene STV11 in ZD88 was highly induced at the initial invasion stage of RSV (1 dpi) at the inoculation site, whereas it remained relatively stable at non-inoculated sites. This finding indicated that STV11 directly responded to RSV invasion to inhibit virus accumulation at the invasion site. We also proved that this approach is suitable for other rice viruses, such as Rice black-streaked dwarf virus (RBSDV). Interestingly, we determined that systemic infection with RSV was faster than that with RBSDV in NPB, which was consistent with findings in field trails. In summary, this approach is suitable for characterizing the viral infection process in rice plants, comparing the local viral accumulation and spread among different cultivars, analyzing the spatiotemporal expression pattern of resistance-associated genes, and monitoring the infection rate for different viruses.
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Affiliation(s)
- Wei Guo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Ministry of Education Key Laboratory of Agriculture Biodiversity for Plant Disease Management, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China; (W.G.); (C.L.)
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (C.L.); (J.L.); (Z.W.); (S.M.); (L.D.); (Y.L.); (F.S.); (S.L.); (Y.Z.)
| | - Chenyang Li
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (C.L.); (J.L.); (Z.W.); (S.M.); (L.D.); (Y.L.); (F.S.); (S.L.); (Y.Z.)
| | - Bo Zeng
- National Agricultural Technology Extension and Service Center, Beijing 100125, China;
| | - Jie Li
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (C.L.); (J.L.); (Z.W.); (S.M.); (L.D.); (Y.L.); (F.S.); (S.L.); (Y.Z.)
| | - Zhaoyun Wang
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (C.L.); (J.L.); (Z.W.); (S.M.); (L.D.); (Y.L.); (F.S.); (S.L.); (Y.Z.)
| | - Shuhui Ma
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (C.L.); (J.L.); (Z.W.); (S.M.); (L.D.); (Y.L.); (F.S.); (S.L.); (Y.Z.)
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Linlin Du
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (C.L.); (J.L.); (Z.W.); (S.M.); (L.D.); (Y.L.); (F.S.); (S.L.); (Y.Z.)
| | - Ying Lan
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (C.L.); (J.L.); (Z.W.); (S.M.); (L.D.); (Y.L.); (F.S.); (S.L.); (Y.Z.)
| | - Feng Sun
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (C.L.); (J.L.); (Z.W.); (S.M.); (L.D.); (Y.L.); (F.S.); (S.L.); (Y.Z.)
| | - Chengye Lu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Ministry of Education Key Laboratory of Agriculture Biodiversity for Plant Disease Management, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China; (W.G.); (C.L.)
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (C.L.); (J.L.); (Z.W.); (S.M.); (L.D.); (Y.L.); (F.S.); (S.L.); (Y.Z.)
| | - Shuo Li
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (C.L.); (J.L.); (Z.W.); (S.M.); (L.D.); (Y.L.); (F.S.); (S.L.); (Y.Z.)
| | - Yijun Zhou
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (C.L.); (J.L.); (Z.W.); (S.M.); (L.D.); (Y.L.); (F.S.); (S.L.); (Y.Z.)
| | - Yunyue Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Ministry of Education Key Laboratory of Agriculture Biodiversity for Plant Disease Management, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China; (W.G.); (C.L.)
- Correspondence: (Y.W.); (T.Z.)
| | - Tong Zhou
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (C.L.); (J.L.); (Z.W.); (S.M.); (L.D.); (Y.L.); (F.S.); (S.L.); (Y.Z.)
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Academy of Agricultural Sciences Joint Laboratory, International Rice Research Institute, Nanjing 210014, China
- Correspondence: (Y.W.); (T.Z.)
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19
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He M, He CQ, Ding NZ. Evolution of Potato virus X. Mol Phylogenet Evol 2021; 167:107336. [PMID: 34757169 DOI: 10.1016/j.ympev.2021.107336] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 10/01/2021] [Accepted: 10/27/2021] [Indexed: 11/18/2022]
Abstract
Potato virus X (PVX) is the type potexvirus of economic significance. The pathogen is distributed worldwide, threatening solanaceous plants in particular. Based on the coat protein (CP) gene, PVX isolates are classified into two major genotypes (I and II). To gain more insights into the molecular epidemiology and evolution of PVX, recombination analyses were conducted and significant signals were detected. Bayesian coalescent method was then applied to the time-stamped entire CP sequences. According to the estimates, the global subtype I-1 went into expansion in the 20th century and was evolving at a moderate rate. Based on the CP phylogenies, a divergence scenario was proposed for PVX. Surveys of codon usage variation showed that PVX genes had additional bias independent of compositional constraint. In codon preference, PVX was both similar to and different from the three major hosts, potato (Solanum tuberosum), tobacco (Nicotiana tabacum), and tomato (S. lycopersicum). Moreover, the suppression of CpG and UpA dinucleotide frequencies was observed in PVX.
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Affiliation(s)
- Mei He
- College of Life Science, Shandong Normal University, Jinan 250014, China
| | - Cheng-Qiang He
- College of Life Science, Shandong Normal University, Jinan 250014, China.
| | - Nai-Zheng Ding
- College of Life Science, Shandong Normal University, Jinan 250014, China.
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20
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Wan X, Yang J, Ahmed W, Liu Q, Wang Y, Wei L, Ji G. Functional analysis of pde gene and its role in the pathogenesis of Xanthomonas oryzae pv. oryzicola. INFECTION GENETICS AND EVOLUTION 2021; 94:105008. [PMID: 34284137 DOI: 10.1016/j.meegid.2021.105008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 05/16/2021] [Accepted: 07/15/2021] [Indexed: 11/16/2022]
Abstract
Bacterial leaf streak caused by Xanthomonas oryzae pv. oryzicola (Xoc) is a devastating disease of rice worldwide, including China. The second messenger c-di-GMP plays an important role in the transduction of intercellular signals. However, little is known about the function of EAL domain protein in c-di-GMP that regulates the virulence in Xoc. In this study, the function of EAL domain protein encoded by pde (FE36_09715) gene in the regulation of c-di-GMP was investigated. Results of this study, showed that the deletion of pde gene led to a significant reduction in the virulence of Xoc and was positively related to the reduction of exopolysaccharides production, biofilm formation, and flagellar motility. However, these significantly impaired properties from the ∆pde mutant strain were partially recovered in the complementary strain. In addition, the deletion of pde gene in Xoc strain YM15 had no visible effect on the colony morphology, amylase, and protease activities of Xoc. It is concluded that, as a regulator for the c-di-GMP level, the pde gene plays an important role in partial biological processes in Xoc and is essential for its virulence.
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Affiliation(s)
- Xiaoyan Wan
- Key Laboratory of Agriculture Biodiversity for Plant Disease Management Under the Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Jun Yang
- Academy of Science and Technology, Chuxiong Normal University, Chuxiong 675000, China
| | - Waqar Ahmed
- Key Laboratory of Agriculture Biodiversity for Plant Disease Management Under the Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Qi Liu
- Key Laboratory of Agriculture Biodiversity for Plant Disease Management Under the Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Yanfang Wang
- Key Laboratory of Agriculture Biodiversity for Plant Disease Management Under the Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Lanfang Wei
- Key Laboratory of Agriculture Biodiversity for Plant Disease Management Under the Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Guanghai Ji
- Key Laboratory of Agriculture Biodiversity for Plant Disease Management Under the Ministry of Education, Yunnan Agricultural University, Kunming 650201, China.
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21
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Membrane association of importin α facilitates viral entry into salivary gland cells of vector insects. Proc Natl Acad Sci U S A 2021; 118:2103393118. [PMID: 34290144 PMCID: PMC8325321 DOI: 10.1073/pnas.2103393118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The importin α family belongs to the conserved nuclear transport pathway in eukaryotes. However, the biological functions of importin α in the plasma membrane are still elusive. Here, we report that importin α, as a plasma membrane-associated protein, is exploited by the rice stripe virus (RSV) to enter vector insect cells, especially salivary gland cells. When the expression of three importin α genes was simultaneously knocked down, few virions entered the salivary glands of the small brown planthopper, Laodelphax striatellus Through hemocoel inoculation of virions, only importin α2 was found to efficiently regulate viral entry into insect salivary-gland cells. Importin α2 bound the nucleocapsid protein of RSV with a relatively high affinity through its importin β-binding (IBB) domain, with a dissociation constant K D of 9.1 μM. Furthermore, importin α2 and its IBB domain showed a distinct distribution in the plasma membrane through binding to heparin in heparan sulfate proteoglycan. When the expression of importin α2 was knocked down in viruliferous planthoppers or in nonviruliferous planthoppers before they acquired virions, the viral transmission efficiency of the vector insects in terms of the viral amount and disease incidence in rice was dramatically decreased. These findings not only reveal the specific function of the importin α family in the plasma membrane utilized by viruses, but also provide a promising target gene in vector insects for manipulation to efficiently control outbreaks of rice stripe disease.
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22
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Chen Q, Liu Y, Ren J, Zhong P, Chen M, Jia D, Chen H, Wei T. Exosomes mediate horizontal transmission of viral pathogens from insect vectors to plant phloem. eLife 2021; 10:64603. [PMID: 34214032 PMCID: PMC8253596 DOI: 10.7554/elife.64603] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 06/21/2021] [Indexed: 12/19/2022] Open
Abstract
Numerous piercing-sucking insects can horizontally transmit viral pathogens together with saliva to plant phloem, but the mechanism remains elusive. Here, we report that an important rice reovirus has hijacked small vesicles, referred to as exosomes, to traverse the apical plasmalemma into saliva-stored cavities in the salivary glands of leafhopper vectors. Thus, virions were horizontally transmitted with exosomes into rice phloem to establish the initial plant infection during vector feeding. The purified exosomes secreted from cultured leafhopper cells were enriched with virions. Silencing the exosomal secretion-related small GTPase Rab27a or treatment with the exosomal biogenesis inhibitor GW4869 strongly prevented viral exosomal release in vivo and in vitro. Furthermore, the specific interaction of the 15-nm-long domain of the viral outer capsid protein with Rab5 induced the packaging of virions in exosomes, ultimately activating the Rab27a-dependent exosomal release pathway. We thus anticipate that exosome-mediated viral horizontal transmission is the conserved strategy hijacked by vector-borne viruses.
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Affiliation(s)
- Qian Chen
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuyan Liu
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiping Ren
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Panpan Zhong
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Manni Chen
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dongsheng Jia
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hongyan Chen
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Taiyun Wei
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
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23
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He Z, Dong Z, Qin L, Gan H. Phylodynamics and Codon Usage Pattern Analysis of Broad Bean Wilt Virus 2. Viruses 2021; 13:v13020198. [PMID: 33525612 PMCID: PMC7912035 DOI: 10.3390/v13020198] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/19/2021] [Accepted: 01/25/2021] [Indexed: 12/13/2022] Open
Abstract
Broad bean wilt virus 2 (BBWV-2), which belongs to the genus Fabavirus of the family Secoviridae, is an important pathogen that causes damage to broad bean, pepper, yam, spinach and other economically important ornamental and horticultural crops worldwide. Previously, only limited reports have shown the genetic variation of BBWV2. Meanwhile, the detailed evolutionary changes, synonymous codon usage bias and host adaptation of this virus are largely unclear. Here, we performed comprehensive analyses of the phylodynamics, reassortment, composition bias and codon usage pattern of BBWV2 using forty-two complete genome sequences of BBWV-2 isolates together with two other full-length RNA1 sequences and six full-length RNA2 sequences. Both recombination and reassortment had a significant influence on the genomic evolution of BBWV2. Through phylogenetic analysis we detected three and four lineages based on the ORF1 and ORF2 nonrecombinant sequences, respectively. The evolutionary rates of the two BBWV2 ORF coding sequences were 8.895 × 10−4 and 4.560 × 10−4 subs/site/year, respectively. We found a relatively conserved and stable genomic composition with a lower codon usage choice in the two BBWV2 protein coding sequences. ENC-plot and neutrality plot analyses showed that natural selection is the key factor shaping the codon usage pattern of BBWV2. Strong correlations between BBWV2 and broad bean and pepper were observed from similarity index (SiD), codon adaptation index (CAI) and relative codon deoptimization index (RCDI) analyses. Our study is the first to evaluate the phylodynamics, codon usage patterns and adaptive evolution of a fabavirus, and our results may be useful for the understanding of the origin of this virus.
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Affiliation(s)
- Zhen He
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (Z.D.); (L.Q.); (H.G.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Correspondence:
| | - Zhuozhuo Dong
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (Z.D.); (L.Q.); (H.G.)
| | - Lang Qin
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (Z.D.); (L.Q.); (H.G.)
| | - Haifeng Gan
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (Z.D.); (L.Q.); (H.G.)
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24
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He Z, Dong Z, Gan H. Comprehensive codon usage analysis of rice black-streaked dwarf virus based on P8 and P10 protein coding sequences. INFECTION GENETICS AND EVOLUTION 2020; 86:104601. [PMID: 33122052 DOI: 10.1016/j.meegid.2020.104601] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 10/05/2020] [Accepted: 10/18/2020] [Indexed: 12/21/2022]
Abstract
Rice black-streaked dwarf virus (RBSDV) belongs to the genus Fijivirus of the family Reoviridae and is an important pathogen that damages rice, maize and wheat worldwide. Previously, several reports have described the genetic variation and population structure of RBSDV. However, the details of the evolutionary changes, synonymous codon usage patterns and host adaptation of the virus are largely unclear. Here, we performed a detailed analysis of the codon usage and host adaptability of RBSDV based on 130 full-length P8 and 234 full-length P10 sequences. Infrequent recombination and frequent segment reassortment influence the genomic evolution of RBSDV. Our phylogenetic analysis found three and four lineages based on the P8 and P10 non-recombinant sequences respectively. We found relatively stable and conserved genomic composition with lower codon usage choice in the RBSDV P8 and P10 protein coding sequences. Both ENC-plot and neutrality-plot analyses showed that natural selection is the key factor that shapes the codon usage pattern of RBSDV. Codon adaptation index (CAI), relative codon deoptimization index (RCDI) and similarity index (SiD) analyses indicated strong correlation between RBSDV and rice rather than maize, wheat or Laodelphax striatellus. Our study provides deep insight into the evaluation of the codon usage pattern and adaptive evolution of RBSDV based on P8 and P10 sequences and should be taken into consideration for the prevention and control of this virus.
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Affiliation(s)
- Zhen He
- School of Horticulture and Plant Protection, Yangzhou University, Wenhui East Road No.48, Yangzhou, 225009, Jiangsu Province, PR China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Wenhui East Road No.48, Yangzhou, 225009, Jiangsu Province, PR China.
| | - Zhuozhuo Dong
- School of Horticulture and Plant Protection, Yangzhou University, Wenhui East Road No.48, Yangzhou, 225009, Jiangsu Province, PR China
| | - Haifeng Gan
- School of Horticulture and Plant Protection, Yangzhou University, Wenhui East Road No.48, Yangzhou, 225009, Jiangsu Province, PR China
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25
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Yang Z, Huang Y, Yang J, Yao S, Zhao K, Wang D, Qin Q, Bian Z, Li Y, Lan Y, Zhou T, Wang H, Liu C, Wang W, Qi Y, Xu Z, Li Y. Jasmonate Signaling Enhances RNA Silencing and Antiviral Defense in Rice. Cell Host Microbe 2020; 28:89-103.e8. [PMID: 32504578 DOI: 10.1016/j.chom.2020.05.001] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/19/2020] [Accepted: 04/30/2020] [Indexed: 12/12/2022]
Abstract
Small RNA-mediated RNA silencing is an important antiviral mechanism in higher plants. It has been shown that RNA silencing components can be upregulated by viral infection. However, the mechanisms underlying the upregulation remain largely unknown. Here, we show that jasmonate (JA) signaling transcriptionally activates Argonaute 18 (AGO18), a core RNA silencing component that promotes rice antiviral defense through sequestering miR168 and miR528, which repress key antiviral defense proteins. Mechanistically, the JA-responsive transcription factor JAMYB directly binds to the AGO18 promoter to activate AGO18 transcription. Rice stripe virus (RSV) coat protein (CP) triggers JA accumulation and upregulates JAMYB to initiate this host defense network. Our study reveals that regulatory crosstalk exists between the JA signaling and antiviral RNA silencing pathways and elucidates a molecular mechanism for CP-mediated viral resistance in monocot crops.
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Affiliation(s)
- Zhirui Yang
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yu Huang
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jialin Yang
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Shengze Yao
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Kun Zhao
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Donghui Wang
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Qingqing Qin
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Zhan Bian
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yan Li
- Center for Plant Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ying Lan
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Tong Zhou
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - He Wang
- Rice Research Institute and College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Chang Liu
- Center for Plant Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wenming Wang
- Rice Research Institute and College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Yijun Qi
- Center for Plant Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhihong Xu
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yi Li
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.
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26
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He Z, Dong Z, Gan H. Genetic changes and host adaptability in sugarcane mosaic virus based on complete genome sequences. Mol Phylogenet Evol 2020; 149:106848. [PMID: 32380283 DOI: 10.1016/j.ympev.2020.106848] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/10/2020] [Accepted: 04/28/2020] [Indexed: 12/15/2022]
Abstract
Sugarcane mosaic virus (SCMV), a member of the genus Potyvirus in the family Potyviridae, is an important pathogen that causes mosaic diseases in maize, sugarcane, canna and other graminaceous species worldwide. Previously, several reports have showed the genetic variation and population structure of SCMV. However, the evolutionary dynamics, synonymous codon usage pattern and adaptive evolution of the virus is unclear. In this study, we performed comprehensive analyses of phylodynamics, composition bias and codon usage of SCMV using 108 complete genomic sequences. Our phylogenetic analysis found six host- and geographically confined phylogenetic lineages within the SCMV non-recombinant isolates. We found a relatively stable and conserved genomic composition with a lower codon usage choice in the SCMV protein coding sequences. Mutation pressure and natural selection have shaped the codon usage patterns of the SCMV protein coding sequences with natural selection being the dominant factor. The codon adaptation index (CAI), relative codon deoptimization index (RCDI) and similarity index (SiD) analyses revealed a stronger correlation between SCMV and maize than between SCMV and sugarcane or canna. Our study is the first to evaluate the codon usage pattern of SCMV based on complete sequences and may provide a better understanding of the origin of SCMV and its evolutionary patterns for future research.
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Affiliation(s)
- Zhen He
- School of Horticulture and Plant Protection, Yangzhou University, Wenhui East Road No. 48, Yangzhou 225009, Jiangsu Province, PR China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Wenhui East Road No. 48, Yangzhou 225009, Jiangsu Province, PR China.
| | - Zhuozhuo Dong
- School of Horticulture and Plant Protection, Yangzhou University, Wenhui East Road No. 48, Yangzhou 225009, Jiangsu Province, PR China
| | - Haifeng Gan
- School of Horticulture and Plant Protection, Yangzhou University, Wenhui East Road No. 48, Yangzhou 225009, Jiangsu Province, PR China
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27
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Analysis of Synonymous Codon Usage Bias in Potato Virus M and Its Adaption to Hosts. Viruses 2019; 11:v11080752. [PMID: 31416257 PMCID: PMC6722529 DOI: 10.3390/v11080752] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/12/2019] [Accepted: 08/13/2019] [Indexed: 02/07/2023] Open
Abstract
Potato virus M (PVM) is a member of the genus Carlavirus of the family Betaflexviridae and causes large economic losses of nightshade crops. Several previous studies have elucidated the population structure, evolutionary timescale and adaptive evolution of PVM. However, the synonymous codon usage pattern of PVM remains unclear. In this study, we performed comprehensive analyses of the codon usage and composition of PVM based on 152 nucleotide sequences of the coat protein (CP) gene and 125 sequences of the cysteine-rich nucleic acid binding protein (NABP) gene. We observed that the PVM CP and NABP coding sequences were GC-and AU-rich, respectively, whereas U- and G-ending codons were preferred in the PVM CP and NABP coding sequences. The lower codon usage of the PVM CP and NABP coding sequences indicated a relatively stable and conserved genomic composition. Natural selection and mutation pressure shaped the codon usage patterns of PVM, with natural selection being the most important factor. The codon adaptation index (CAI) and relative codon deoptimization index (RCDI) analysis revealed that the greatest adaption of PVM was to pepino, followed by tomato and potato. Moreover, similarity Index (SiD) analysis showed that pepino had a greater impact on PVM than tomato and potato. Our study is the first attempt to evaluate the codon usage pattern of the PVM CP and NABP genes to better understand the evolutionary changes of a carlavirus.
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28
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Common Carp mef2 Genes: Evolution and Expression. Genes (Basel) 2019; 10:genes10080588. [PMID: 31374988 PMCID: PMC6723361 DOI: 10.3390/genes10080588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 06/30/2019] [Accepted: 07/30/2019] [Indexed: 02/08/2023] Open
Abstract
The MEF2 (myocyte enhancer factor 2) family belongs to the MADS-box superfamily of eukaryotic transcription factors. The vertebrate genes compose four distinct subfamilies designated MEF2A, -B, -C, and -D. There are multiple mef2 genes in the common carp (Cyprinus carpio). So far, the embryonic expression patterns of these genes and the evolution of fish mef2 genes have been barely investigated. In this study, we completed the coding information of C. carpio mef2ca2 and mef2d1 genes via gene cloning and presented two mosaic mef2 sequences as evidence for recombination. We also analyzed the phylogenetic relationship and conserved synteny of mef2 genes and proposed a new evolutionary scenario. In our version, MEF2B and the other three vertebrate subfamilies were generated in parallel from the single last ancestor via two rounds of whole genome duplication events that occurred at the dawn of vertebrates. Moreover, we examined the expression patterns of C. carpio mef2 genes during embryogenesis, by using whole-mount in situ hybridization, and found the notochord to be a new expression site for these genes except for mef2ca1&2. Our results thus provide new insights into the evolution and expression of mef2 genes.
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29
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Mao Q, Wu W, Liao Z, Li J, Jia D, Zhang X, Chen Q, Chen H, Wei J, Wei T. Viral pathogens hitchhike with insect sperm for paternal transmission. Nat Commun 2019; 10:955. [PMID: 30814506 PMCID: PMC6393494 DOI: 10.1038/s41467-019-08860-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 02/03/2019] [Indexed: 01/09/2023] Open
Abstract
Arthropod-borne viruses (arboviruses) can be maternally transmitted by female insects to their offspring, however, it is unknown whether male sperm can directly interact with the arbovirus and mediate its paternal transmission. Here we report that an important rice arbovirus is paternally transmitted by the male leafhoppers by hitchhiking with the sperm. The virus-sperm binding is mediated by the interaction of viral capsid protein and heparan sulfate proteoglycan on the sperm head surfaces. Mating experiments reveal that paternal virus transmission is more efficient than maternal transmission. Such paternal virus transmission scarcely affects the fitness of adult males or their offspring, and plays a pivotal role in maintenance of viral population during seasons unfavorable for rice hosts in the field. Our findings reveal that a preferred mode of vertical arbovirus transmission has been evolved by hitchhiking with insect sperm without disturbing sperm functioning, facilitating the long-term viral epidemic and persistence in nature.
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Affiliation(s)
- Qianzhuo Mao
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.,State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops and College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wei Wu
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Zhenfeng Liao
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Jiajia Li
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Dongsheng Jia
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.,State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops and College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaofeng Zhang
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Qian Chen
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Hongyan Chen
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Jing Wei
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
| | - Taiyun Wei
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China. .,State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops and College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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30
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Wainaina JM, Kubatko L, Harvey J, Ateka E, Makori T, Karanja D, Boykin LM, Kehoe MA. Evolutionary insights of Bean common mosaic necrosis virus and Cowpea aphid-borne mosaic virus. PeerJ 2019; 7:e6297. [PMID: 30783563 PMCID: PMC6377593 DOI: 10.7717/peerj.6297] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 12/18/2018] [Indexed: 11/20/2022] Open
Abstract
Plant viral diseases are one of the major limitations in legume production within sub-Saharan Africa (SSA), as they account for up to 100% in production losses within smallholder farms. In this study, field surveys were conducted in the western highlands of Kenya with viral symptomatic leaf samples collected. Subsequently, next-generation sequencing was carried out to gain insights into the molecular evolution and evolutionary relationships of Bean common mosaic necrosis virus (BCMNV) and Cowpea aphid-borne mosaic virus (CABMV) present within symptomatic common bean and cowpea. Eleven near-complete genomes of BCMNV and two for CABMV were obtained from western Kenya. Bayesian phylogenomic analysis and tests for differential selection pressure within sites and across tree branches of the viral genomes were carried out. Three well-supported clades in BCMNV and one supported clade for CABMNV were resolved and in agreement with individual gene trees. Selection pressure analysis within sites and across phylogenetic branches suggested both viruses were evolving independently, but under strong purifying selection, with a slow evolutionary rate. These findings provide valuable insights on the evolution of BCMNV and CABMV genomes and their relationship to other viral genomes globally. The results will contribute greatly to the knowledge gap involving the phylogenomic relationship of these viruses, particularly for CABMV, for which there are few genome sequences available, and inform the current breeding efforts towards resistance for BCMNV and CABMV.
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Affiliation(s)
- James M Wainaina
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, Australia
| | - Laura Kubatko
- Ohio State University, Columbus, OH, United States of America
| | - Jagger Harvey
- Feed the Future Innovation Lab for the Reduction of Post-Harvest Loss, Kansas State University, Manhattan, KS, United States of America
| | - Elijah Ateka
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Timothy Makori
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - David Karanja
- Kenya Agricultural and Livestock Research Organization (KARLO), Machakos, Kenya
| | - Laura M Boykin
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, Australia
| | - Monica A Kehoe
- Plant Pathology, Department of Primary Industries and Regional Development Diagnostic Laboratory Service, South Perth, Australia
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Abstract
Reproduction of RNA viruses is typically error-prone due to the infidelity of their replicative machinery and the usual lack of proofreading mechanisms. The error rates may be close to those that kill the virus. Consequently, populations of RNA viruses are represented by heterogeneous sets of genomes with various levels of fitness. This is especially consequential when viruses encounter various bottlenecks and new infections are initiated by a single or few deviating genomes. Nevertheless, RNA viruses are able to maintain their identity by conservation of major functional elements. This conservatism stems from genetic robustness or mutational tolerance, which is largely due to the functional degeneracy of many protein and RNA elements as well as to negative selection. Another relevant mechanism is the capacity to restore fitness after genetic damages, also based on replicative infidelity. Conversely, error-prone replication is a major tool that ensures viral evolvability. The potential for changes in debilitated genomes is much higher in small populations, because in the absence of stronger competitors low-fit genomes have a choice of various trajectories to wander along fitness landscapes. Thus, low-fit populations are inherently unstable, and it may be said that to run ahead it is useful to stumble. In this report, focusing on picornaviruses and also considering data from other RNA viruses, we review the biological relevance and mechanisms of various alterations of viral RNA genomes as well as pathways and mechanisms of rehabilitation after loss of fitness. The relationships among mutational robustness, resilience, and evolvability of viral RNA genomes are discussed.
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Lan H, Hong X, Huang R, Lin X, Li Q, Li K, Zhou T. RNA interference-mediated knockdown and virus-induced suppression of Troponin C gene adversely affect the behavior or fitness of the green rice leafhopper, Nephotettix cincticeps. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2018; 97:e21438. [PMID: 29193300 DOI: 10.1002/arch.21438] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The green rice leafhopper, Nephotettix cincticeps, is a major rice pest in Southeast Asia and Southern China. Novel control strategies must be explored to control the rice pest. Behavior or fitness regulation of insect by modulating the Troponin C (TnC) may be a novel strategy in the comprehensive management of the insect pest. However, characterizations and functions of TnC, especially regarding effect of its RNA interference-mediated gene knockdown on the behavior or fitness of N. cincticeps remain unknown. Here, we successfully cloned and characterized TnC gene from N. cincticeps (Nc-TnC). We demonstrated that Nc-TnC ubiquitously transcribed at all development stages and special tissues in adult insects, with relative higher levels at the adult stage and in the intestinal canal. Microinjection- or oral membrane feeding-based transient knockdown of Nc-TnC adversely affected the performance or fitness, such as the decreased survival, feeding capacity, weight, and fecundity of N. cincticeps. Furthermore, we revealed that the expression of Nc-TnC was suppressed by its interaction with rice dwarf virus-encoded nonstructural protein 10, which ultimately affected detrimentally the corresponding parameters of the performance or fitness of N. cincticeps. In conclusion, our data deepen understanding of Nc-TnC functions during the development of and viral infection in N. cincticeps. It imply Nc-TnC may serve as a potential target for N. cincticeps control in future.
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Affiliation(s)
- Hanhong Lan
- School of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou, PR China
| | - Xiaojing Hong
- School of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou, PR China
| | - Ranran Huang
- School of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou, PR China
| | - Xin Lin
- School of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou, PR China
| | - Qinghuang Li
- School of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou, PR China
| | - Kaihui Li
- School of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou, PR China
| | - Tao Zhou
- School of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou, PR China
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