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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] [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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da Silva JPH, Zerbini FM. Taxonomic Classification of Geminiviruses Based on Pairwise Sequence Comparisons. Methods Mol Biol 2024; 2724:21-31. [PMID: 37987895 DOI: 10.1007/978-1-0716-3485-1_2] [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] [Indexed: 11/22/2023]
Abstract
Geminiviridae is the largest and one of the most diverse families of plant viruses, comprising 14 genera demarcated based on host range, type of insect vector, and phylogenetic relationships. The use of unbiased, whole-genome multiple displacement amplification techniques coupled with high-throughput sequencing has greatly expanded our knowledge of geminivirus diversity over the last two decades. As a result, a large number of new species have been described in recent years. Species demarcation criteria in the family are entirely based on sequence comparisons, but the specific cutoff values vary for each genus. The purpose of this chapter is to provide a step-by-step pipeline to classify new species in the family Geminiviridae.
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Affiliation(s)
| | - F Murilo Zerbini
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil.
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3
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Iqbal Z, Shafiq M, Sattar MN, Ali I, Khurshid M, Farooq U, Munir M. Genetic Diversity, Evolutionary Dynamics, and Ongoing Spread of Pedilanthus Leaf Curl Virus. Viruses 2023; 15:2358. [PMID: 38140599 PMCID: PMC10747432 DOI: 10.3390/v15122358] [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: 10/28/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Pedilanthus leaf curl virus (PeLCV) is a monopartite begomovirus (family Geminiviridae) discovered just a few decades ago. Since then, it has become a widely encountered virus, with reports from ca. 25 plant species across Pakistan and India, indicative of its notable evolutionary success. Viruses mutate at such a swift rate that their ecological and evolutionary behaviors are inextricably linked, and all of these behaviors are imprinted on their genomes as genetic diversity. So, all these imprints can be mapped by computational methods. This study was designed to map the sequence variation dynamics, genetic heterogeneity, regional diversity, phylogeny, and recombination events imprinted on the PeLCV genome. Phylogenetic and network analysis grouped the full-length genome sequences of 52 PeLCV isolates into 7 major clades, displaying some regional delineation but lacking host-specific demarcation. The progenitor of PeLCV was found to have originated in Multan, Pakistan, in 1977, from where it spread concurrently to India and various regions of Pakistan. A high proportion of recombination events, distributed unevenly throughout the genome and involving both inter- and intraspecies recombinants, were inferred. The findings of this study highlight that the PeLCV population is expanding under a high degree of genetic diversity (π = 0.073%), a high rate of mean nucleotide substitution (1.54 × 10-3), demographic selection, and a high rate of recombination. This sets PeLCV apart as a distinctive begomovirus among other begomoviruses. These factors could further exacerbate the PeLCV divergence and adaptation to new hosts. The insights of this study that pinpoint the emergence of PeLCV are outlined.
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Affiliation(s)
- Zafar Iqbal
- Central Laboratories, King Faisal University, Al-Ahsa P.O. Box 55110, Saudi Arabia;
| | - Muhammad Shafiq
- Department of Biotechnology, University of Management and Technology, Sialkot Campus, Sialkot P.O. Box 51340, Pakistan;
| | | | - Irfan Ali
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad P.O. Box 38000, Pakistan;
| | - Muhammad Khurshid
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore P.O. Box 54590, Pakistan;
| | - Umer Farooq
- Department of Biotechnology, University of Sialkot, Sialkot P.O. Box 51340, Pakistan;
| | - Muhammad Munir
- Date Palm Research Center of Excellence, King Faisal University, Al-Ahsa P.O. Box 31982, Saudi Arabia;
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Rajabu CA, Dallas MM, Chiunga E, De León L, Ateka EM, Tairo F, Ndunguru J, Ascencio-Ibanez JT, Hanley-Bowdoin L. SEGS-1 a cassava genomic sequence increases the severity of African cassava mosaic virus infection in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2023; 14:1250105. [PMID: 37915512 PMCID: PMC10616593 DOI: 10.3389/fpls.2023.1250105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/04/2023] [Indexed: 11/03/2023]
Abstract
Cassava is a major crop in Sub-Saharan Africa, where it is grown primarily by smallholder farmers. Cassava production is constrained by Cassava mosaic disease (CMD), which is caused by a complex of cassava mosaic begomoviruses (CMBs). A previous study showed that SEGS-1 (sequences enhancing geminivirus symptoms), which occurs in the cassava genome and as episomes during viral infection, enhances CMD symptoms and breaks resistance in cassava. We report here that SEGS-1 also increases viral disease severity in Arabidopsis thaliana plants that are co-inoculated with African cassava mosaic virus (ACMV) and SEGS-1 sequences. Viral disease was also enhanced in Arabidopsis plants carrying a SEGS-1 transgene when inoculated with ACMV alone. Unlike cassava, no SEGS-1 episomal DNA was detected in the transgenic Arabidopsis plants during ACMV infection. Studies using Nicotiana tabacum suspension cells showed that co-transfection of SEGS-1 sequences with an ACMV replicon increases viral DNA accumulation in the absence of viral movement. Together, these results demonstrated that SEGS-1 can function in a heterologous host to increase disease severity. Moreover, SEGS-1 is active in a host genomic context, indicating that SEGS-1 episomes are not required for disease enhancement.
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Affiliation(s)
- Cyprian A. Rajabu
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Mary M. Dallas
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Evangelista Chiunga
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Leandro De León
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, United States
| | - Elijah M. Ateka
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Fred Tairo
- Tanzania Agricultural Research Institute-Mikocheni, Dar Es Salaam, Tanzania
| | - Joseph Ndunguru
- Tanzania Agricultural Research Institute-Mikocheni, Dar Es Salaam, Tanzania
| | - Jose T. Ascencio-Ibanez
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, United States
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
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da Silva JPH, de Resende FMP, da Silva JCF, de Breuil S, Nome C, Bejerman N, Zerbini FM. Amesuviridae: a new family of plant-infecting viruses in the phylum Cressdnaviricota, realm Monodnaviria. Arch Virol 2023; 168:223. [PMID: 37561218 DOI: 10.1007/s00705-023-05852-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
The phylum Cressdnaviricota comprises viruses with single-stranded, circular DNA genomes that encode an HUH-type endonuclease (known as Rep). The phylum includes two classes, eight orders, and 11 families. Here, we report the creation of a twelfth family in the order Mulpavirales, class Arfiviricetes of the phylum Cressdnaviricota. The family Amesuviridae comprises viruses that infect plants and is divided into two genera: Temfrudevirus, including the species Temfrudevirus temperatum (with temperate fruit decay-associated virus as a member), and Yermavirus, including the species Yermavirus ilicis (with yerba mate-associated circular DNA virus as a member). Both viruses encode Rep proteins with HUH endonuclease and SH3 superfamily helicase domains. Phylogenetic analysis indicates that the replicative module of amesuviruses constitutes a well-supported monophyletic clade related to Rep proteins from viruses in the order Mulpavirales. Furthermore, both viruses encode a single capsid protein (CP) related to geminivirus CPs. Phylogenetic incongruence between the replicative and structural modules of amesuviruses suggests a chimeric origin resulting from remote recombination events between ancestral mulpavirales and geminivirids. The creation of the family Amesuviridae has been ratified by the International Committee on Taxonomy of Viruses (ICTV).
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Affiliation(s)
| | | | | | - Soledad de Breuil
- Instituto de Patología Vegetal, Centro de Investigaciones, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5.5, X5020ICA, Agropecuarias, Córdoba, Argentina
| | - Claudia Nome
- Instituto de Patología Vegetal, Centro de Investigaciones, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5.5, X5020ICA, Agropecuarias, Córdoba, Argentina
| | - Nicolas Bejerman
- Instituto de Patología Vegetal, Centro de Investigaciones, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5.5, X5020ICA, Agropecuarias, Córdoba, Argentina
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6
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Fan Y, Zhong Y, Pan L, Wang X, Ding M, Liu S. A shift of vector specificity acquired by a begomovirus through natural homologous recombination. MOLECULAR PLANT PATHOLOGY 2023; 24:882-895. [PMID: 37191666 PMCID: PMC10346445 DOI: 10.1111/mpp.13351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 04/26/2023] [Accepted: 04/26/2023] [Indexed: 05/17/2023]
Abstract
Recombination is common in plant viruses such as geminiviruses, but the ecological and pathogenic consequences have been explored only in a few cases. Here, we found that a new begomovirus, tomato yellow leaf curl Shuangbai virus (TYLCSbV), probably originated from the recombination of Ageratum yellow vein China virus (AYVCNV) and tobacco curl shoot virus (TbCSV). Agrobacterium-mediated inoculation showed that TYLCSbV and AYVCNV have similar levels of infectivity on tomato and tobacco plants. However, the two viruses exhibit contrasting specificities for vector transmission, that is, TYLCSbV was efficiently transmitted by the whitefly Bemisia tabaci Mediterranean (MED) rather than by the whitefly B. tabaci Middle East-Asia Minor 1 (MEAM1), whereas AYVCNV was more efficiently transmitted by MEAM1. We also showed that the transmission efficiencies of TYLCSbV and AYVCNV are positively correlated with the accumulation of the viruses in whitefly whole bodies and organs/tissues. The key coat protein amino acids that determine their accumulation are between positions 147 and 256. Moreover, field surveys suggest that MED has displaced MEAM1 in some regions where TYLCSbV was collected. Viral competition assays indicated that TYLCSbV outcompeted AYVCNV when transmitted by MED, while the outcome was the opposite when transmitted by MEAM1. Our findings suggest that recombination has resulted in a shift of vector specificity that could provide TYLCSbV with a potential selective transmission advantage, and the population shift of whitefly cryptic species could have influenced virus evolution towards an extended trajectory of transmission.
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Affiliation(s)
- Yun‐Yun Fan
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang ProvinceInstitute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Yu‐Wei Zhong
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang ProvinceInstitute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Li‐Long Pan
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang ProvinceInstitute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Xiao‐Wei Wang
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang ProvinceInstitute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Ming Ding
- Biotechnology and Germplasm Resources InstituteYunnan Academy of Agricultural SciencesKunmingChina
| | - Shu‐Sheng Liu
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang ProvinceInstitute of Insect Sciences, Zhejiang UniversityHangzhouChina
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7
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Iqbal MJ, Zia-Ur-Rehman M, Ilyas M, Hameed U, Herrmann HW, Chingandu N, Manzoor MT, Haider MS, Brown JK. Sentinel plot surveillance of cotton leaf curl disease in Pakistan- a case study at the cultivated cotton-wild host plant interface. Virus Res 2023; 333:199144. [PMID: 37271420 PMCID: PMC10352719 DOI: 10.1016/j.virusres.2023.199144] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/06/2023]
Abstract
A sentinel plot case study was carried out to identify and map the distribution of begomovirus-betasatellite complexes in sentinel plots and commercial cotton fields over a four-year period using molecular and high-throughput DNA 'discovery' sequencing approaches. Samples were collected from 15 study sites in the two major cotton-producing areas of Pakistan. Whitefly- and leafhopper-transmitted geminiviruses were detected in previously unreported host plant species and locations. The most prevalent begomovirus was cotton leaf curl Kokhran virus-Burewala (CLCuKoV-Bu). Unexpectedly, a recently recognized recombinant, cotton leaf curl Multan virus-Rajasthan (CLCuMuV-Ra) was prevalent in five of 15 sites. cotton leaf curl Alabad virus (CLCuAlV) and cotton leaf curl Kokhran virus-Kokhran, 'core' members of CLCuD-begomoviruses that co-occurred with CLCuMuV in the 'Multan' epidemic were detected in one of 15 sentinel plots. Also identified were chickpea chlorotic dwarf virus and 'non-core' CLCuD-begomoviruses, okra enation leaf curl virus, squash leaf curl virus, and tomato leaf curl New Delhi virus. Cotton leaf curl Multan betasatellite (CLCuMuB) was the most prevalent CLCuD-betasatellite, and less commonly, two 'non-core' betasatellites. Recombination analysis revealed previously uncharacterized recombinants among helper virus-betasatellite complexes consisting of CLCuKoV, CLCuMuV, CLCuAlV and CLCuMuB. Population analyses provided early evidence for CLCuMuV-Ra expansion and displacement of CLCuKoV-Bu in India and Pakistan from 2012-2017. Identification of 'core' and non-core CLCuD-species/strains in cotton and other potential reservoirs, and presence of the now predominant CLCuMuV-Ra strain are indicative of ongoing diversification. Investigating the phylodynamics of geminivirus emergence in cotton-vegetable cropping systems offers an opportunity to understand the driving forces underlying disease outbreaks and reconcile viral evolution with epidemiological relationships that also capture pathogen population shifts.
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Affiliation(s)
- Muhammad Javed Iqbal
- School of Plant Sciences, The University of Arizona, 1140 E South Campus Drive, Tucson, AZ 85721 USA; Faculty of Agricultural Sciences, University of the Punjab, New Campus Canal Road Lahore, Pakistan
| | - Muhammad Zia-Ur-Rehman
- Faculty of Agricultural Sciences, University of the Punjab, New Campus Canal Road Lahore, Pakistan
| | - Muhammad Ilyas
- School of Plant Sciences, The University of Arizona, 1140 E South Campus Drive, Tucson, AZ 85721 USA
| | - Usman Hameed
- Faculty of Agricultural Sciences, University of the Punjab, New Campus Canal Road Lahore, Pakistan
| | - Hans Werner Herrmann
- School of Plant Sciences, The University of Arizona, 1140 E South Campus Drive, Tucson, AZ 85721 USA
| | - Nomatter Chingandu
- School of Plant Sciences, The University of Arizona, 1140 E South Campus Drive, Tucson, AZ 85721 USA
| | - Muhammad Tariq Manzoor
- Faculty of Agricultural Sciences, University of the Punjab, New Campus Canal Road Lahore, Pakistan
| | - Muhammad Saleem Haider
- Faculty of Agricultural Sciences, University of the Punjab, New Campus Canal Road Lahore, Pakistan
| | - Judith K Brown
- School of Plant Sciences, The University of Arizona, 1140 E South Campus Drive, Tucson, AZ 85721 USA.
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Srivastava A, Pandey V, Al-Sadi AM, Shahid MS, Gaur R. An Insight into Emerging Begomoviruses and their Satellite Complex causing Papaya Leaf Curl Disease. Curr Genomics 2023; 24:2-17. [PMID: 37920727 PMCID: PMC10334704 DOI: 10.2174/1389202924666230207111530] [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: 09/29/2022] [Revised: 01/02/2023] [Accepted: 01/27/2023] [Indexed: 02/10/2023] Open
Abstract
Papaya leaf curl disease (PaLCD) was primarily detected in India and causes major economic damage to agriculture crops grown globally, seriously threatening food security. Begomoviruses are communicated by the vector Bemisia tabaci, and their transmission efficiency and persistence in the vector are the highest, exhibiting the widest host range due to adaptation and evolution. Symptoms induced during PaLCD include leaf curl, leaf yellowing, interveinal chlorosis, and reduced fruit quality and yield. Consequently, plants have evolved several multi-layered defense mechanisms to resist Begomovirus infection and distribution. Subsequently, Begomovirus genomes organise circular ssDNA of size ~2.5-2.7 kb of overlapping viral transcripts and carry six-seven ORFs encoding multifunctional proteins, which are precisely evolved by the viruses to maintain the genome-constraint and develop complex but integrated interactions with a variety of host components to expand and facilitate successful infection cycles, i.e., suppression of host defense strategies. Geographical distribution is continuing to increase due to the advent and evolution of new Begomoviruses, and sweep to new regions is a future scenario. This review summarizes the current information on the biological functions of papaya-infecting Begomoviruses and their encoded proteins in transmission through vectors and modulating host-mediated responses, which may improve our understanding of how to challenge these significant plant viruses by revealing new information on the development of antiviral approaches against Begomoviruses associated with PaLCD.
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Affiliation(s)
- Aarshi Srivastava
- Department of Biotechnology, D.D.U. Gorakhpur University, Gorakhpur, India
| | - Vineeta Pandey
- Department of Biotechnology, D.D.U. Gorakhpur University, Gorakhpur, India
| | - Abdullah. M. Al-Sadi
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khod, Oman
| | - Muhammad S. Shahid
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khod, Oman
| | - R.K. Gaur
- Department of Biotechnology, D.D.U. Gorakhpur University, Gorakhpur, India
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Dye AE, Muga B, Mwangi J, Hoyer JS, Ly V, Rosado Y, Sharpee W, Mware B, Wambugu M, Labadie P, Deppong D, Jackai L, Jacobson A, Kennedy G, Ateka E, Duffy S, Hanley-Bowdoin L, Carbone I, Ascencio-Ibáñez JT. Cassava begomovirus species diversity changes during plant vegetative cycles. Front Microbiol 2023; 14:1163566. [PMID: 37303798 PMCID: PMC10248227 DOI: 10.3389/fmicb.2023.1163566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 04/17/2023] [Indexed: 06/13/2023] Open
Abstract
Cassava is a root crop important for global food security and the third biggest source of calories on the African continent. Cassava production is threatened by Cassava mosaic disease (CMD), which is caused by a complex of single-stranded DNA viruses (family: Geminiviridae, genus: Begomovirus) that are transmitted by the sweet potato whitefly (Bemisia tabaci). Understanding the dynamics of different cassava mosaic begomovirus (CMB) species through time is important for contextualizing disease trends. Cassava plants with CMD symptoms were sampled in Lake Victoria and coastal regions of Kenya before transfer to a greenhouse setting and regular propagation. The field-collected and greenhouse samples were sequenced using Illumina short-read sequencing and analyzed on the Galaxy platform. In the field-collected samples, African cassava mosaic virus (ACMV), East African cassava mosaic virus (EACMV), East African cassava mosaic Kenya virus (EACMKV), and East African cassava mosaic virus-Uganda variant (EACMV-Ug) were detected in samples from the Lake Victoria region, while EACMV and East African mosaic Zanzibar virus (EACMZV) were found in the coastal region. Many of the field-collected samples had mixed infections of EACMV and another begomovirus. After 3 years of regrowth in the greenhouse, only EACMV-like viruses were detected in all samples. The results suggest that in these samples, EACMV becomes the dominant virus through vegetative propagation in a greenhouse. This differed from whitefly transmission results. Cassava plants were inoculated with ACMV and another EACMV-like virus, East African cassava mosaic Cameroon virus (EACMCV). Only ACMV was transmitted by whiteflies from these plants to recipient plants, as indicated by sequencing reads and copy number data. These results suggest that whitefly transmission and vegetative transmission lead to different outcomes for ACMV and EACMV-like viruses.
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Affiliation(s)
- Anna E. Dye
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Brenda Muga
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Jenniffer Mwangi
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - J. Steen Hoyer
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ, United States
| | - Vanessa Ly
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, United States
| | - Yamilex Rosado
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, United States
| | - William Sharpee
- International Livestock Research Institute (ILRI), Nairobi, Kenya
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - Benard Mware
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Mary Wambugu
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Paul Labadie
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - David Deppong
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Louis Jackai
- Department of Natural Resources and Environmental Design, North Carolina Agricultural and Technical State University, Greensboro, NC, United States
| | - Alana Jacobson
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, United States
| | - George Kennedy
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - Elijah Ateka
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ, United States
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Ignazio Carbone
- Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
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Sun PP, Zhang L, Xu XZ, Zhu M, Zhang B, Li ZN. Molecular Characterization of Three Apple Geminivirus Isolates in Crabapples Detected in Inner Mongolia, China. PLANTS (BASEL, SWITZERLAND) 2023; 12:195. [PMID: 36616324 PMCID: PMC9824349 DOI: 10.3390/plants12010195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Apple geminivirus 1 (AGV) in the genus Maldovirus of the family Geminiviridae was first identified infecting apple trees in the year 2015 in China. In this work, we characterized three isolates of the AGV in the Chinese pearleaf crabapple (Malus asiatica) in Inner Mongolia Autonomous Region. The viruses were detected by Illumina sequencing and its existence was confirmed by reverse transcription-polymerase chain reaction (RT-PCR) amplification of an AGV fragment. Between the three AGV isolates and the initially characterized AGV isolate PL2015, the nucleotide sequence identities of the complete genome ranged from 91.2 to 91.7%, of the coat protein gene (V1) ranged from 95.4% to 97.3%, and of the replicase gene (C1) ranged from 87.3% to 88.0%. Phylogenetic analysis indicated that the three isolates formed a monophyletic group together with the AGV, separated from the current genera in the family Geminiviridae. This is the first description of the AGV infecting crabapples.
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Affiliation(s)
- Ping-Ping Sun
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Lei Zhang
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Xiao-Zhao Xu
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Mo Zhu
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Bin Zhang
- College of Life Sciences & Technology, Inner Mongolia Normal University, Hohhot 010028, China
| | - Zheng-Nan Li
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot 010018, China
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11
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Quadros AFF, Ferro CG, de Rezende RR, Godinho MT, Xavier CAD, Nogueira AM, Alfenas-Zerbini P, Zerbini FM. Begomovirus populations in single plants are complex and may include both well-adapted and poorly-adapted viruses. Virus Res 2023; 323:198969. [PMID: 36257487 PMCID: PMC10194161 DOI: 10.1016/j.virusres.2022.198969] [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: 06/28/2022] [Revised: 10/10/2022] [Accepted: 10/13/2022] [Indexed: 11/05/2022]
Abstract
Begomoviruses (single-stranded DNA plant viruses transmitted by whiteflies) are economically important pathogens causing epidemics worldwide. Tomato-infecting begomoviruses emerged in Brazil in the 1990's following the introduction of Bemisia tabaci Middle East-Asia Minor 1. It is believed that these viruses evolved from indigenous viruses infecting non-cultivated hosts. However, tomato-infecting viruses are rarely found in non-cultivated hosts, and vice-versa. It is possible that viral populations in a given host are composed primarily of viruses which are well adapted to this host, but also include a small proportion of poorly adapted viruses. Following transfer to a new host, the composition of the viral population would shift rapidly, with the viruses which are better adapted to the new host becoming predominant. To test this hypothesis, we collected tomato and Sida plants growing next to each other at two locations in 2014 and 2018. Total DNA was extracted from tomato and Sida samples from each location and year and used as a template for high-throughput sequencing. Reads were mapped following a highly stringent set of criteria. For the 2014 samples, >98% of the Sida reads mapped to Sida micrantha mosaic virus (SiMMV), but 0.1% of the reads mapped to tomato severe rugose virus (ToSRV). Conversely, >99% of the tomato reads mapped to ToSRV, with 0.18% mapping to SiMMV. For the 2018 samples, 41% of the Sida reads mapped to three Sida-adapted viruses and 0.1% of the reads mapped to ToSRV, while 99.9% of the tomato reads mapped to ToSRV. These results are consistent with the hypothesis that viral populations in a single plant are composed primarily of the virus that is better adapted to the host but also include a small proportion of viruses that are poorly adapted.
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Affiliation(s)
- Ayane F F Quadros
- Dep. de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Camila G Ferro
- Dep. de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Rafael R de Rezende
- Dep. de Microbiologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Márcio T Godinho
- Dep. de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - César A D Xavier
- Dep. de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Angélica M Nogueira
- Dep. de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - P Alfenas-Zerbini
- Dep. de Microbiologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - F Murilo Zerbini
- Dep. de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil.
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12
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Doizy A, Prin A, Cornu G, Chiroleu F, Rieux A. Phylostems: a new graphical tool to investigate temporal signal of heterochronous sequences datasets. BIOINFORMATICS ADVANCES 2023; 3:vbad026. [PMID: 36936370 PMCID: PMC10017117 DOI: 10.1093/bioadv/vbad026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/16/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023]
Abstract
Motivation Molecular tip-dating of phylogenetic trees is a growing discipline that uses DNA sequences sampled at different points in time to co-estimate the timing of evolutionary events with rates of molecular evolution. Importantly, such inferences should only be performed on datasets displaying sufficient temporal signal, a feature important to test prior to any tip-dating inference. For this purpose, the most popular method considered to-date has been the 'root-to-tip regression' which consist in fitting a linear regression of the number of substitutions accumulated from the root to the tips of a phylogenetic tree as a function of sampling times. The main limitation of the regression method, in its current implementation, relies in the fact that the temporal signal can only be tested at the whole-tree scale (i.e. its root). Results To overcome this limitation we introduce Phylostems, a new graphical user-friendly tool developed to investigate temporal signal within every clade of a phylogenetic tree. We provide a 'how to' guide by running Phylostems on an empirical dataset and supply guidance for results interpretation. Availability and implementation Phylostems is freely available at https://pvbmt-apps.cirad.fr/apps/phylostems.
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Affiliation(s)
- Anna Doizy
- CIRAD, UMR PVBMT, La Réunion, St Pierre 97410, France
- DoAna—Statistiques Réunion, Reunion Island, Saint-Joseph F-97480, France
| | - Amaury Prin
- CIRAD, UMR PVBMT, La Réunion, St Pierre 97410, France
| | - Guillaume Cornu
- CIRAD, Univ Montpellier, UR Forests and Societies, 34398 Montpellier Cedex 5, France
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13
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Thompson JR. Analysis of the genome of grapevine red blotch virus and related grabloviruses indicates diversification prior to the arrival of Vitis vinifera in North America. J Gen Virol 2022; 103. [PMID: 36205485 DOI: 10.1099/jgv.0.001789] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this study 163 complete whole-genome sequences of the emerging pathogen grapevine red blotch virus (GRBV; genus Grablovirus, family Geminiviridae) were used to reconstruct phylogenies using Bayesian analyses on time-tipped (heterochronous) data. Using different combinations of priors, Bayes factors identified heterochronous datasets (3×200 million chains) generated from strict clock and exponential tree priors as being the most robust. Substitution rates of 3.2×10-5 subsitutions per site per year (95% HPD 4.3-2.1×10-5) across the whole of the GRBV genome were estimated, suggesting ancestral GRBV diverged from ancestral wild Vitis latent virus 1 around 9 000 years ago, well before the first documented arrival of Vitis vinifera in North America. Whole-genome analysis of GRBV isolates in a single infected field-grown grapevine across 12 years identified 12 single nucleotide polymorphisms none of which were fixed substitutions: an observation not discordant with the in silico estimate. The substitution rate estimated here is lower than those estimated for other geminiviruses and is the first for a woody-host-infecting geminivirus.
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Affiliation(s)
- Jeremy R Thompson
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.,Present address: Plant Health and Environment Laboratory, Ministry for Primary Industries, Auckland 1140, New Zealand
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14
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Li Q, Zhang Y, Lu W, Han X, Yang L, Shi Y, Li H, Chen L, Liu Y, Yang X, Shi Y. Identification and characterization of a new geminivirus from soybean plants and determination of V2 as a pathogenicity factor and silencing suppressor. BMC PLANT BIOLOGY 2022; 22:362. [PMID: 35869422 PMCID: PMC9308217 DOI: 10.1186/s12870-022-03745-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Soybean is one of the four major crops in China. The occurrence of viruses in soybean causes significant economic losses. RESULTS In this study, the soybean leaves from stay-green plants showing crinkle were collected for metatranscriptomic sequencing. A novel geminivirus, tentatively named soybean geminivirus A (SGVA), was identified in soybean stay-green plants. Sequence analysis of the full-length SGVA genome revealed a genome of 2762 nucleotides that contain six open reading frames. Phylogenetic analyses revealed that SGVA was located adjacent to the clade of begomoviruses in both the full genome-based and C1-based phylogenetic tree, while in the CP-based phylogenetic tree, SGVA was located adjacent to the clade of becurtoviruses. SGVA was proposed as a new recombinant geminivirus. Agroinfectious clone of SGVA was constructed. Typical systemic symptoms of curly leaves were observed at 11 dpi in Nicotiana benthamiana plants and severe dwarfism was observed after 3 weeks post inoculation. Expression of the SGVA encoded V2 and C1 proteins through a potato virus X (PVX) vector caused severe symptoms in N. benthamiana. The V2 protein inhibited local RNA silencing in co-infiltration assays in GFP transgenic 16C N. benthamiana plants. Further study revealed mild symptoms in N. benthamiana plants inoculated with SGVA-ZZ V2-STOP and SGVA-ZZ V2-3738AA mutants. Both the relative viral DNA and CP protein accumulation levels significantly decreased when compared with SGVA-inoculated plants. CONCLUSIONS This work identified a new geminivirus in soybean stay-green plants and determined V2 as a pathogenicity factor and silencing suppressor.
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Affiliation(s)
- Qinglun Li
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yuyang Zhang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China
| | - Weiguo Lu
- Institute of Crops Molecular Breeding, Henan Academy of Agricultural Sciences/ National Centre for Plant Breeding, Zhengzhou, 450002, China
| | - Xiaoyu Han
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China
| | - Lingling Yang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yajuan Shi
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China
| | - Honglian Li
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China
| | - Linlin Chen
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yiqing Liu
- Guangdong Baiyun University, Guangzhou, 510550, China
| | - Xue Yang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Yan Shi
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China.
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15
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Phylodynamics and Coat Protein Analysis of Babaco Mosaic Virus in Ecuador. PLANTS 2022; 11:plants11131646. [PMID: 35807598 PMCID: PMC9268947 DOI: 10.3390/plants11131646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/07/2022] [Accepted: 06/10/2022] [Indexed: 11/17/2022]
Abstract
Babaco is a fast-growing herbaceous shrub with great commercial potential because of the organoleptic properties of its fruit. Babaco mosaic virus (BabMV) is a potexvirus in the family Alphaflexiviridae affecting babaco in all the provinces that produce this crop in Ecuador. BabMV was recently described but it has been affecting babaco for decades and, since many potexviruses are serologically indistinguishable, it may have been previously misidentified as papaya mosaic virus. Based on the coat protein (CP) gene, we aimed to study the distribution and epidemiological patterns of BabMV in babaco and chamburo over the years and to model its three-dimensional structure. Sequences of the CP were obtained from thirty-six isolates from plants collected in the main babaco-producing provinces of Ecuador between 2016 and 2021. The evolution rate of BabMV was estimated at 1.21 × 10−3 nucleotide substitutions site−1 year−1 and a time of origin of the most recent common ancestor around 1958.80. From molecular dynamics simulations, compared to other proteins of BabMV—RDRP, TGB1, and Alkb domain—the CP exhibited a higher flexibility with the C and N terminals as the most flexible regions. The reconstructed viral distribution provides dispersion patterns which have implications for control approaches of BabMV.
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16
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Srivastava A, Pandey V, Sahu AK, Yadav D, Al-Sadi AM, Shahid MS, Gaur RK. Evolutionary Dynamics of Begomoviruses and Its Satellites Infecting Papaya in India. Front Microbiol 2022; 13:879413. [PMID: 35685936 PMCID: PMC9171567 DOI: 10.3389/fmicb.2022.879413] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
The genus Begomovirus represents a group of multipartite viruses that significantly damage many agricultural crops, including papaya, and influence overall production. Papaya leaf curl disease (PaLCD) caused by the complex begomovirus species has several important implications and substantial losses in papaya production in many developing countries, including India. The increase in the number of begomovirus species poses a continuous threat to the overall production of papaya. Here, we attempted to map the genomic variation, mutation, evolution rate, and recombination to know the disease complexity and successful adaptation of PaLCD in India. For this, we retrieved 44 DNA-A and 26 betasatellite sequences from GenBank reported from India. An uneven distribution of evolutionary divergence has been observed using the maximum-likelihood algorithm across the branch length. Although there were phylogenetic differences, we found high rates of nucleotide substitution mutation in both viral and sub-viral genome datasets. We demonstrated frequent recombination of begomovirus species, with a maximum in intra-species recombinants. Furthermore, our results showed a high degree of genetic variability, demographic selection, and mean substitution rate acting on the population, supporting the emergence of a diverse and purifying selection of viruses and associated betasatellites. Moreover, variation in the genetic composition of all begomovirus datasets revealed a predominance of nucleotide diversity principally driven by mutation, which might further accelerate the advent of new strains and species and their adaption to various hosts with unique pathogenicity. Therefore, the finding of genetic variation and selection emphases on factors that contribute to the universal spread and evolution of Begomovirus and this unanticipated diversity may also provide guidelines toward future evolutionary trend analyses and the development of wide-ranging disease control strategies for begomoviruses associated with PaLCD.
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Affiliation(s)
- Aarshi Srivastava
- Department of Biotechnology, D.D.U. Gorakhpur University, Gorakhpur, India
| | - Vineeta Pandey
- Department of Biotechnology, D.D.U. Gorakhpur University, Gorakhpur, India
| | - Anurag Kumar Sahu
- International Center for Genetic Engineering and Biotechnology, New Delhi, India
| | - Dinesh Yadav
- Department of Biotechnology, D.D.U. Gorakhpur University, Gorakhpur, India
| | - Abdullah M. Al-Sadi
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khod, Oman
| | - Muhammad Shafiq Shahid
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khod, Oman
- *Correspondence: Muhammad Shafiq Shahid,
| | - R. K. Gaur
- Department of Biotechnology, D.D.U. Gorakhpur University, Gorakhpur, India
- R. K. Gaur,
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Mishra M, Verma RK, Pandey V, Srivastava A, Sharma P, Gaur R, Ali A. Role of Diversity and Recombination in the Emergence of Chilli Leaf Curl Virus. Pathogens 2022; 11:pathogens11050529. [PMID: 35631050 PMCID: PMC9146097 DOI: 10.3390/pathogens11050529] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/16/2022] [Accepted: 04/27/2022] [Indexed: 02/01/2023] Open
Abstract
Chilli leaf curl virus (ChiLCV), (Genus Begomovirus, family Geminiviridae) and associated satellites pose a serious threat to chilli production, worldwide. This study highlights the factors accountable for genetic diversity, recombination, and evolution of ChiLCV, and associated chilli leaf curl alphasatellite (ChiLCA) and chilli leaf curl betasatellite (ChiLCB). Phylogenetic analysis of complete genome (DNA-A) sequences of 132 ChiLCV isolates from five countries downloaded from NCBI database clustered into three major clades and showed high population diversity. The dN/dS ratio and Tajima D value of all viral DNA-A and associated betasatellite showed selective control on evolutionary relationships. Negative values of neutrality tests indicated purified selection and an excess of low-frequency polymorphism. Nucleotide diversity (π) for C4 and Rep genes was higher than other genes of ChiLCV with an average value of π = 18.37 × 10−2 and π = 17.52 × 10−2 respectively. A high number of mutations were detected in TrAP and Rep genes, while ChiLCB has a greater number of mutations than ChiLCA. In addition, significant recombination breakpoints were detected in all regions of ChiLCV genome, ChiLCB and, ChiLCA. Our findings indicate that ChiLCV has the potential for rapid evolution and adaptation to a range of geographic conditions and could be adopted to infect a wide range of crops, including diverse chilli cultivars.
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Affiliation(s)
- Megha Mishra
- Department of Biosciences, School of Liberal Arts and Sciences, Mody University of Science and Technology, Lakshmangarh, Sikar 332311, Rajasthan, India; (M.M.); (R.K.V.)
| | - Rakesh Kumar Verma
- Department of Biosciences, School of Liberal Arts and Sciences, Mody University of Science and Technology, Lakshmangarh, Sikar 332311, Rajasthan, India; (M.M.); (R.K.V.)
| | - Vineeta Pandey
- Department of Biotechnology, D.D.U. Gorakhpur University, Gorakhpur 273006, Uttar Pradesh, India; (V.P.); (A.S.)
| | - Aarshi Srivastava
- Department of Biotechnology, D.D.U. Gorakhpur University, Gorakhpur 273006, Uttar Pradesh, India; (V.P.); (A.S.)
| | - Pradeep Sharma
- Department of Biotechnology, ICAR—Indian Institute of Wheat & Barley Research, Agarsain Road, Karnal 132001, Haryana, India;
| | - Rajarshi Gaur
- Department of Biotechnology, D.D.U. Gorakhpur University, Gorakhpur 273006, Uttar Pradesh, India; (V.P.); (A.S.)
- Correspondence: (R.G.); (A.A.); Tel.: +1-918-631-2018 (A.A.)
| | - Akhtar Ali
- Department of Biological Science, The University of Tulsa, 800 S Tucker Drive, Tulsa, OK 74104-3189, USA
- Correspondence: (R.G.); (A.A.); Tel.: +1-918-631-2018 (A.A.)
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18
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Pandey V, Srivastava A, Mishra M, Gaur RK. Chilli leaf curl disease populations in India are highly recombinant, and rapidly segregated. 3 Biotech 2022; 12:83. [PMID: 35251885 PMCID: PMC8882514 DOI: 10.1007/s13205-022-03139-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 02/02/2022] [Indexed: 11/01/2022] Open
Abstract
Capsicum annuum, a valuable spice and vegetable crop belonging to the Solanaceae family, is extensively grown across the Indian subcontinent. Chilli production is restricted by a begomoviral infection named as chilli leaf curl disease (ChiLCD) mainly in tropical and subtropical regions which leads to considerable economic losses, thus affecting chilli cultivation. Here, we studied the genetic diversity with structural evaluation of chilli leaf curl disease and satellite molecules infecting Chilli in India. We retrieved 121 reference sequences of ChiLCD including DNA-A, DNA-B, beta-satellite and alpha-satellites from GenBank reported from India. The population diversity and genetic variation were estimated through various parameters which decipher the four major groups of phylogenetic divergence for DNA-A and five groups of beta-satellite showing percentage similarity with isolates within and across India. Further, transitional and transversional bias for ORFs were observed highest in C4 and REn genes, respectively, and for DNA-A and DNA-B, these values were 1.07 and 1.22, respectively. The recombination breakpoints for DNA-A were estimated 49 majorly in V1, C1,C2 and C4 genome region and highest 22 breakpoints were determined for Rep (AC1) of ORFs, similarly 9 events for beta-satellite were found less around βC1ORF. Moreover, the evolution and genetic variability were also contributed through parameters such as nucleotide substitution which were found within the range of RNA viruses for DNA-A, DNA-B, for all 6 ORFs (relaxed clock) and beta-satellite. Additionally, total numbers of mutations (η) for DNA-A, DNA-B, alpha-satellites and beta-satellites were 2505, 419, 807 and 1288 detected, respectively, while it was found 987 highest for Rep gene among all ORFs. Further, neutrality tests determine the dominant nature of population expansion and purifying selection for all the genes of begomovirus associated with ChiLCD and satellite molecules supporting conserved nature of gene. The combined Tajima's D and Fu and Li'S D* negative values in tests indicated that population are under purified selection and an excess of low-frequency polymorphism. Our analysis indicates the potential contribution of genetic mutations and recombination of ChiLCD which leads to rapid adaptation and evolution of begomovirus and its satellite molecules accelerating its host range and diversity within and across the Indian subcontinent. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-022-03139-w.
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Affiliation(s)
- Vineeta Pandey
- grid.411985.00000 0001 0662 4146Department of Biotechnology, D.D.U. Gorakhpur University, Gorakhpur, Uttar Pradesh 273009 India
| | - Aarshi Srivastava
- grid.411985.00000 0001 0662 4146Department of Biotechnology, D.D.U. Gorakhpur University, Gorakhpur, Uttar Pradesh 273009 India
| | - Megha Mishra
- grid.444560.70000 0004 1793 810XDepartment of Biosciences, Mody University of Science and Technology, Lakshmangarh, Sikar, Rajasthan 332311 India
| | - R. K. Gaur
- grid.411985.00000 0001 0662 4146Department of Biotechnology, D.D.U. Gorakhpur University, Gorakhpur, Uttar Pradesh 273009 India
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Rieux A, Campos P, Duvermy A, Scussel S, Martin D, Gaudeul M, Lefeuvre P, Becker N, Lett JM. Contribution of historical herbarium small RNAs to the reconstruction of a cassava mosaic geminivirus evolutionary history. Sci Rep 2021; 11:21280. [PMID: 34711837 PMCID: PMC8553777 DOI: 10.1038/s41598-021-00518-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 10/13/2021] [Indexed: 12/30/2022] Open
Abstract
Emerging viral diseases of plants are recognised as a growing threat to global food security. However, little is known about the evolutionary processes and ecological factors underlying the emergence and success of viruses that have caused past epidemics. With technological advances in the field of ancient genomics, it is now possible to sequence historical genomes to provide a better understanding of viral plant disease emergence and pathogen evolutionary history. In this context, herbarium specimens represent a valuable source of dated and preserved material. We report here the first historical genome of a crop pathogen DNA virus, a 90-year-old African cassava mosaic virus (ACMV), reconstructed from small RNA sequences bearing hallmarks of small interfering RNAs. Relative to tip-calibrated dating inferences using only modern data, those performed with the historical genome yielded both molecular evolution rate estimates that were significantly lower, and lineage divergence times that were significantly older. Crucially, divergence times estimated without the historical genome appeared in discordance with both historical disease reports and the existence of the historical genome itself. In conclusion, our study reports an updated time-frame for the history and evolution of ACMV and illustrates how the study of crop viral diseases could benefit from natural history collections.
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Affiliation(s)
- Adrien Rieux
- CIRAD, UMR PVBMT, 97410, St Pierre, La Réunion, France.
| | - Paola Campos
- CIRAD, UMR PVBMT, 97410, St Pierre, La Réunion, France
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 Rue Cuvier, CP 50, 75005, Paris, France
| | | | - Sarah Scussel
- CIRAD, UMR PVBMT, 97410, St Pierre, La Réunion, France
| | - Darren Martin
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, Cape Town, South Africa
| | - Myriam Gaudeul
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 Rue Cuvier, CP 50, 75005, Paris, France
- Herbier national (P), Muséum national d'Histoire Naturelle, CP39, 57 Rue Cuvier, 75005, Paris, France
| | | | - Nathalie Becker
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 Rue Cuvier, CP 50, 75005, Paris, France
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20
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Aimone CD, De León L, Dallas MM, Ndunguru J, Ascencio-Ibáñez JT, Hanley-Bowdoin L. A New Type of Satellite Associated with Cassava Mosaic Begomoviruses. J Virol 2021; 95:e0043221. [PMID: 34406866 PMCID: PMC8513466 DOI: 10.1128/jvi.00432-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 08/10/2021] [Indexed: 12/29/2022] Open
Abstract
Cassava mosaic disease (CMD), which is caused by single-stranded DNA begomoviruses, severely limits cassava production across Africa. A previous study showed that CMD symptom severity and viral DNA accumulation increase in cassava in the presence of a DNA sequence designated SEGS-2 (sequence enhancing geminivirus symptoms). We report here that when SEGS-2 is coinoculated with African cassava mosaic virus (ACMV) onto Arabidopsis thaliana, viral symptoms increase. Transgenic Arabidopsis with an integrated copy of SEGS-2 inoculated with ACMV also display increased symptom severity and viral DNA levels. Moreover, SEGS-2 enables Cabbage leaf curl virus (CaLCuV) to infect a geminivirus-resistant Arabidopsis thaliana accession. Although SEGS-2 is related to cassava genomic sequences, an earlier study showed that it occurs as episomes and is packaged into virions in CMD-infected cassava and viruliferous whiteflies. We identified SEGS-2 episomes in SEGS-2 transgenic Arabidopsis. The episomes occur as both double-stranded and single-stranded DNA, with the single-stranded form packaged into virions. In addition, SEGS-2 episomes replicate in tobacco protoplasts in the presence, but not the absence, of ACMV DNA-A. SEGS-2 episomes contain a SEGS-2 derived promoter and an open reading frame with the potential to encode a 75-amino acid protein. An ATG mutation at the beginning of the SEGS-2 coding region does not enhance ACMV infection in A. thaliana. Together, the results established that SEGS-2 is a new type of begomovirus satellite that enhances viral disease through the action of an SEGS-2-encoded protein that may also be encoded by the cassava genome. IMPORTANCE Cassava is an important root crop in the developing world and a food and income crop for more than 300 million African farmers. Cassava is rising in global importance and trade as the demands for biofuels and commercial starch increase. More than half of the world's cassava is produced in Africa, where it is primarily grown by smallholder farmers, many of whom are from the poorest villages. Although cassava can grow under high temperature, drought, and poor soil conditions, its production is severely limited by viral diseases. Cassava mosaic disease (CMD) is one of the most important viral diseases of cassava and can cause up to 100% yield losses. We provide evidence that SEGS-2, which was originally isolated from cassava crops displaying severe and atypical CMD symptoms in Tanzanian fields, is a novel begomovirus satellite that can compromise the development of durable CMD resistance.
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Affiliation(s)
- Catherine D. Aimone
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Leandro De León
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, USA
| | - Mary M. Dallas
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | | | - José T. Ascencio-Ibáñez
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, USA
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
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Crespo-Bellido A, Hoyer JS, Dubey D, Jeannot RB, Duffy S. Interspecies Recombination Has Driven the Macroevolution of Cassava Mosaic Begomoviruses. J Virol 2021; 95:e0054121. [PMID: 34106000 PMCID: PMC8354330 DOI: 10.1128/jvi.00541-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/01/2021] [Indexed: 11/20/2022] Open
Abstract
Begomoviruses (family Geminiviridae, genus Begomovirus) significantly hamper crop production and threaten food security around the world. The frequent emergence of new begomovirus genotypes is facilitated by high mutation frequencies and the propensity to recombine and reassort. Homologous recombination has been especially implicated in the emergence of novel cassava mosaic begomovirus (CMB) genotypes, which cause cassava mosaic disease (CMD). Cassava (Manihot esculenta) is a staple food crop throughout Africa and an important industrial crop in Asia, two continents where production is severely constrained by CMD. The CMD species complex is comprised of 11 bipartite begomovirus species with ample distribution throughout Africa and the Indian subcontinent. While recombination is regarded as a frequent occurrence for CMBs, a revised, systematic assessment of recombination and its impact on CMB phylogeny is currently lacking. We assembled data sets of all publicly available, full-length DNA-A (n = 880) and DNA-B (n = 369) nucleotide sequences from the 11 recognized CMB species. Phylogenetic networks and complementary recombination detection methods revealed extensive recombination among the CMB sequences. Six out of the 11 species descended from unique interspecies recombination events. Estimates of recombination and mutation rates revealed that all species experience mutation more frequently than recombination, but measures of population divergence indicate that recombination is largely responsible for the genetic differences between species. Our results support that recombination has significantly impacted the CMB phylogeny and has driven speciation in the CMD species complex. IMPORTANCE Cassava mosaic disease (CMD) is a significant threat to cassava production throughout Africa and Asia. CMD is caused by a complex comprised of 11 recognized virus species exhibiting accelerated rates of evolution, driven by high frequencies of mutation and genetic exchange. Here, we present a systematic analysis of the contribution of genetic exchange to cassava mosaic virus species-level diversity. Most of these species emerged as a result of genetic exchange. This is the first study to report the significant impact of genetic exchange on speciation in a group of viruses.
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Affiliation(s)
- Alvin Crespo-Bellido
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers State University of New Jersey, New Brunswick, New Jersey, USA
| | - J. Steen Hoyer
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers State University of New Jersey, New Brunswick, New Jersey, USA
| | - Divya Dubey
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers State University of New Jersey, New Brunswick, New Jersey, USA
| | - Ronica B. Jeannot
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers State University of New Jersey, New Brunswick, New Jersey, USA
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers State University of New Jersey, New Brunswick, New Jersey, USA
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22
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Kinship networks of seed exchange shape spatial patterns of plant virus diversity. Nat Commun 2021; 12:4505. [PMID: 34301941 PMCID: PMC8302746 DOI: 10.1038/s41467-021-24720-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 06/28/2021] [Indexed: 12/02/2022] Open
Abstract
By structuring farmers’ informal networks of seed exchange, kinship systems play a key role in the dynamics of crop genetic diversity in smallholder farming systems. However, because many crop diseases are propagated through infected germplasm, local seed systems can also facilitate the dissemination of seedborne pathogens. Here, we investigate how the interplay of kinship systems and local networks of germplasm exchange influences the metapopulation dynamics of viruses responsible for the cassava mosaic disease (CMD), a major threat to food security in Africa. Combining anthropological, genetic and plant epidemiological data, we analyzed the genetic structure of local populations of the African cassava mosaic virus (ACMV), one of the main causal agents of CMD. Results reveal contrasted patterns of viral diversity in patrilineal and matrilineal communities, consistent with local modes of seed exchange. Our results demonstrate that plant virus ecosystems have also a cultural component and that social factors that shape regional seed exchange networks influence the genetic structure of plant virus populations. This study combines ethnobotanical and epidemiological data to understand how social networks of seed exchange influence the genetic structure of the African cassava mosaic virus in Gabon. Results reveal contrasted patterns of viral diversity in patrilineal and matrilineal communities, consistent with cultural differences in modes of seed exchange.
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23
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Aimone CD, Lavington E, Hoyer JS, Deppong DO, Mickelson-Young L, Jacobson A, Kennedy GG, Carbone I, Hanley-Bowdoin L, Duffy S. Population diversity of cassava mosaic begomoviruses increases over the course of serial vegetative propagation. J Gen Virol 2021; 102:001622. [PMID: 34310272 PMCID: PMC8491896 DOI: 10.1099/jgv.0.001622] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 06/05/2021] [Indexed: 01/06/2023] Open
Abstract
Cassava mosaic disease (CMD) represents a serious threat to cassava, a major root crop for more than 300 million Africans. CMD is caused by single-stranded DNA begomoviruses that evolve rapidly, making it challenging to develop durable disease resistance. In addition to the evolutionary forces of mutation, recombination and reassortment, factors such as climate, agriculture practices and the presence of DNA satellites may impact viral diversity. To gain insight into the factors that alter and shape viral diversity in planta, we used high-throughput sequencing to characterize the accumulation of nucleotide diversity after inoculation of infectious clones corresponding to African cassava mosaic virus (ACMV) and East African cassava mosaic Cameroon virus (EACMCV) in the susceptible cassava landrace Kibandameno. We found that vegetative propagation had a significant effect on viral nucleotide diversity, while temperature and a satellite DNA did not have measurable impacts in our study. EACMCV diversity increased linearly with the number of vegetative propagation passages, while ACMV diversity increased for a time and then decreased in later passages. We observed a substitution bias toward C→T and G→A for mutations in the viral genomes consistent with field isolates. Non-coding regions excluding the promoter regions of genes showed the highest levels of nucleotide diversity for each genome component. Changes in the 5' intergenic region of DNA-A resembled the sequence of the cognate DNA-B sequence. The majority of nucleotide changes in coding regions were non-synonymous, most with predicted deleterious effects on protein structure, indicative of relaxed selection pressure over six vegetative passages. Overall, these results underscore the importance of knowing how cropping practices affect viral evolution and disease progression.
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Affiliation(s)
- Catherine D. Aimone
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh NC 27695, USA
| | - Erik Lavington
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USA
| | - J. Steen Hoyer
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USA
| | - David O. Deppong
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh NC 27695, USA
| | - Leigh Mickelson-Young
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh NC 27695, USA
| | - Alana Jacobson
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA
| | - George G. Kennedy
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
| | - Ignazio Carbone
- Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh NC 27695, USA
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh NC 27695, USA
| | - Siobain Duffy
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USA
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24
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Xavier CAD, Godinho MT, Mar TB, Ferro CG, Sande OFL, Silva JC, Ramos-Sobrinho R, Nascimento RN, Assunção I, Lima GSA, Lima ATM, Murilo Zerbini F. Evolutionary dynamics of bipartite begomoviruses revealed by complete genome analysis. Mol Ecol 2021; 30:3747-3767. [PMID: 34021651 DOI: 10.1111/mec.15997] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 05/07/2021] [Accepted: 05/14/2021] [Indexed: 12/17/2022]
Abstract
Several key evolutionary events marked the evolution of geminiviruses, culminating with the emergence of divided (bipartite) genomes represented by viruses classified in the genus Begomovirus. This genus represents the most abundant group of multipartite viruses, contributing significantly to the observed abundance of multipartite species in the virosphere. Although aspects related to virus-host interactions and evolutionary dynamics have been extensively studied, the bipartite nature of these viruses has been little explored in evolutionary studies. Here, we performed a parallel evolutionary analysis of the DNA-A and DNA-B segments of New World begomoviruses. A total of 239 full-length DNA-B sequences obtained in this study, combined with 292 DNA-A and 76 DNA-B sequences retrieved from GenBank, were analysed. The results indicate that the DNA-A and DNA-B respond differentially to evolutionary processes, with the DNA-B being more permissive to variation and more prone to recombination than the DNA-A. Although a clear geographic segregation was observed for both segments, differences in the genetic structure between DNA-A and DNA-B were also observed, with cognate segments belonging to distinct genetic clusters. DNA-B coding regions evolve under the same selection pressures than DNA-A coding regions. Together, our results indicate an interplay between reassortment and recombination acting at different levels across distinct subpopulations and segments.
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Affiliation(s)
- César A D Xavier
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Márcio T Godinho
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Talita B Mar
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Camila G Ferro
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Osvaldo F L Sande
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - José C Silva
- Dep. de Bioquímica e Biologia Molecular/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Roberto Ramos-Sobrinho
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Renato N Nascimento
- Centro de Ciências Agrárias/Fitossanidade, Universidade Federal de Alagoas, Rio Largo, Alagoas, Brazil
| | - Iraildes Assunção
- Centro de Ciências Agrárias/Fitossanidade, Universidade Federal de Alagoas, Rio Largo, Alagoas, Brazil
| | - Gaus S A Lima
- Centro de Ciências Agrárias/Fitossanidade, Universidade Federal de Alagoas, Rio Largo, Alagoas, Brazil
| | - Alison T M Lima
- Instituto de Ciências Agrárias, Universidade Federal de Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - F Murilo Zerbini
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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25
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Farooq T, Umar M, She X, Tang Y, He Z. Molecular phylogenetics and evolutionary analysis of a highly recombinant begomovirus, Cotton leaf curl Multan virus, and associated satellites. Virus Evol 2021; 7:veab054. [PMID: 34532058 PMCID: PMC8438885 DOI: 10.1093/ve/veab054] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/24/2021] [Accepted: 06/04/2021] [Indexed: 11/12/2022] Open
Abstract
Cotton leaf curl Multan virus (CLCuMuV) and its associated satellites are a major part of the cotton leaf curl disease (CLCuD) caused by the begomovirus species complex. Despite the implementation of potential disease management strategies, the incessant resurgence of resistance-breaking variants of CLCuMuV imposes a continuous threat to cotton production. Here, we present a focused effort to map the geographical prevalence, genomic diversity, and molecular evolutionary endpoints that enhance disease complexity by facilitating the successful adaptation of CLCuMuV populations to the diversified ecosystems. Our results demonstrate that CLCuMuV populations are predominantly distributed in China, while the majority of alphasatellites and betasatellites exist in Pakistan. We demonstrate that together with frequent recombination, an uneven genetic variation mainly drives CLCuMuV and its satellite's virulence and evolvability. However, the pattern and distribution of recombination breakpoints greatly vary among viral and satellite sequences. The CLCuMuV, Cotton leaf curl Multan alphasatellite, and Cotton leaf curl Multan betasatellite populations arising from distinct regions exhibit high mutation rates. Although evolutionarily linked, these populations are independently evolving under strong purifying selection. These findings will facilitate to comprehensively understand the standing genetic variability and evolutionary patterns existing among CLCuMuV populations across major cotton-producing regions of the world.
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Affiliation(s)
- Tahir Farooq
- Plant Protection Research Institute and Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P.R. China
| | - Muhammad Umar
- Tasmanian Institute of Agriculture, New Town Research Laboratories, University of Tasmania, 13 St. Johns Avenue, New Town, TAS 7008, Australia
| | - Xiaoman She
- Plant Protection Research Institute and Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P.R. China
| | - Yafei Tang
- Plant Protection Research Institute and Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P.R. China
| | - Zifu He
- Plant Protection Research Institute and Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P.R. China
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26
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Maliano MR, Macedo MA, Rojas MR, Gilbertson RL. Weed-infecting viruses in a tropical agroecosystem present different threats to crops and evolutionary histories. PLoS One 2021; 16:e0250066. [PMID: 33909644 PMCID: PMC8081230 DOI: 10.1371/journal.pone.0250066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/30/2021] [Indexed: 01/21/2023] Open
Abstract
In the Caribbean Basin, malvaceous weeds commonly show striking golden/yellow mosaic symptoms. Leaf samples from Malachra sp. and Abutilon sp. plants with these symptoms were collected in Hispaniola from 2014 to 2020. PCR tests with degenerate primers revealed that all samples were infected with a bipartite begomovirus, and sequence analyses showed that Malachra sp. plants were infected with tobacco leaf curl Cuba virus (TbLCuCV), whereas the Abutilon sp. plants were infected with a new bipartite begomovirus, tentatively named Abutilon golden yellow mosaic virus (AbGYMV). Phylogenetic analyses showed that TbLCuCV and AbGYMV are distinct but closely related species, which are most closely related to bipartite begomoviruses infecting weeds in the Caribbean Basin. Infectious cloned DNA-A and DNA-B components were used to fulfilled Koch's postulates for these diseases of Malachra sp. and Abutilon sp. In host range studies, TbLCuCV also induced severe symptoms in Nicotiana benthamiana, tobacco and common bean plants; whereas AbGYMV induced few or no symptoms in plants of these species. Pseudorecombinants generated with the infectious clones of these viruses were highly infectious and induced severe symptoms in N. benthamiana and Malachra sp., and both viruses coinfected Malachra sp., and possibly facilitating virus evolution via recombination and pseudorecombination. Together, our results suggest that TbLCuCV primarily infects Malachra sp. in the Caribbean Basin, and occasionally spills over to infect and cause disease in crops; whereas AbGYMV is well-adapted to an Abutilon sp. in the Dominican Republic and has not been reported infecting crops.
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Affiliation(s)
- Minor R. Maliano
- Department of Plant Pathology, University of California, Davis, California, United States of America
| | - Mônica A. Macedo
- Department of Plant Pathology, University of California, Davis, California, United States of America
- Federal Institute of Education, Science and Technology Goiano, Campus Urutaí, Goias, Brazil
| | - Maria R. Rojas
- Department of Plant Pathology, University of California, Davis, California, United States of America
| | - Robert L. Gilbertson
- Department of Plant Pathology, University of California, Davis, California, United States of America
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27
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Avedi EK, Adediji AO, Kilalo DC, Olubayo FM, Macharia I, Ateka EM, Machuka EM, Mutuku JM. Metagenomic analyses and genetic diversity of Tomato leaf curl Arusha virus affecting tomato plants in Kenya. Virol J 2021; 18:2. [PMID: 33407584 PMCID: PMC7789182 DOI: 10.1186/s12985-020-01466-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/04/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tomato production is threatened worldwide by the occurrence of begomoviruses which are associated with tomato leaf curl diseases. There is little information on the molecular properties of tomato begomoviruses in Kenya, hence we investigated the population and genetic diversity of begomoviruses associated with tomato leaf curl in Kenya. METHODS Tomato leaf samples with virus-like symptoms were obtained from farmers' field across the country in 2018 and Illumina sequencing undertaken to determine the genetic diversity of associated begomoviruses. Additionally, the occurrence of selection pressure and recombinant isolates within the population were also evaluated. RESULTS Twelve complete begomovirus genomes were obtained from our samples with an average coverage of 99.9%. The sequences showed 95.7-99.7% identity among each other and 95.9-98.9% similarities with a Tomato leaf curl virus Arusha virus (ToLCArV) isolate from Tanzania. Analysis of amino acid sequences showed the highest identities in the regions coding for the coat protein gene (98.5-100%) within the isolates, and 97.1-100% identity with the C4 gene of ToLCArV. Phylogenetic algorithms clustered all Kenyan isolates in the same clades with ToLCArV, thus confirming the isolates to be a variant of the virus. There was no evidence of recombination within our isolates. Estimation of selection pressure within the virus population revealed the occurrence of negative or purifying selection in five out of the six coding regions of the sequences. CONCLUSIONS The begomovirus associated with tomato leaf curl diseases of tomato in Kenya is a variant of ToLCArV, possibly originating from Tanzania. There is low genetic diversity within the virus population and this information is useful in the development of appropriate management strategies for the disease in the country.
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Affiliation(s)
- Edith Khamonya Avedi
- Department of Phytosanitary Services and Biosafety, Kenya Plant Health Inspectorate Service, Nairobi, Kenya. .,Department of Plant Science and Crop Protection, University of Nairobi, Nairobi, Kenya. .,Biosciences Eastern and Central Africa, International Livestock Research Institute, Nairobi, Kenya.
| | - Adedapo Olutola Adediji
- Department of Crop Protection and Environmental Biology, Faculty of Agriculture, University of Ibadan, Ibadan, Nigeria.
| | - Dora Chao Kilalo
- Department of Plant Science and Crop Protection, University of Nairobi, Nairobi, Kenya
| | | | - Isaac Macharia
- Department of Phytosanitary Services and Biosafety, Kenya Plant Health Inspectorate Service, Nairobi, Kenya
| | - Elijah Miinda Ateka
- Department of Horticulture and Food Security, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Eunice Magoma Machuka
- Biosciences Eastern and Central Africa, International Livestock Research Institute, Nairobi, Kenya
| | - Josiah Musembi Mutuku
- Biosciences Eastern and Central Africa, International Livestock Research Institute, Nairobi, Kenya.,Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK.,The Central and West African Virus Epidemiology (WAVE), Pôle Scientifique et d'Innovation de Bingerville, Université Félix Houphouët-Boigny, Abidjan, Côte d'Ivoire
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28
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Pinto VB, Quadros AFF, Godinho MT, Silva JC, Alfenas-Zerbini P, Zerbini FM. Intra-host evolution of the ssDNA virus tomato severe rugose virus (ToSRV). Virus Res 2020; 292:198234. [PMID: 33232784 DOI: 10.1016/j.virusres.2020.198234] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/10/2020] [Accepted: 11/13/2020] [Indexed: 01/17/2023]
Abstract
To evaluate and quantify the evolutionary dynamics of the bipartite begomovirus tomato severe rugose virus (ToSRV) in a cultivated and a non-cultivated host, plants of tomato and Nicandra physaloides were biolistically inoculated with an infectious clone and systemically infected leaves were sampled at 30, 75 and 120 days after inoculation. Total DNA was extracted and sequenced in the Illumina HiSeq 2000 platform. The datasets were trimmed with the quality score limit set to 0.01, and the assembly was performed using the infectious clone sequence as reference. SNPs were filtered using a minimum p-value of 0.001 and the sum frequencies were used to calculate the deviation from the original clone sequence. Nucleotide substitution rates were calculated for the two DNA components in both hosts: 1.73 × 10-3 and 3.07 × 10-4 sub/site/year for the DNA-A and DNA-B, respectively, in N. physaloides, and 8.05 × 10-4 and 7.02 × 10-5 sub/site/year the for DNA-A and DNA-B, respectively, in tomato. These values are in the same range of those estimated for viruses with single-stranded RNA genomes and for other begomoviruses. Strikingly, the number of substitutions decreased over time, suggesting the presence of bottlenecks during systemic infection. Determination of Shannon's entropy indicated different patterns of variation in the DNA-A and the DNA-B, suggesting distinct evolutionary forces acting upon each component.
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Affiliation(s)
- Vitor Batista Pinto
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil; National Research Institute for Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Ayane Fernanda Ferreira Quadros
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil; National Research Institute for Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Márcio Tadeu Godinho
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil; National Research Institute for Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - José Cleydson Silva
- National Research Institute for Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Poliane Alfenas-Zerbini
- National Research Institute for Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil; Dep. de Microbiologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - F Murilo Zerbini
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil; National Research Institute for Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil.
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29
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Sun S, Hu Y, Jiang G, Tian Y, Ding M, Yu C, Zhou X, Qian Y. Molecular Characterization and Genomic Function of Grapevine Geminivirus A. Front Microbiol 2020; 11:555194. [PMID: 32983075 PMCID: PMC7493466 DOI: 10.3389/fmicb.2020.555194] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/12/2020] [Indexed: 11/20/2022] Open
Abstract
A new grapevine geminivirus A (GGVA) isolate (named as GGVA-17YM1) and its associated defective genome (GGVA-D) were identified from a grapevine sample collected in Yuanmou, Yunnan Province, using sRNA high throughput sequencing and traditional Sanger sequencing. To explore the pathogenicity of GGVA and GGVA-D, infectious clones of GGVA-17YM1 and GGVA-D-17YM1 were constructed. Infection assays indicated that Nicotiana benthamiana plants inoculated with GGVA alone or a combination of GGVA and GGVA-D exhibited upward curled apical leaves and dwarfism. Southern blotting and quantitative real-time polymerase chain reaction analysis revealed that GGVA-D increased the accumulation level of GGVA DNA. Transient expression using a PVX-derived recombinant vector indicated that C2 and C4 encoded by GGVA are involved in symptom induction in N. benthamiana. Furthermore, the V2 protein inhibited local RNA silencing in co-infiltration assays in GFP transgenic N. benthamiana plants. Subsequently, full-length genome sequencing resulted in the identification of 11 different isolates of GGVA and 9 associated defective DNA molecules. Phylogenetic analysis based on whole genome sequences showed that all GGVA isolates, including our sequences, clustered into two distinct branches with no geographical grouping. Analyses of molecular variation indicated single nucleotide polymorphisms (SNPs) with more transitions (55.97%) than transversions (44.03%). Furthermore, the main variants for ORF C1, C3, or V1 were synonymous mutations, and non-synonymous mutations for ORF C2, C4, and V2. Genetic selection analysis indicated that negative selection acted on four ORFs (V1, C1, C2, and C3), while V2 and C4 were under positive selection. Our results contribute to the characterization of the genetic diversity of GGVA and provide insights into its pathogenicity.
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Affiliation(s)
- Suwei Sun
- Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Ya Hu
- Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | | | - Yimin Tian
- Technical Center for Animal, Plant and Food Inspection and Quarantine, Shanghai Customs District, Shanghai, China
| | - Ming Ding
- Institute of Biotechnology and Germplasm Resources, Yunnan Academy of Agricultural Science, Kunming, China
| | - Cui Yu
- Technical Center for Animal, Plant and Food Inspection and Quarantine, Shanghai Customs District, Shanghai, China
| | - Xueping Zhou
- Institute of Biotechnology, Zhejiang University, Hangzhou, China.,Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yajuan Qian
- Institute of Biotechnology, Zhejiang University, Hangzhou, China
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30
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Godfroid M, Dagan T, Merker M, Kohl TA, Diel R, Maurer FP, Niemann S, Kupczok A. Insertion and deletion evolution reflects antibiotics selection pressure in a Mycobacterium tuberculosis outbreak. PLoS Pathog 2020; 16:e1008357. [PMID: 32997707 PMCID: PMC7549793 DOI: 10.1371/journal.ppat.1008357] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 10/12/2020] [Accepted: 08/18/2020] [Indexed: 11/18/2022] Open
Abstract
In genome evolution, genetic variants are the source of diversity, which natural selection acts upon. Treatment of human tuberculosis (TB) induces a strong selection pressure for the emergence of antibiotic resistance-conferring variants in the infecting Mycobacterium tuberculosis (MTB) strains. MTB evolution in response to treatment has been intensively studied and mainly attributed to point substitutions. However, the frequency and contribution of insertions and deletions (indels) to MTB genome evolution remains poorly understood. Here, we analyzed a multi-drug resistant MTB outbreak for the presence of high-quality indels and substitutions. We find that indels are significantly enriched in genes conferring antibiotic resistance. Furthermore, we show that indels are inherited during the outbreak and follow a molecular clock with an evolutionary rate of 5.37e-9 indels/site/year, which is 23 times lower than the substitution rate. Inherited indels may co-occur with substitutions in genes along related biological pathways; examples are iron storage and resistance to second-line antibiotics. This suggests that epistatic interactions between indels and substitutions affect antibiotic resistance and compensatory evolution in MTB.
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Affiliation(s)
- Maxime Godfroid
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Tal Dagan
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Thomas A. Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Roland Diel
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Institute for Epidemiology, University Medical Hospital Schleswig-Holstein, Kiel, Germany
- Lungenclinic Grosshansdorf, Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Großhansdorf, Germany
| | - Florian P. Maurer
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Anne Kupczok
- Institute of General Microbiology, Kiel University, Kiel, Germany
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Miozzi L, Vaira AM, Brilli F, Casarin V, Berti M, Ferrandino A, Nerva L, Accotto GP, Lanfranco L. Arbuscular Mycorrhizal Symbiosis Primes Tolerance to Cucumber Mosaic Virus in Tomato. Viruses 2020; 12:E675. [PMID: 32580438 PMCID: PMC7354615 DOI: 10.3390/v12060675] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 06/19/2020] [Accepted: 06/20/2020] [Indexed: 01/30/2023] Open
Abstract
Tomato plants can establish symbiotic interactions with arbuscular mycorrhizal fungi (AMF) able to promote plant nutrition and prime systemic plant defenses against pathogens attack; the mechanism involved is known as mycorrhiza-induced resistance (MIR). However, studies on the effect of AMF on viral infection, still limited and not conclusive, indicate that AMF colonization may have a detrimental effect on plant defenses against viruses, so that the term "mycorrhiza-induced susceptibility" (MIS) has been proposed for these cases. To expand the case studies to a not yet tested viral family, that is, Bromoviridae, we investigated the effect of the colonization by the AMF Funneliformis mosseae on cucumber mosaic virus (CMV) infection in tomato by phenotypic, physiological, biochemical, and transcriptional analyses. Our results showed that the establishment of a functional AM symbiosis is able to limit symptoms development. Physiological and transcriptomic data highlighted that AMF mitigates the drastic downregulation of photosynthesis-related genes and the reduction of photosynthetic CO2 assimilation rate caused by CMV infection. In parallel, an increase of salicylic acid level and a modulation of reactive oxygen species (ROS)-related genes, toward a limitation of ROS accumulation, was specifically observed in CMV-infected mycorrhizal plants. Overall, our data indicate that the AM symbiosis influences the development of CMV infection in tomato plants and exerts a priming effect able to enhance tolerance to viral infection.
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Affiliation(s)
- Laura Miozzi
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Torino, Strada delle Cacce 73, 10135 Torino, Italy; (A.M.V.); (V.C.); (M.B.); (L.N.); (G.P.A.)
| | - Anna Maria Vaira
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Torino, Strada delle Cacce 73, 10135 Torino, Italy; (A.M.V.); (V.C.); (M.B.); (L.N.); (G.P.A.)
| | - Federico Brilli
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Unit of Sesto Fiorentino (FI), Via Madonna del Piano 10, 50019 Sesto Fiorentino (FI), Italy;
| | - Valerio Casarin
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Torino, Strada delle Cacce 73, 10135 Torino, Italy; (A.M.V.); (V.C.); (M.B.); (L.N.); (G.P.A.)
| | - Mara Berti
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Torino, Strada delle Cacce 73, 10135 Torino, Italy; (A.M.V.); (V.C.); (M.B.); (L.N.); (G.P.A.)
| | - Alessandra Ferrandino
- Department of Agricultural, Forestry and Food Sciences, University of Torino, Largo Paolo Braccini 2, 10095 Grugliasco (TO), Italy;
| | - Luca Nerva
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Torino, Strada delle Cacce 73, 10135 Torino, Italy; (A.M.V.); (V.C.); (M.B.); (L.N.); (G.P.A.)
- Council for Agricultural Research and Economics—Research Centre for Viticulture and Enology CREA-VE, Via XXVIII Aprile 26, 31015 Conegliano (TV), Italy
| | - Gian Paolo Accotto
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Torino, Strada delle Cacce 73, 10135 Torino, Italy; (A.M.V.); (V.C.); (M.B.); (L.N.); (G.P.A.)
| | - Luisa Lanfranco
- Department of Life Sciences and Systems Biology, University of Torino, Viale Mattioli 25, 10125 Torino, Italy
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Evolutionary timescale and geographical movement of cucumber mosaic virus, with focus on Iranian strains. Arch Virol 2019; 165:185-192. [PMID: 31637514 DOI: 10.1007/s00705-019-04439-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 09/16/2019] [Indexed: 10/25/2022]
Abstract
Cucumber mosaic virus (CMV) is a geographically widespread plant virus with a very broad host range. The virus has been detected in diverse crops all over Iran. In this study, we estimated the timescale of the evolution of CMV subgroup I and the geographical movement of the virus with a focus on Iranian strains. Analyses using the MP and CP genes and their concatenation revealed that the CMV population within subgroup I had a single ancestor dating back to about 450-550 years ago. The Iranian strains formed three clusters in a maximum-clade-credibility phylogenetic tree. It was found that the most recent common ancestor of the Iranian strains within each cluster dates back to less than 100 years ago. Our results also suggest that both short- and long-distance migration of Iranian CMV strains has occurred in the last 100 years.
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Melgarejo TA, Rojas MR, Gilbertson RL. A Bipartite Begomovirus Infecting Boerhavia erecta (Family Nyctaginaceae) in the Dominican Republic Represents a Distinct Phylogenetic Lineage and has a High Degree of Host Specificity. PHYTOPATHOLOGY 2019; 109:1464-1474. [PMID: 30995160 DOI: 10.1094/phyto-02-19-0061-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Boerhavia erecta plants in and around agricultural fields in the Azua Valley of the southeastern Dominican Republic often show striking golden mosaic symptoms. Leaf samples from B. erecta plants showing these symptoms were collected in 2012 and 2013, and PCR tests with degenerate primers revealed begomovirus DNA-A and DNA-B components. The complete sequences of the DNA-A and DNA-B components of four isolates show a high degree of sequence identity (>96%) and a genome organization typical of New World (NW) bipartite begomoviruses. Sequence comparisons and phylogenetic analyses revealed that these isolates composed a new phylogenetic lineage of NW bipartite begomoviruses. The most closely related begomovirus is Merremia mosaic virus, a weed-infecting species from Puerto Rico. Because DNA-A sequence identities are well below the 91% threshold, these isolates represent a new begomovirus species, for which the name Boerhavia golden mosaic virus (BoGMV) is proposed. Infectious cloned BoGMV DNA-A and DNA-B components induced golden mosaic symptoms in agroinoculated B. erecta plants, thereby fulfilling Koch's postulates for this disease. Agroinoculation and mechanical transmission experiments revealed that BoGMV has an unusually narrow host range, limited to members of the family Nyctaginaceae and not including the permissive host Nicotiana benthamiana. The inability of BoGMV to infect N. benthamiana was due to a deficiency in cell-to-cell movement but not to a unique amino acid residue in the movement protein.
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Affiliation(s)
- Tomas A Melgarejo
- 1Department of Plant Pathology, University of California, Davis, One Shield Ave., CA 95616, U.S.A
- 2Departamento de Fitopatologia, Universidad Nacional Agraria La Molina, Av. La Molina s/n La Molina, Lima, Peru
| | - Maria R Rojas
- 1Department of Plant Pathology, University of California, Davis, One Shield Ave., CA 95616, U.S.A
| | - Robert L Gilbertson
- 1Department of Plant Pathology, University of California, Davis, One Shield Ave., CA 95616, U.S.A
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García-Arenal F, Zerbini FM. Life on the Edge: Geminiviruses at the Interface Between Crops and Wild Plant Hosts. Annu Rev Virol 2019; 6:411-433. [PMID: 31180812 DOI: 10.1146/annurev-virology-092818-015536] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Viruses constitute the largest group of emerging pathogens, and geminiviruses (plant viruses with circular, single-stranded DNA genomes) are the major group of emerging plant viruses. With their high potential for genetic variation due to mutation and recombination, their efficient spread by vectors, and their wide host range as a group, including both wild and cultivated hosts, geminiviruses are attractive models for the study of the evolutionary and ecological factors driving virus emergence. Studies on the epidemiological features of geminivirus diseases have traditionally focused primarily on crop plants. Nevertheless, knowledge of geminivirus infection in wild plants, and especially at the interface between wild and cultivated plants, is necessary to provide a complete view of their ecology, evolution, and emergence. In this review, we address the most relevant aspects of geminivirus variability and evolution in wild and crop plants and geminiviruses' potential to emerge in crops.
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Affiliation(s)
- Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas UPM-INIA and Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain;
| | - Francisco Murilo Zerbini
- Departamento de Fitopatologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), and National Research Institute for Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil;
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35
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Salvador LCM, O'Brien DJ, Cosgrove MK, Stuber TP, Schooley AM, Crispell J, Church SV, Gröhn YT, Robbe-Austerman S, Kao RR. Disease management at the wildlife-livestock interface: Using whole-genome sequencing to study the role of elk in Mycobacterium bovis transmission in Michigan, USA. Mol Ecol 2019; 28:2192-2205. [PMID: 30807679 DOI: 10.1111/mec.15061] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 01/16/2019] [Accepted: 02/14/2019] [Indexed: 12/30/2022]
Abstract
The role of wildlife in the persistence and spread of livestock diseases is difficult to quantify and control. These difficulties are exacerbated when several wildlife species are potentially involved. Bovine tuberculosis (bTB), caused by Mycobacterium bovis, has experienced an ecological shift in Michigan, with spillover from cattle leading to an endemically infected white-tailed deer (deer) population. It has potentially substantial implications for the health and well-being of both wildlife and livestock and incurs a significant economic cost to industry and government. Deer are known to act as a reservoir of infection, with evidence of M. bovis transmission to sympatric elk and cattle populations. However, the role of elk in the circulation of M. bovis is uncertain; they are few in number, but range further than deer, so may enable long distance spread. Combining Whole Genome Sequences (WGS) for M. bovis isolates from exceptionally well-observed populations of elk, deer and cattle with spatiotemporal locations, we use spatial and Bayesian phylogenetic analyses to show strong spatiotemporal admixture of M. bovis isolates. Clustering of bTB in elk and cattle suggests either intraspecies transmission within the two populations, or exposure to a common source. However, there is no support for significant pathogen transfer amongst elk and cattle, and our data are in accordance with existing evidence that interspecies transmission in Michigan is likely only maintained by deer. This study demonstrates the value of whole genome population studies of M. bovis transmission at the wildlife-livestock interface, providing insights into bTB management in an endemic system.
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Affiliation(s)
- Liliana C M Salvador
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.,Ecology and Evolutionary Biology Department, Princeton University, Princeton, New Jersey.,Royal (Dick) Veterinary School of Veterinary Studies, University of Edinburgh, Midlothian, UK.,Department of Infectious Diseases, College of Veterinary Medicine, Institute of Bioinformatics, University of Georgia, Athens, Georgia
| | - Daniel J O'Brien
- Wildlife Disease Laboratory, Michigan Department of Natural Resources, Lansing, Michigan
| | - Melinda K Cosgrove
- Wildlife Disease Laboratory, Michigan Department of Natural Resources, Lansing, Michigan
| | - Tod P Stuber
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, Iowa
| | - Angie M Schooley
- Mycobacteriology Laboratory, Infectious Disease Division, Michigan Department of Health and Human Services, Lansing, Michigan
| | - Joseph Crispell
- School of Veterinary Medicine, College of Health and Agricultural Sciences, University College Dublin, Dublin, Ireland
| | - Steven V Church
- Mycobacteriology Laboratory, Infectious Disease Division, Michigan Department of Health and Human Services, Lansing, Michigan
| | - Yrjö T Gröhn
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Suelee Robbe-Austerman
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, Iowa
| | - Rowland R Kao
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.,Royal (Dick) Veterinary School of Veterinary Studies, University of Edinburgh, Midlothian, UK
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36
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Mukiibi DR, Alicai T, Kawuki R, Okao-Okuja G, Tairo F, Sseruwagi P, Ndunguru J, Ateka EM. Resistance of advanced cassava breeding clones to infection by major viruses in Uganda. CROP PROTECTION (GUILDFORD, SURREY) 2019; 115:104-112. [PMID: 30739973 PMCID: PMC6358137 DOI: 10.1016/j.cropro.2018.09.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 09/12/2018] [Accepted: 09/24/2018] [Indexed: 05/21/2023]
Abstract
Cassava brown streak disease (CBSD) and cassava mosaic disease (CMD) are two viral diseases that cause severe yield losses in cassava of up to 100%, thereby persistently threatening food and income security in sub-Saharan Africa. For effective management of these diseases, there is a critical need to develop and deploy varieties with dual resistance to CBSD and CMD. In this study, we determined the response of advanced breeding lines to field infection by cassava brown streak viruses (CBSVs) and cassava mosaic begomoviruses (CMBs). This aim helped in identifying superior clones for downstream breeding. In total, 220 cassava clones, three in uniform yield trials (UYTs) and 217 in a crossing block trial (CBT), were evaluated for virus and disease resistance. Field data were collected on disease incidence and severity. To detect and quantify CBSVs, 448 and 128 leaf samples from CBSD symptomatic and symptomless plants were analyzed by reverse transcription PCR and real-time quantitative PCR, respectively. In addition, 93 leaf samples from CMD symptomatic plants in the CBT were analyzed by conventional PCR using CMB species-specific primers. In the CBT, 124 (57%) cassava clones did not express CMD symptoms. Of the affected plants, 44 (55%) had single African cassava mosaic virus infection. Single Cassava brown streak virus (CBSV) infections were more prevalent (81.6%) in CBT clones than single Ugandan cassava brown streak virus (UCBSV) infection (3.2%). Of the three advanced clones in the UYT, NAROCASS 1 and NAROCASS 2 had significantly lower (P < 0.05) CBSD severity, incidence, and CBSV load than MH04/0300. In the UYT, only 22% of samples tested had CBSVs, and all showed a negative result for CMBs. The low disease incidence, severity, and viral load associated with NAROCASS 1 and NAROCASS 2 is evidence of their tolerance to both CBSD and CMD. Therefore, these two cassava clones should be utilized in CBSD and CMD management in Uganda, including their utilization as progenitors in further virus resistance breeding.
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Affiliation(s)
- Daniel Rogers Mukiibi
- Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Nairobi, Kenya
- National Crops Resources Research Institute, P.O. Box 7084, Kampala, Uganda
| | - Titus Alicai
- National Crops Resources Research Institute, P.O. Box 7084, Kampala, Uganda
| | - Robert Kawuki
- National Crops Resources Research Institute, P.O. Box 7084, Kampala, Uganda
| | | | - Fred Tairo
- Mikocheni Agricultural Research Institute, P.O. Box 6226, Dar es Salaam, Tanzania
| | - Peter Sseruwagi
- Mikocheni Agricultural Research Institute, P.O. Box 6226, Dar es Salaam, Tanzania
| | - Joseph Ndunguru
- Mikocheni Agricultural Research Institute, P.O. Box 6226, Dar es Salaam, Tanzania
| | - Elijah Miinda Ateka
- Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Nairobi, Kenya
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37
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Yang X, Chen B, Zhang T, Li Z, Xu C, Zhou G. Geographic Distribution and Genetic Diversity of Rice Stripe Mosaic Virus in Southern China. Front Microbiol 2018; 9:3068. [PMID: 30619153 PMCID: PMC6295562 DOI: 10.3389/fmicb.2018.03068] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 11/28/2018] [Indexed: 01/21/2023] Open
Abstract
Rice stripe mosaic virus (RSMV) transmitted by the leafhopper Recilia dorsalis is a tentative new species in the genus Cytorhabdovirus identified recently in South China. To explore its geographic distribution and genetic diversity, field investigation and viral whole-genome sequencing were conducted in this study. The results indicated that RSMV was present in the rice samples collected across southern China. Twelve representative samples from different geographical regions were selected for viral whole-genome sequencing and the viral genome variation was analyzed in combination with a previously reported RSMV isolate. Identity analysis showed that the genome sequences of 13 RSMV isolates were highly conserved with nucleotide identities over 99.4%. There was a strong negative selection pressure during the evolution of RSMV with more transitions (72.08%) than transversions (27.92%) found between the RSMV isolates. Among the seven genes encoded by RSMV, the P gene was the most variable, followed by N, M, L, and G; the P3 and P6 amino acid sequences were not found to be mutated and no mutations were found in the non-coding region. A phylogenetic tree based on the RSMV whole-genome nucleotide sequences revealed that all RSMV isolates clustered in two groups based on geographical origin. Notably, the L proteins of the Guangxi and Hainan isolates had five and one specific amino acid sites, respectively, suggesting that the L gene has undergone environmental adaptive variation during the dispersal of RSMV.
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Affiliation(s)
- Xin Yang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Biao Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Tong Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Zhanbiao Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Chenhui Xu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Guohui Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, China
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38
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Zhao L, Rosario K, Breitbart M, Duffy S. Eukaryotic Circular Rep-Encoding Single-Stranded DNA (CRESS DNA) Viruses: Ubiquitous Viruses With Small Genomes and a Diverse Host Range. Adv Virus Res 2018; 103:71-133. [PMID: 30635078 DOI: 10.1016/bs.aivir.2018.10.001] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
While single-stranded DNA (ssDNA) was once thought to be a relatively rare genomic architecture for viruses, modern metagenomics sequencing has revealed circular ssDNA viruses in most environments and in association with diverse hosts. In particular, circular ssDNA viruses encoding a homologous replication-associated protein (Rep) have been identified in the majority of eukaryotic supergroups, generating interest in the ecological effects and evolutionary history of circular Rep-encoding ssDNA viruses (CRESS DNA) viruses. This review surveys the explosion of sequence diversity and expansion of eukaryotic CRESS DNA taxonomic groups over the last decade, highlights similarities between the well-studied geminiviruses and circoviruses with newly identified groups known only through their genome sequences, discusses the ecology and evolution of eukaryotic CRESS DNA viruses, and speculates on future research horizons.
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Affiliation(s)
- Lele Zhao
- Department of Ecology, Evolution and Natural Resources, Rutgers, the State University of New Jersey, New Brunswick, NJ, United States
| | - Karyna Rosario
- College of Marine Science, University of South Florida, Saint Petersburg, FL, United States
| | - Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, FL, United States
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, Rutgers, the State University of New Jersey, New Brunswick, NJ, United States.
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39
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Domingo-Calap P, Schubert B, Joly M, Solis M, Untrau M, Carapito R, Georgel P, Caillard S, Fafi-Kremer S, Paul N, Kohlbacher O, González-Candelas F, Bahram S. An unusually high substitution rate in transplant-associated BK polyomavirus in vivo is further concentrated in HLA-C-bound viral peptides. PLoS Pathog 2018; 14:e1007368. [PMID: 30335851 PMCID: PMC6207329 DOI: 10.1371/journal.ppat.1007368] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 10/30/2018] [Accepted: 09/28/2018] [Indexed: 11/18/2022] Open
Abstract
Infection with human BK polyomavirus, a small double-stranded DNA virus, potentially results in severe complications in immunocompromised patients. Here, we describe the in vivo variability and evolution of the BK polyomavirus by deep sequencing. Our data reveal the highest genomic evolutionary rate described in double-stranded DNA viruses, i.e., 10−3–10−5 substitutions per nucleotide site per year. High mutation rates in viruses allow their escape from immune surveillance and adaptation to new hosts. By combining mutational landscapes across viral genomes with in silico prediction of viral peptides, we demonstrate the presence of significantly more coding substitutions within predicted cognate HLA-C-bound viral peptides than outside. This finding suggests a role for HLA-C in antiviral immunity, perhaps through the action of killer cell immunoglobulin-like receptors. The present study provides a comprehensive view of viral evolution and immune escape in a DNA virus. Little is known about the mechanisms of evolution and viral immune escape in double-stranded DNA (dsDNA) viruses. Here, we study the evolution of BK polyomavirus and observe the highest genomic evolutionary rate described so far for a dsDNA virus, in the range of RNA viruses, which usually evolve rapidly. Furthermore, the prediction of viral peptides to determine immune escape suggests a specific role of HLA-C in antiviral immunity. These findings are helpful for future advances in antiviral therapies and provide a step forward in our understanding of in vivo viral evolution in humans.
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Affiliation(s)
- Pilar Domingo-Calap
- Plateforme GENOMAX, Laboratoire d’ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d’Immunologie et d’Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire, OMICARE, Centre de Recherche d’Immunologie et d’Hématologie, Strasbourg, France
- * E-mail: (PDC); (SB)
| | - Benjamin Schubert
- Center for Bioinformatics, University of Tübingen, Tübingen, Germany
- Applied Bioinformatics, Department of Computer Science, Tübingen, Germany
| | - Mélanie Joly
- Plateforme GENOMAX, Laboratoire d’ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d’Immunologie et d’Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire, OMICARE, Centre de Recherche d’Immunologie et d’Hématologie, Strasbourg, France
- Service de Néphrologie et Transplantation Rénale, Hôpitaux Universitaires de Strasbourg, France
| | - Morgane Solis
- Plateforme GENOMAX, Laboratoire d’ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d’Immunologie et d’Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire, OMICARE, Centre de Recherche d’Immunologie et d’Hématologie, Strasbourg, France
- Laboratoire de Virologie, Plateau Technique de Microbiologie, Pôle de Biologie, Hôpitaux Universitaires de Strasbourg, France
| | - Meiggie Untrau
- Plateforme GENOMAX, Laboratoire d’ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d’Immunologie et d’Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire, OMICARE, Centre de Recherche d’Immunologie et d’Hématologie, Strasbourg, France
| | - Raphael Carapito
- Plateforme GENOMAX, Laboratoire d’ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d’Immunologie et d’Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire, OMICARE, Centre de Recherche d’Immunologie et d’Hématologie, Strasbourg, France
- Laboratoire Central d’Immunologie, Plateau Technique de Biologie, Nouvel Hôpital Civil, France
| | - Philippe Georgel
- Plateforme GENOMAX, Laboratoire d’ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d’Immunologie et d’Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire, OMICARE, Centre de Recherche d’Immunologie et d’Hématologie, Strasbourg, France
| | - Sophie Caillard
- Plateforme GENOMAX, Laboratoire d’ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d’Immunologie et d’Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire, OMICARE, Centre de Recherche d’Immunologie et d’Hématologie, Strasbourg, France
- Service de Néphrologie et Transplantation Rénale, Hôpitaux Universitaires de Strasbourg, France
| | - Samira Fafi-Kremer
- Plateforme GENOMAX, Laboratoire d’ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d’Immunologie et d’Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire, OMICARE, Centre de Recherche d’Immunologie et d’Hématologie, Strasbourg, France
- Laboratoire de Virologie, Plateau Technique de Microbiologie, Pôle de Biologie, Hôpitaux Universitaires de Strasbourg, France
| | - Nicodème Paul
- Plateforme GENOMAX, Laboratoire d’ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d’Immunologie et d’Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire, OMICARE, Centre de Recherche d’Immunologie et d’Hématologie, Strasbourg, France
| | - Oliver Kohlbacher
- Center for Bioinformatics, University of Tübingen, Tübingen, Germany
- Applied Bioinformatics, Department of Computer Science, Tübingen, Germany
- Quantitative Biology Center, Tübingen, Germany
- Faculty of Medicine, University of Tübingen, Tübingen, Germany
- Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany
- Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany
| | - Fernando González-Candelas
- Unidad Mixta Infección y Salud Pública FISABIO/Universitat de València, Institute for Integrative Systems Biology I2SysBio (CSIC-UV) and CIBER en Epidemiología y Salud Pública, Valencia, Spain
| | - Seiamak Bahram
- Plateforme GENOMAX, Laboratoire d’ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d’Immunologie et d’Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire, OMICARE, Centre de Recherche d’Immunologie et d’Hématologie, Strasbourg, France
- Laboratoire Central d’Immunologie, Plateau Technique de Biologie, Nouvel Hôpital Civil, France
- * E-mail: (PDC); (SB)
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40
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Rosario K, Mettel KA, Benner BE, Johnson R, Scott C, Yusseff-Vanegas SZ, Baker CCM, Cassill DL, Storer C, Varsani A, Breitbart M. Virus discovery in all three major lineages of terrestrial arthropods highlights the diversity of single-stranded DNA viruses associated with invertebrates. PeerJ 2018; 6:e5761. [PMID: 30324030 PMCID: PMC6186406 DOI: 10.7717/peerj.5761] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/16/2018] [Indexed: 11/20/2022] Open
Abstract
Viruses encoding a replication-associated protein (Rep) within a covalently closed, single-stranded (ss)DNA genome are among the smallest viruses known to infect eukaryotic organisms, including economically valuable agricultural crops and livestock. Although circular Rep-encoding ssDNA (CRESS DNA) viruses are a widespread group for which our knowledge is rapidly expanding, biased sampling toward vertebrates and land plants has limited our understanding of their diversity and evolution. Here, we screened terrestrial arthropods for CRESS DNA viruses and report the identification of 44 viral genomes and replicons associated with specimens representing all three major terrestrial arthropod lineages, namely Euchelicerata (spiders), Hexapoda (insects), and Myriapoda (millipedes). We identified virus genomes belonging to three established CRESS DNA viral families (Circoviridae, Genomoviridae, and Smacoviridae); however, over half of the arthropod-associated viral genomes are only distantly related to currently classified CRESS DNA viral sequences. Although members of viral and satellite families known to infect plants (Geminiviridae, Nanoviridae, Alphasatellitidae) were not identified in this study, these plant-infecting CRESS DNA viruses and replicons are transmitted by hemipterans. Therefore, members from six out of the seven established CRESS DNA viral families circulate among arthropods. Furthermore, a phylogenetic analysis of Reps, including endogenous viral sequences, reported to date from a wide array of organisms revealed that most of the known CRESS DNA viral diversity circulates among invertebrates. Our results highlight the vast and unexplored diversity of CRESS DNA viruses among invertebrates and parallel findings from RNA viral discovery efforts in undersampled taxa.
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Affiliation(s)
- Karyna Rosario
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
| | - Kaitlin A Mettel
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
| | - Bayleigh E Benner
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
| | - Ryan Johnson
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
| | - Catherine Scott
- Department of Biological Sciences, University of Toronto, Scarborough, Scarborough, ON, Canada
| | | | - Christopher C M Baker
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Deby L Cassill
- Department of Biological Sciences, University of South Florida Saint Petersburg, Saint Petersburg, FL, USA
| | - Caroline Storer
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.,Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa
| | - Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
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41
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Jacobson AL, Duffy S, Sseruwagi P. Whitefly-transmitted viruses threatening cassava production in Africa. Curr Opin Virol 2018; 33:167-176. [PMID: 30243102 DOI: 10.1016/j.coviro.2018.08.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 08/28/2018] [Accepted: 08/31/2018] [Indexed: 10/28/2022]
Abstract
Emerging plant viruses are one of the greatest problems facing crop production worldwide, and have severe consequences in the developing world where subsistence farming is a major source of food production, and knowledge and resources for management are limited. In Africa, evolution of two viral disease complexes, cassava mosaic begomoviruses (CMBs) (Geminiviridae) and cassava brown streak viruses (CBSVs) (Potyviridae), have resulted in severe pandemics that continue to spread and threaten cassava production. Identification of genetically diverse and rapidly evolving CMBs and CBSVs, extensive genetic variation in the vector, Bemisia tabaci (Hemiptera: Aleyrodidae), and numerous secondary endosymbiont profiles that influence vector phenotypes suggest that complex local and regional vector-virus-plant-environment interactions may be driving the evolution and epidemiology of these viruses.
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Affiliation(s)
- Alana Lynn Jacobson
- Department of Entomology and Plant Pathology, Auburn University, 301 Funchess Hall, Auburn, AL 36849, USA.
| | - Siobain Duffy
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, 14 College Farm Rd, New Brunswick, NJ 08901, USA
| | - Peter Sseruwagi
- Mikocheni Agricultural Research Institute, P.O. Box 6226, Dar es Salaam, Tanzania
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42
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Pagán I. The diversity, evolution and epidemiology of plant viruses: A phylogenetic view. INFECTION GENETICS AND EVOLUTION 2018; 65:187-199. [PMID: 30055330 DOI: 10.1016/j.meegid.2018.07.033] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 07/24/2018] [Accepted: 07/24/2018] [Indexed: 10/28/2022]
Abstract
During the past four decades, the scientific community has seen an exponential advance in the number, sophistication, and quality of molecular techniques and bioinformatics tools for the genetic characterization of plant virus populations. Predating these advances, the field of Phylogenetics has significantly contributed to understand important aspects of plant virus evolution. This review aims at summarizing the impact of Phylogenetics in the current knowledge on three major aspects of plant virus evolution that have benefited from the development of phylogenetic inference: (1) The identification and classification of plant virus diversity. (2) The mechanisms and forces shaping the evolution of plant virus populations. (3) The understanding of the interaction between plant virus evolution, epidemiology and ecology. The work discussed here highlights the important role of phylogenetic approaches in the study of the dynamics of plant virus populations.
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Affiliation(s)
- Israel Pagán
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, E.T.S. Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid 28223, Spain.
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43
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Sánchez-Campos S, Domínguez-Huerta G, Díaz-Martínez L, Tomás DM, Navas-Castillo J, Moriones E, Grande-Pérez A. Differential Shape of Geminivirus Mutant Spectra Across Cultivated and Wild Hosts With Invariant Viral Consensus Sequences. FRONTIERS IN PLANT SCIENCE 2018; 9:932. [PMID: 30013589 PMCID: PMC6036239 DOI: 10.3389/fpls.2018.00932] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 06/11/2018] [Indexed: 05/12/2023]
Abstract
Geminiviruses (family Geminiviridae) possess single-stranded circular DNA genomes that are replicated by cellular polymerases in plant host cell nuclei. In their hosts, geminivirus populations behave as ensembles of mutant and recombinant genomes, known as viral quasispecies. This favors the emergence of new geminiviruses with altered host range, facilitating new or more severe diseases or overcoming resistance traits. In warm and temperate areas several whitefly-transmitted geminiviruses of the genus Begomovirus cause the tomato yellow leaf curl disease (TYLCD) with significant economic consequences. TYLCD is frequently controlled in commercial tomatoes by using the dominant Ty-1 resistance gene. Over a 45 day period we have studied the diversification of three begomoviruses causing TYLCD: tomato yellow leaf curl virus (TYLCV), tomato yellow leaf curl Sardinia virus (TYLCSV) and tomato yellow leaf curl Malaga virus (TYLCMaV, a natural recombinant between TYLCV and TYLCSV). Viral quasispecies resulting from inoculation of geminivirus infectious clones were examined in plants of susceptible tomato (ty-1/ty-1), heterozygous resistant tomato (Ty-1/ty-1), common bean, and the wild reservoir Solanum nigrum. Differences in virus fitness across hosts were observed while viral consensus sequences remained invariant. However, the complexity and heterogeneity of the quasispecies were high, especially in common bean and the wild host. Interestingly, the presence or absence of the Ty-1 allele in tomato did not lead to differences in begomovirus mutant spectra. However, the fitness decrease of TYLCSV and TYLCV in tomato at 45 dpi might be related to an increase in CP (Coat protein) mutation frequency. In Solanum nigrum the recombinant TYLCMaV, which showed lower fitness than TYLCSV, at 45 dpi actively explored Rep (Replication associated protein) ORF but not the overlapping C4. Our results underline the importance of begomovirus mutant spectra during infections. This is especially relevant in the wild reservoir of the viruses, which has the potential to maintain highly diverse mutant spectra without modifying their consensus sequences.
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Affiliation(s)
- Sonia Sánchez-Campos
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” Consejo Superior de Investigaciones Científicas-Universidad de Málaga, Estación Experimental “La Mayora,” Algarrobo-Costa, Málaga, Spain
| | - Guillermo Domínguez-Huerta
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” Consejo Superior de Investigaciones Científicas-Universidad de Málaga, Estación Experimental “La Mayora,” Algarrobo-Costa, Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” Consejo Superior de Investigaciones Científicas-Universidad de Málaga, Área de Genética, Facultad de Ciencias, Campus de Teatinos, Málaga, Spain
| | - Luis Díaz-Martínez
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” Consejo Superior de Investigaciones Científicas-Universidad de Málaga, Área de Genética, Facultad de Ciencias, Campus de Teatinos, Málaga, Spain
| | - Diego M. Tomás
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” Consejo Superior de Investigaciones Científicas-Universidad de Málaga, Estación Experimental “La Mayora,” Algarrobo-Costa, Málaga, Spain
| | - Jesús Navas-Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” Consejo Superior de Investigaciones Científicas-Universidad de Málaga, Estación Experimental “La Mayora,” Algarrobo-Costa, Málaga, Spain
| | - Enrique Moriones
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” Consejo Superior de Investigaciones Científicas-Universidad de Málaga, Estación Experimental “La Mayora,” Algarrobo-Costa, Málaga, Spain
| | - Ana Grande-Pérez
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora,” Consejo Superior de Investigaciones Científicas-Universidad de Málaga, Área de Genética, Facultad de Ciencias, Campus de Teatinos, Málaga, Spain
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44
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Mauck KE, Chesnais Q, Shapiro LR. Evolutionary Determinants of Host and Vector Manipulation by Plant Viruses. Adv Virus Res 2018; 101:189-250. [PMID: 29908590 DOI: 10.1016/bs.aivir.2018.02.007] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Plant viruses possess adaptations for facilitating acquisition, retention, and inoculation by vectors. Until recently, it was hypothesized that these adaptations are limited to virus proteins that enable virions to bind to vector mouthparts or invade their internal tissues. However, increasing evidence suggests that viruses can also manipulate host plant phenotypes and vector behaviors in ways that enhance their own transmission. Manipulation of vector-host interactions occurs through virus effects on host cues that mediate vector orientation, feeding, and dispersal behaviors, and thereby, the probability of virus transmission. Effects on host phenotypes vary by pathosystem but show a remarkable degree of convergence among unrelated viruses whose transmission is favored by the same vector behaviors. Convergence based on transmission mechanism, rather than phylogeny, supports the hypothesis that virus effects are adaptive and not just by-products of infection. Based on this, it has been proposed that viruses manipulate hosts through multifunctional proteins that facilitate exploitation of host resources and elicitation of specific changes in host phenotypes. But this proposition is rarely discussed in the context of the numerous constraints on virus evolution imposed by molecular and environmental factors, which figure prominently in research on virus-host interactions not dealing with host manipulation. To explore the implications of this oversight, we synthesized available literature to identify patterns in virus effects among pathogens with shared transmission mechanisms and discussed the results of this synthesis in the context of molecular and environmental constraints on virus evolution, limitations of existing studies, and prospects for future research.
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Affiliation(s)
- Kerry E Mauck
- Department of Entomology, University of California, Riverside, Riverside, CA, United States.
| | - Quentin Chesnais
- Department of Entomology, University of California, Riverside, Riverside, CA, United States
| | - Lori R Shapiro
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States
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45
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Kazlauskas D, Varsani A, Krupovic M. Pervasive Chimerism in the Replication-Associated Proteins of Uncultured Single-Stranded DNA Viruses. Viruses 2018; 10:v10040187. [PMID: 29642587 PMCID: PMC5923481 DOI: 10.3390/v10040187] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 04/04/2018] [Accepted: 04/08/2018] [Indexed: 12/16/2022] Open
Abstract
Numerous metagenomic studies have uncovered a remarkable diversity of circular replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses, the majority of which are uncultured and unclassified. Unlike capsid proteins, the Reps show significant similarity across different groups of CRESS DNA viruses and have conserved domain organization with the N-terminal nuclease and the C-terminal helicase domain. Consequently, Rep is widely used as a marker for identification, classification and assessment of the diversity of CRESS DNA viruses. However, it has been shown that in certain viruses the Rep nuclease and helicase domains display incongruent evolutionary histories. Here, we systematically evaluated the co-evolutionary patterns of the two Rep domains across classified and unclassified CRESS DNA viruses. Our analysis indicates that the Reps encoded by members of the families Bacilladnaviridae, Circoviridae, Geminiviridae, Genomoviridae, Nanoviridae and Smacoviridae display largely congruent evolutionary patterns in the two domains. By contrast, among the unclassified CRESS DNA viruses, 71% appear to have chimeric Reps. Such massive chimerism suggests that unclassified CRESS DNA viruses represent a dynamic population in which exchange of gene fragments encoding the nuclease and helicase domains is extremely common. Furthermore, purging of the chimeric sequences uncovered six monophyletic Rep groups that may represent new families of CRESS DNA viruses.
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Affiliation(s)
- Darius Kazlauskas
- Institute of Biotechnology, Vilnius University, Saulėtekio Av. 7, Vilnius 10257, Lithuania.
- Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Department of Microbiology, Institut Pasteur, 25 rue du Docteur Roux, Paris 75015, France.
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA.
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory 7700, South Africa.
| | - Mart Krupovic
- Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Department of Microbiology, Institut Pasteur, 25 rue du Docteur Roux, Paris 75015, France.
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46
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Yang X, Wang B, Luan J, Xie Y, Liu S, Zhou X. Molecular variation of tomato yellow leaf curl virus in the insect vector Bemisia tabaci. Sci Rep 2017; 7:16427. [PMID: 29180745 PMCID: PMC5703973 DOI: 10.1038/s41598-017-16330-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 11/08/2017] [Indexed: 12/19/2022] Open
Abstract
Insect vectors play significant roles in geminivirus spread and evolution in nature. To date little is known about the population dynamics of begomoviruses in their insect vector Bemisia tabaci. In this study we analyzed the genetic variation of tomato yellow leaf curl virus (TYLCV) in its host plant, Solanum lycopersicum, in its transmission vector B. tabaci raised on TYLCV-infected S. lycopersicum plants, and in B. tabaci after being transferred from S. lycopersicum to Gossypium hirsutum. We found that the levels of variability of TYLCV remained stable in S. lycopersicum plants, but increased significantly in both invasive and indigenous species of B. tabaci. We also presented evidence that the elevated mutation frequencies in TYLCV populations from vector whiteflies were caused mainly by mutations that occurred at several distinct sites within the TYLCV genome. Simultaneous introduction of mutations in the hot spots did not affect the ability of TYLCV to be transmitted by B. tabaci, but reduced its pathogenicity in both S. lycopersicum and Nicotiana benthamiana. Our findings provide new information on population variability of TYLCV in its insect vector, extending the knowledge of the influence of insect vector on plant virus population dynamics.
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Affiliation(s)
- Xiuling Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Bi Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Junbo Luan
- Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yan Xie
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Shusheng Liu
- Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.
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47
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The Evolutionary History and Spatiotemporal Dynamics of the NC Lineage of Citrus Tristeza Virus. Viruses 2017; 9:v9100272. [PMID: 29023368 PMCID: PMC5691624 DOI: 10.3390/v9100272] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/04/2017] [Accepted: 09/21/2017] [Indexed: 12/19/2022] Open
Abstract
Citrus tristeza virus (CTV) is a major pathogen affecting citrus trees worldwide. However, few studies have focused on CTV's evolutionary history and geographic behavior. CTV is locally dispersed by an aphid vector and long distance dispersion due to transportation of contaminated material. With the aim to delve deeper into the CTV-NC (New Clade) genotype evolution, we estimated an evolution rate of 1.19 × 10-3 subs/site/year and the most common recent ancestor in 1977. Furthermore, the place of origin of the genotype was in the United States, and a great expansion of the population was observed in Uruguay. This expansion phase could be a consequence of the increment in the number of naïve citrus trees in Uruguayan orchards encompassing citrus industry growth in the past years.
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48
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Genetic variability and population structure of the New World begomovirus Euphorbia yellow mosaic virus. J Gen Virol 2017; 98:1537-1551. [DOI: 10.1099/jgv.0.000784] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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49
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Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain. Nat Commun 2017; 8:15483. [PMID: 28537263 PMCID: PMC5458099 DOI: 10.1038/ncomms15483] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 03/30/2017] [Indexed: 11/26/2022] Open
Abstract
An atypically large outbreak of Elizabethkingia anophelis infections occurred in Wisconsin. Here we show that it was caused by a single strain with thirteen characteristic genomic regions. Strikingly, the outbreak isolates show an accelerated evolutionary rate and an atypical mutational spectrum. Six phylogenetic sub-clusters with distinctive temporal and geographic dynamics are revealed, and their last common ancestor existed approximately one year before the first recognized human infection. Unlike other E. anophelis, the outbreak strain had a disrupted DNA repair mutY gene caused by insertion of an integrative and conjugative element. This genomic change probably contributed to the high evolutionary rate of the outbreak strain and may have increased its adaptability, as many mutations in protein-coding genes occurred during the outbreak. This unique discovery of an outbreak caused by a naturally occurring mutator bacterial pathogen provides a dramatic example of the potential impact of pathogen evolutionary dynamics on infectious disease epidemiology. Elizabethkingia anophelis is an emerging pathogen of high antimicrobial resistance. Perrin and colleagues sequenced isolates of a 2015/2016 E. anophelis outbreak in Wisconsin and found substantial genetic diversity, accelerated evolutionary rate and a disruptive mutation in the DNA repair gene mutY.
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50
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Evolutionary history of ssDNA bacilladnaviruses features horizontal acquisition of the capsid gene from ssRNA nodaviruses. Virology 2017; 504:114-121. [DOI: 10.1016/j.virol.2017.02.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 02/01/2017] [Accepted: 02/02/2017] [Indexed: 11/21/2022]
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