51
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Gantuz M, Lorenzetti MA, Chabay PA, Preciado MV. A novel recombinant variant of latent membrane protein 1 from Epstein Barr virus in Argentina denotes phylogeographical association. PLoS One 2017; 12:e0174221. [PMID: 28328987 PMCID: PMC5362222 DOI: 10.1371/journal.pone.0174221] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/05/2017] [Indexed: 12/15/2022] Open
Abstract
Epstein Barr virus (EBV) infection in Argentina occurs at an early age and occasionally develops infectious mononucleosis (IM). EBV is also related with lymphomas. LMP1, the viral oncoprotein is polymorphic and is used to define viral variants.
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Affiliation(s)
- Magdalena Gantuz
- Instituto Multidisciplinario de Investigaciones en Patologías Pediátricas (IMIPP), CONICET-GCBA, Laboratorio de Biología Molecular, División Patología, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina
| | - Mario Alejandro Lorenzetti
- Instituto Multidisciplinario de Investigaciones en Patologías Pediátricas (IMIPP), CONICET-GCBA, Laboratorio de Biología Molecular, División Patología, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina
| | - Paola Andrea Chabay
- Instituto Multidisciplinario de Investigaciones en Patologías Pediátricas (IMIPP), CONICET-GCBA, Laboratorio de Biología Molecular, División Patología, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina
| | - María Victoria Preciado
- Instituto Multidisciplinario de Investigaciones en Patologías Pediátricas (IMIPP), CONICET-GCBA, Laboratorio de Biología Molecular, División Patología, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina
- * E-mail:
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52
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Lima ATM, Silva JCF, Silva FN, Castillo-Urquiza GP, Silva FF, Seah YM, Mizubuti ESG, Duffy S, Zerbini FM. The diversification of begomovirus populations is predominantly driven by mutational dynamics. Virus Evol 2017; 3:vex005. [PMID: 28458915 PMCID: PMC5399926 DOI: 10.1093/ve/vex005] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Begomoviruses (single-stranded DNA plant viruses) are responsible for serious agricultural threats. Begomovirus populations exhibit a high degree of within-host genetic variation and evolve as quickly as RNA viruses. Although the recombination-prone nature of begomoviruses has been extensively demonstrated, the relative contribution of recombination and mutation to the genetic variation of begomovirus populations has not been assessed. We estimated the genetic variability of begomovirus datasets from around the world. An uneven distribution of genetic variation across the length of the cp and rep genes due to recombination was evident from our analyses. To estimate the relative contributions of recombination and mutation to the genetic variability of begomoviruses, we mapped all substitutions over maximum likelihood trees and counted the number of substitutions on branches which were associated with recombination (ηr) and mutation (ημ). In addition, we also estimated the per generation relative rates of both evolutionary mechanisms (r/μ) to express how frequently begomovirus genomes are affected by recombination relative to mutation. We observed that the composition of genetic variation in all begomovirus datasets was dominated by mutation. Additionally, the low correlation between the estimates indicated that the relative contributions of recombination and mutation are not necessarily a function of their relative rates. Our results show that, although a considerable fraction of the genetic variation levels could be assigned to recombination, it was always lower than that due to mutation, indicating that the diversification of begomovirus populations is predominantly driven by mutational dynamics.
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Affiliation(s)
- Alison T M Lima
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Av. P.H. Rolfs, s/n, Viçosa, MG 36570-900, Brazil.,National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Av. P.H. Rolfs, s/n, Viçosa, MG 36570-900, Brazil
| | - José C F Silva
- National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Av. P.H. Rolfs, s/n, Viçosa, MG 36570-900, Brazil
| | - Fábio N Silva
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Av. P.H. Rolfs, s/n, Viçosa, MG 36570-900, Brazil.,National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Av. P.H. Rolfs, s/n, Viçosa, MG 36570-900, Brazil
| | - Gloria P Castillo-Urquiza
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Av. P.H. Rolfs, s/n, Viçosa, MG 36570-900, Brazil.,National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Av. P.H. Rolfs, s/n, Viçosa, MG 36570-900, Brazil
| | - Fabyano F Silva
- Departamento de Zootecnia, Universidade Federal de Viçosa, Av. P.H. Rolfs, s/n, Viçosa, MG 36570-900, Brazil
| | - Yee M Seah
- Department of Ecology, Evolution and Natural Resources, Rutgers, The State University of New Jersey, 14 College Farm Rd, New Brunswick, NJ 08901, USA
| | - Eduardo S G Mizubuti
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Av. P.H. Rolfs, s/n, Viçosa, MG 36570-900, Brazil
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, Rutgers, The State University of New Jersey, 14 College Farm Rd, New Brunswick, NJ 08901, USA
| | - F Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Av. P.H. Rolfs, s/n, Viçosa, MG 36570-900, Brazil.,National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Av. P.H. Rolfs, s/n, Viçosa, MG 36570-900, Brazil
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53
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Varsani A, Krupovic M. Sequence-based taxonomic framework for the classification of uncultured single-stranded DNA viruses of the family Genomoviridae. Virus Evol 2017; 3:vew037. [PMID: 28458911 PMCID: PMC5399927 DOI: 10.1093/ve/vew037] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
With the advent of metagenomics approaches, a large diversity of known and unknown viruses has been identified in various types of environmental, plant, and animal samples. One such widespread virus group is the recently established family Genomoviridae which includes viruses with small (∼2-2.4 kb), circular ssDNA genomes encoding rolling-circle replication initiation proteins (Rep) and unique capsid proteins. Here, we propose a sequence-based taxonomic framework for classification of 121 new virus genomes within this family. Genomoviruses display ∼47% sequence diversity, which is very similar to that within the well-established and extensively studied family Geminiviridae (46% diversity). Based on our analysis, we establish a 78% genome-wide pairwise identity as a species demarcation threshold. Furthermore, using a Rep sequence phylogeny-based analysis coupled with the current knowledge on the classification of geminiviruses, we establish nine genera within the Genomoviridae family. These are Gemycircularvirus (n = 73), Gemyduguivirus (n = 1), Gemygorvirus (n = 9), Gemykibivirus (n = 29), Gemykolovirus (n = 3), Gemykrogvirus (n = 3), Gemykroznavirus (n = 1), Gemytondvirus (n = 1), Gemyvongvirus (n = 1). The presented taxonomic framework offers rational classification of genomoviruses based on the sequence information alone and sets an example for future classification of other groups of uncultured viruses discovered using metagenomics approaches.
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Affiliation(s)
- 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 Clinical Laboratory 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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54
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Rao LX, Guo Y, Zhang LL, Zhou XP, Hong J, Wu JX. Genetic variation and population structure of Cucumber green mottle mosaic virus. Arch Virol 2017; 162:1159-1168. [PMID: 28054163 DOI: 10.1007/s00705-016-3207-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 12/01/2016] [Indexed: 11/26/2022]
Abstract
Cucumber green mottle mosaic virus (CGMMV) is a single-stranded, positive sense RNA virus infecting cucurbitaceous plants. In recent years, CGMMV has become an important pathogen of cucurbitaceous crops including watermelon, pumpkin, cucumber and bottle gourd in China, causing serious losses to their production. In this study, we surveyed CGMMV infection in various cucurbitaceous crops grown in Zhejiang Province and in several seed lots purchased from local stores with the dot enzyme-linked immunosorbent assay (dot-ELISA), using a CGMMV specific monoclonal antibody. Seven CGMMV isolates obtained from watermelon, grafted watermelon or oriental melon samples were cloned and sequenced. Identity analysis showed that the nucleotide identities of the seven complete genome sequences ranged from 99.2 to 100%. Phylogenetic analysis of seven CGMMV isolates as well as 24 other CGMMV isolates from the GenBank database showed that all CGMMV isolates could be grouped into two distinct monophyletic clades according to geographic distribution, i.e. Asian isolates for subtype I and European isolates for subtype II, indicating that population diversification of CGMMV isolates may be affected by geographical distribution. Site variation rate analysis of CGMMV found that the overall variation rate was below 8% and mainly ranged from 2 to 5%, indicating that the CGMMV genomic sequence was conservative. Base substitution type analysis of CGMMV showed a mutational bias, with more transitions (A↔G and C↔T) than transversions (A↔C, A↔T, G↔C and G↔T). Most of the variation occurring in the CGMMV genome resulted in non-synonymous substitutions, and the variation rate of some sites was higher than 30% because of this mutational bias. Selection constraint analysis of CGMMV ORFs showed strong negative selection acting on the replication-associated protein, similar to what occurs for other plant RNA viruses. Finally, potential recombination analysis identified isolate Ec as a recombinant with a low degree of confidence.
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Affiliation(s)
- Li-Xia Rao
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Yushuang Guo
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Li-Li Zhang
- Hangzhou City Plant Protection and Soil and Fertilizer Station, Hangzhou, 310020, People's Republic of China
| | - Xue-Ping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Jian Hong
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Jian-Xiang Wu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China.
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55
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Molecular genetic analysis and evolution of begomoviruses and betasatellites causing yellow mosaic disease of bhendi. Virus Genes 2016; 53:275-285. [DOI: 10.1007/s11262-016-1414-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 11/22/2016] [Indexed: 01/08/2023]
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56
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De Bruyn A, Harimalala M, Zinga I, Mabvakure BM, Hoareau M, Ravigné V, Walters M, Reynaud B, Varsani A, Harkins GW, Martin DP, Lett JM, Lefeuvre P. Divergent evolutionary and epidemiological dynamics of cassava mosaic geminiviruses in Madagascar. BMC Evol Biol 2016; 16:182. [PMID: 27600545 PMCID: PMC5012068 DOI: 10.1186/s12862-016-0749-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 08/18/2016] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Cassava mosaic disease (CMD) in Madagascar is caused by a complex of at least six African cassava mosaic geminivirus (CMG) species. This provides a rare opportunity for a comparative study of the evolutionary and epidemiological dynamics of distinct pathogenic crop-infecting viral species that coexist within the same environment. The genetic and spatial structure of CMG populations in Madagascar was studied and Bayesian phylogeographic modelling was applied to infer the origins of Madagascan CMG populations within the epidemiological context of related populations situated on mainland Africa and other south western Indian Ocean (SWIO) islands. RESULTS The isolation and analysis of 279 DNA-A and 117 DNA-B sequences revealed the presence in Madagascar of four prevalent CMG species (South African cassava mosaic virus, SACMV; African cassava mosaic virus, ACMV; East African cassava mosaic Kenya virus, EACMKV; and East African cassava mosaic Cameroon virus, EACMCV), and of numerous CMG recombinants that have, to date, only ever been detected on this island. SACMV and ACMV, the two most prevalent viruses, displayed low degrees of genetic diversity and have most likely been introduced to the island only once. By contrast, EACMV-like CMG populations (consisting of East African cassava mosaic virus, EAMCKV, EACMCV and complex recombinants of these) were more diverse, more spatially structured, and displayed evidence of at least three independent introductions from mainland Africa. Although there were no statistically supported virus movement events between Madagascar and the other SWIO islands, at least one mainland African ACMV variant likely originated in Madagascar. CONCLUSIONS Our study highlights both the complexity of CMD in Madagascar, and the distinct evolutionary and spatial dynamics of the different viral species that collectively are associated with this disease. Given that more distinct CMG species and recombinants have been found in Madagascar than any other similarly sized region of the world, the risks of recombinant CMG variants emerging on this island are likely to be higher than elsewhere. Evidence of an epidemiological link between Madagascan and mainland African CMGs suggests that the consequences of such emergence events could reach far beyond the shores of this island.
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Affiliation(s)
- Alexandre De Bruyn
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 chemin de l’IRAT, Saint-Pierre, Ile de la Réunion 97410 France
- Université de la Réunion, UMR PVBMT, Pôle de Protection des Plantes, 7 chemin de l’IRAT, Saint-Pierre, Ile de la Réunion 97410 France
| | - Mireille Harimalala
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 chemin de l’IRAT, Saint-Pierre, Ile de la Réunion 97410 France
- Université de la Réunion, UMR PVBMT, Pôle de Protection des Plantes, 7 chemin de l’IRAT, Saint-Pierre, Ile de la Réunion 97410 France
- FOFIFA, Laboratoire de Pathologie Végétale, BP 1444 Ambatobe, Madagascar
| | - Innocent Zinga
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 chemin de l’IRAT, Saint-Pierre, Ile de la Réunion 97410 France
- LSBAD, Université de Bangui, BP908 Bangui, Centrafrique France
| | - Batsirai M. Mabvakure
- South African National Bioinformatics Institute, Medical Research Council Bioinformatics Unit, University of the Western Cape, Cape Town, South Africa
| | - Murielle Hoareau
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 chemin de l’IRAT, Saint-Pierre, Ile de la Réunion 97410 France
| | - Virginie Ravigné
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 chemin de l’IRAT, Saint-Pierre, Ile de la Réunion 97410 France
- CIRAD, UMR BGPI, Campus International de Baillarguet, Montpellier, 34398 France
| | - Matthew Walters
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Bernard Reynaud
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 chemin de l’IRAT, Saint-Pierre, Ile de la Réunion 97410 France
- Université de la Réunion, UMR PVBMT, Pôle de Protection des Plantes, 7 chemin de l’IRAT, Saint-Pierre, Ile de la Réunion 97410 France
| | - Arvind Varsani
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
- Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611 USA
- Structural Biology Research Unit, University of Cape Town, Rondebosch, 7701 Cape Town, South Africa
| | - Gordon W. Harkins
- South African National Bioinformatics Institute, Medical Research Council Bioinformatics Unit, University of the Western Cape, Cape Town, South Africa
| | - Darren P. Martin
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory 7925, Cape Town, South Africa
| | - Jean-Michel Lett
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 chemin de l’IRAT, Saint-Pierre, Ile de la Réunion 97410 France
| | - Pierre Lefeuvre
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 chemin de l’IRAT, Saint-Pierre, Ile de la Réunion 97410 France
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57
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Perry KL, McLane H, Hyder MZ, Dangl GS, Thompson JR, Fuchs MF. Grapevine red blotch-associated virus is Present in Free-Living Vitis spp. Proximal to Cultivated Grapevines. PHYTOPATHOLOGY 2016; 106:663-70. [PMID: 26960112 DOI: 10.1094/phyto-01-16-0035-r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Red blotch is an emerging disease of grapevine associated with grapevine red blotch-associated virus (GRBaV). The virus spreads with infected planting stocks but no vector of epidemiological significance has been conclusively identified. A vineyard block of red-blotch-affected Vitis vinifera 'Cabernet franc' clone 214 was observed in California, with a clustering of infected, symptomatic vines focused along one edge of the field proximal to a riparian habitat with free-living Vitis spp. No genetic heterogeneity was observed in a 587-nucleotide region of the GRBaV genome in a population of 44 Cabernet franc clone 214 isolates. By contrast, genetic differences were observed in isolates from other cultivars and clones growing in adjacent blocks. GRBaV was confirmed infecting four free-living vines, two of which were shown to be V. californica × V. vinifera hybrids. The genomes of three free-living GRBaV vine isolates and seven from V. vinifera cultivars were compared; free-living vine isolates were shown to be more similar to each other and a 'Merlot' isolate than to the other cultivated vine isolates. The finding that GRBaV is present in free-living Vitis spp. indicates the virus can be spread by natural (nonhuman-mediated) means, and we hypothesize that in-field spread of GRBaV is occurring.
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Affiliation(s)
- Keith L Perry
- First, second, third, and fifth authors: Department of Plant Pathology and Plant-Microbe Biology, 334 Plant Science, Cornell University, Ithaca, NY 14853; fourth author: Foundation Plant Services, University of California Davis, One Shields Ave., Davis 95616; sixth author: Department of Plant Pathology and Plant-Microbe Biology, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456
| | - Heather McLane
- First, second, third, and fifth authors: Department of Plant Pathology and Plant-Microbe Biology, 334 Plant Science, Cornell University, Ithaca, NY 14853; fourth author: Foundation Plant Services, University of California Davis, One Shields Ave., Davis 95616; sixth author: Department of Plant Pathology and Plant-Microbe Biology, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456
| | - Muhammad Z Hyder
- First, second, third, and fifth authors: Department of Plant Pathology and Plant-Microbe Biology, 334 Plant Science, Cornell University, Ithaca, NY 14853; fourth author: Foundation Plant Services, University of California Davis, One Shields Ave., Davis 95616; sixth author: Department of Plant Pathology and Plant-Microbe Biology, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456
| | - Gerald S Dangl
- First, second, third, and fifth authors: Department of Plant Pathology and Plant-Microbe Biology, 334 Plant Science, Cornell University, Ithaca, NY 14853; fourth author: Foundation Plant Services, University of California Davis, One Shields Ave., Davis 95616; sixth author: Department of Plant Pathology and Plant-Microbe Biology, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456
| | - Jeremy R Thompson
- First, second, third, and fifth authors: Department of Plant Pathology and Plant-Microbe Biology, 334 Plant Science, Cornell University, Ithaca, NY 14853; fourth author: Foundation Plant Services, University of California Davis, One Shields Ave., Davis 95616; sixth author: Department of Plant Pathology and Plant-Microbe Biology, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456
| | - Marc F Fuchs
- First, second, third, and fifth authors: Department of Plant Pathology and Plant-Microbe Biology, 334 Plant Science, Cornell University, Ithaca, NY 14853; fourth author: Foundation Plant Services, University of California Davis, One Shields Ave., Davis 95616; sixth author: Department of Plant Pathology and Plant-Microbe Biology, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456
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58
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Rieux A, Balloux F. Inferences from tip-calibrated phylogenies: a review and a practical guide. Mol Ecol 2016; 25:1911-24. [PMID: 26880113 PMCID: PMC4949988 DOI: 10.1111/mec.13586] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 02/01/2016] [Accepted: 02/04/2016] [Indexed: 12/25/2022]
Abstract
Molecular dating of phylogenetic trees is a growing discipline using sequence data to co‐estimate the timing of evolutionary events and rates of molecular evolution. All molecular‐dating methods require converting genetic divergence between sequences into absolute time. Historically, this could only be achieved by associating externally derived dates obtained from fossil or biogeographical evidence to internal nodes of the tree. In some cases, notably for fast‐evolving genomes such as viruses and some bacteria, the time span over which samples were collected may cover a significant proportion of the time since they last shared a common ancestor. This situation allows phylogenetic trees to be calibrated by associating sampling dates directly to the sequences representing the tips (terminal nodes) of the tree. The increasing availability of genomic data from ancient DNA extends the applicability of such tip‐based calibration to a variety of taxa including humans, extinct megafauna and various microorganisms which typically have a scarce fossil record. The development of statistical models accounting for heterogeneity in different aspects of the evolutionary process while accommodating very large data sets (e.g. whole genomes) has allowed using tip‐dating methods to reach inferences on divergence times, substitution rates, past demography or the age of specific mutations on a variety of spatiotemporal scales. In this review, we summarize the current state of the art of tip dating, discuss some recent applications, highlight common pitfalls and provide a ‘how to’ guide to thoroughly perform such analyses.
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Affiliation(s)
- Adrien Rieux
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, Gower Street, London, WC1E 6BT, UK
| | - François Balloux
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, Gower Street, London, WC1E 6BT, UK
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59
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Civetta A, Ostapchuk DCM, Nwali B. Genome Hotspots for Nucleotide Substitutions and the Evolution of Influenza A (H1N1) Human Strains. Genome Biol Evol 2016; 8:986-93. [PMID: 26988249 PMCID: PMC4860693 DOI: 10.1093/gbe/evw061] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In recent years a number of studies have brought attention to the role of positive selection during the evolution of antigenic escape by influenza strains. Particularly, the identification of positively selected sites within antigenic domains of viral surface proteins has been used to suggest that the evolution of viral–host receptor binding specificity is driven by selection. Here we show that, following the 1918 outbreak, the antigenic sites of the hemagglutinin (HA) viral surface protein and the stalk region of neuraminidase became substitution hotspots. The hotspots show similar patterns of nucleotide substitution bias at synonymous and nonsynonymous sites. Such bias imposes directionality in amino acid replacements that can influence signals of selection at antigenic sites. Our results suggest that the high accumulation of substitutions within the antigenic sites of HA can explain not only cases of antigenic escape by antigenic drift but also lead to occasional episodes of viral extinction.
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Affiliation(s)
- Alberto Civetta
- Department of Biology, University of Winnipeg, Winnipeg, Manitoba R3B 2G3, Canada
| | | | - Basil Nwali
- Department of Biology, University of Winnipeg, Winnipeg, Manitoba R3B 2G3, Canada Department of Biochemistry, Ebonyi State University, Abakaliki, Nigeria
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60
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Ndunguru J, De León L, Doyle CD, Sseruwagi P, Plata G, Legg JP, Thompson G, Tohme J, Aveling T, Ascencio-Ibáñez JT, Hanley-Bowdoin L. Two Novel DNAs That Enhance Symptoms and Overcome CMD2 Resistance to Cassava Mosaic Disease. J Virol 2016; 90:4160-4173. [PMID: 26865712 PMCID: PMC4810563 DOI: 10.1128/jvi.02834-15] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 02/03/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Cassava mosaic begomoviruses (CMBs) cause cassava mosaic disease (CMD) across Africa and the Indian subcontinent. Like all members of the geminivirus family, CMBs have small, circular single-stranded DNA genomes. We report here the discovery of two novel DNA sequences, designated SEGS-1 and SEGS-2 (forsequencesenhancinggeminivirussymptoms), that enhance symptoms and break resistance to CMD. The SEGS are characterized by GC-rich regions and the absence of long open reading frames. Both SEGS enhanced CMD symptoms in cassava (Manihot esculentaCrantz) when coinoculated withAfrican cassava mosaic virus(ACMV),East African cassava mosaic Cameroon virus(EACMCV), orEast African cassava mosaic virus-Uganda(EACMV-UG). SEGS-1 also overcame resistance of a cassava landrace carrying the CMD2 resistance locus when coinoculated with EACMV-UG. Episomal forms of both SEGS were detected in CMB-infected cassava but not in healthy cassava. SEGS-2 episomes were also found in virions and whiteflies. SEGS-1 has no homology to geminiviruses or their associated satellites, but the cassava genome contains a sequence that is 99% identical to full-length SEGS-1. The cassava genome also includes three sequences with 84 to 89% identity to SEGS-2 that together encompass all of SEGS-2 except for a 52-bp region, which includes the episomal junction and a 26-bp sequence related to alphasatellite replication origins. These results suggest that SEGS-1 is derived from the cassava genome and facilitates CMB infection as an integrated copy and/or an episome, while SEGS-2 was originally from the cassava genome but now is encapsidated into virions and transmitted as an episome by whiteflies. IMPORTANCE Cassava is a major crop in the developing world, with its production in Africa being second only to maize. CMD is one of the most important diseases of cassava and a serious constraint to production across Africa. CMD2 is a major CMD resistance locus that has been deployed in many cassava cultivars through large-scale breeding programs. In recent years, severe, atypical CMD symptoms have been observed occasionally on resistant cultivars, some of which carry the CMD2 locus, in African fields. In this report, we identified and characterized two DNA sequences, SEGS-1 and SEGS-2, which produce similar symptoms when coinoculated with cassava mosaic begomoviruses onto a susceptible cultivar or a CMD2-resistant landrace. The ability of SEGS-1 to overcome CMD2 resistance and the transmission of SEGS-2 by whiteflies has major implications for the long-term durability of CMD2 resistance and underscore the need for alternative sources of resistance in cassava.
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Affiliation(s)
- Joseph Ndunguru
- Mikocheni Agricultural Research Institute, Dar es Salaam, Tanzania
| | - Leandro De León
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, USA
| | - Catherine D Doyle
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Peter Sseruwagi
- Mikocheni Agricultural Research Institute, Dar es Salaam, Tanzania
| | - German Plata
- Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, USA
| | - James P Legg
- International Institute of Tropical Agriculture-Tanzania, Dar es Salaam, Tanzania
| | - Graham Thompson
- ARC-Institute for Industrial Crops, Rusternburg, South Africa
| | - Joe Tohme
- International Center for Tropical Agriculture, Cali, Colombia
| | - Theresa Aveling
- University of Pretoria, Department of Microbiology and Plant Pathology, Pretoria, South Africa
| | - Jose 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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61
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Richter KS, Serra H, White CI, Jeske H. The recombination mediator RAD51D promotes geminiviral infection. Virology 2016; 493:113-27. [PMID: 27018825 DOI: 10.1016/j.virol.2016.03.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 03/15/2016] [Accepted: 03/18/2016] [Indexed: 11/28/2022]
Abstract
To study a possible role for homologous recombination in geminivirus replication, we challenged Arabidopsis recombination gene knockouts by Euphorbia yellow mosaic virus infection. Our results show that the RAD51 paralog RAD51D, rather than RAD51 itself, promotes viral replication at early stages of infection. Blot hybridization analyses of replicative intermediates using one- and two-dimensional gels and deep sequencing point to an unexpected facet of recombination-dependent replication, the repair by single-strand annealing (SSA) during complementary strand replication. A significant decrease of both intramolecular, yielding defective DNAs and intermolecular recombinant molecules between the two geminiviral DNA components (A, B) were observed in the absence of RAD51D. By contrast, DNA A and B reacted differentially with the generation of inversions. A model to implicate single-strand annealing recombination in geminiviral recombination-dependent replication is proposed.
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Affiliation(s)
- Kathrin S Richter
- Institute of Biomaterials and Biomolecular Systems, Department of Molecular Biology and Plant Virology, University of Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany
| | - Heϊdi Serra
- Génétique, Reproduction et Développement, UMR CNRS 6293-Clermont Université- INSERM U1103 Aubière, France
| | - Charles I White
- Génétique, Reproduction et Développement, UMR CNRS 6293-Clermont Université- INSERM U1103 Aubière, France
| | - Holger Jeske
- Institute of Biomaterials and Biomolecular Systems, Department of Molecular Biology and Plant Virology, University of Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany.
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62
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Saleem H, Nahid N, Shakir S, Ijaz S, Murtaza G, Khan AA, Mubin M, Nawaz-ul-Rehman MS. Diversity, Mutation and Recombination Analysis of Cotton Leaf Curl Geminiviruses. PLoS One 2016; 11:e0151161. [PMID: 26963635 PMCID: PMC4872795 DOI: 10.1371/journal.pone.0151161] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 02/23/2016] [Indexed: 12/20/2022] Open
Abstract
The spread of cotton leaf curl disease in China, India and Pakistan is a recent phenomenon. Analysis of available sequence data determined that there is a substantial diversity of cotton-infecting geminiviruses in Pakistan. Phylogenetic analyses indicated that recombination between two major groups of viruses, cotton leaf curl Multan virus (CLCuMuV) and cotton leaf curl Kokhran virus (CLCuKoV), led to the emergence of several new viruses. Recombination detection programs and phylogenetic analyses showed that CLCuMuV and CLCuKoV are highly recombinant viruses. Indeed, CLCuKoV appeared to be a major donor virus for the coat protein (CP) gene, while CLCuMuV donated the Rep gene in the majority of recombination events. Using recombination free nucleotide datasets the substitution rates for CP and Rep genes were determined. We inferred similar nucleotide substitution rates for the CLCuMuV-Rep gene (4.96X10-4) and CLCuKoV-CP gene (2.706X10-4), whereas relatively higher substitution rates were observed for CLCuMuV-CP and CLCuKoV-Rep genes. The combination of sequences with equal and relatively low substitution rates, seemed to result in the emergence of viral isolates that caused epidemics in Pakistan and India. Our findings also suggest that CLCuMuV is spreading at an alarming rate, which can potentially be a threat to cotton production in the Indian subcontinent.
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Affiliation(s)
- Huma Saleem
- Virology Lab, Center for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Nazia Nahid
- Department of Bioinformatics and Biotechnology, GC University Faisalabad, Faisalabad, Pakistan
| | - Sara Shakir
- Virology Lab, Center for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Sehrish Ijaz
- Virology Lab, Center for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Ghulam Murtaza
- Virology Lab, Center for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Asif Ali Khan
- Virology Lab, Center for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Mubin
- Virology Lab, Center for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Shah Nawaz-ul-Rehman
- Virology Lab, Center for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
- * E-mail:
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63
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Meena CK, Borkotoky S, Murali A. Insight into virus encapsulation mechanism through in silico interaction study between coat protein and RNA operator loops of Sesbania mosaic virus. MOLECULAR BIOSYSTEMS 2016; 12:1996-2009. [DOI: 10.1039/c6mb00206d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Viruses are parasite by nature and they are responsible for many diseases. Inhibitor development is very difficult for viruses due to their rapid mutative nature.
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Affiliation(s)
- Chetan Kumar Meena
- Centre for Bioinformatics
- School of Life Sciences
- Pondicherry University
- Puducherry - 605 014
- India
| | - Subhomoi Borkotoky
- Centre for Bioinformatics
- School of Life Sciences
- Pondicherry University
- Puducherry - 605 014
- India
| | - Ayaluru Murali
- Centre for Bioinformatics
- School of Life Sciences
- Pondicherry University
- Puducherry - 605 014
- India
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64
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Trovão NS, Baele G, Vrancken B, Bielejec F, Suchard MA, Fargette D, Lemey P. Host ecology determines the dispersal patterns of a plant virus. Virus Evol 2015; 1:vev016. [PMID: 27774287 PMCID: PMC5014491 DOI: 10.1093/ve/vev016] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Since its isolation in 1966 in Kenya, rice yellow mottle virus (RYMV) has been reported throughout Africa resulting in one of the economically most important tropical plant emerging diseases. A thorough understanding of RYMV evolution and dispersal is critical to manage viral spread in tropical areas that heavily rely on agriculture for subsistence. Phylogenetic analyses have suggested a relatively recent expansion, perhaps driven by the intensification of agricultural practices, but this has not yet been examined in a coherent statistical framework. To gain insight into the historical spread of RYMV within Africa rice cultivations, we analyse a dataset of 300 coat protein gene sequences, sampled from East to West Africa over a 46-year period, using Bayesian evolutionary inference. Spatiotemporal reconstructions date the origin of RMYV back to 1852 (1791-1903) and confirm Tanzania as the most likely geographic origin. Following a single long-distance transmission event from East to West Africa, separate viral populations have been maintained for about a century. To identify the factors that shaped the RYMV distribution, we apply a generalised linear model (GLM) extension of discrete phylogenetic diffusion and provide strong support for distances measured on a rice connectivity landscape as the major determinant of RYMV spread. Phylogeographic estimates in continuous space further complement this by demonstrating more pronounced expansion dynamics in West Africa that are consistent with agricultural intensification and extensification. Taken together, our principled phylogeographic inference approach shows for the first time that host ecology dynamics have shaped the historical spread of a plant virus.
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Affiliation(s)
- Nídia Sequeira Trovão
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Guy Baele
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Bram Vrancken
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Filip Bielejec
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Marc A. Suchard
- Departments of Biomathematics and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 0095-1766, USA
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA 0095-1766, USA and
| | - Denis Fargette
- Institut de Recherches pour le Développement (IRD), UMR IPME (IRD, CIRAD, Université de Montpellier), 34394 Montpellier, France
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium
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65
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Richter KS, Götz M, Winter S, Jeske H. The contribution of translesion synthesis polymerases on geminiviral replication. Virology 2015; 488:137-48. [PMID: 26638018 DOI: 10.1016/j.virol.2015.10.027] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 10/26/2015] [Accepted: 10/28/2015] [Indexed: 12/25/2022]
Abstract
Geminiviruses multiply primarily in the plant phloem, but never in meristems. Their Rep protein can activate DNA synthesis in differentiated cells. However, when their single-stranded DNA is injected into the phloem by insects, no Rep is present for inducing initial complementary strand replication. Considering a contribution of translesion synthesis (TLS) polymerases in plants, four of them (Polη, Polζ, Polκ, Rev1) are highly and constitutively expressed in differentiated tissues like the phloem. Two geminiviruses (Euphorbia yellow mosaic virus, Cleome leaf crumple virus), inoculated either biolistically or by whiteflies, replicated in Arabidopsis thaliana mutant lines of these genes to the same extent as in wild type plants. Comparative deep sequencing of geminiviral DNAs, however, showed a high exchange rate (10(-4)-10(-3)) similar to the phylogenetic variation described before and a significant difference in nucleotide substation rates if Polη and Polζ were absent, with a differential response to the viral DNA components.
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Affiliation(s)
- Kathrin S Richter
- Institute of Biomaterials and Biomolecular Systems, Department of Molecular Biology and Plant Virology, University of Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany
| | - Monika Götz
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Messeweg 11-12, D-38104 Braunschweig, Germany
| | - Stephan Winter
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Messeweg 11-12, D-38104 Braunschweig, Germany
| | - Holger Jeske
- Institute of Biomaterials and Biomolecular Systems, Department of Molecular Biology and Plant Virology, University of Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany.
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66
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Rosario K, Seah YM, Marr C, Varsani A, Kraberger S, Stainton D, Moriones E, Polston JE, Duffy S, Breitbart M. Vector-Enabled Metagenomic (VEM) Surveys Using Whiteflies (Aleyrodidae) Reveal Novel Begomovirus Species in the New and Old Worlds. Viruses 2015; 7:5553-70. [PMID: 26516898 PMCID: PMC4632403 DOI: 10.3390/v7102895] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 10/16/2015] [Accepted: 10/19/2015] [Indexed: 01/16/2023] Open
Abstract
Whitefly-transmitted viruses belonging to the genus Begomovirus (family Geminiviridae) represent a substantial threat to agricultural food production. The rapid evolutionary potential of these single-stranded DNA viruses combined with the polyphagous feeding behavior of their whitefly vector (Bemisia tabaci) can lead to the emergence of damaging viral strains. Therefore, it is crucial to characterize begomoviruses circulating in different regions and crops globally. This study utilized vector-enabled metagenomics (VEM) coupled with high-throughput sequencing to survey begomoviruses directly from whiteflies collected in various locations (California (USA), Guatemala, Israel, Puerto Rico, and Spain). Begomoviruses were detected in all locations, with the highest diversity identified in Guatemala where up to seven different species were identified in a single field. Both bipartite and monopartite viruses were detected, including seven new begomovirus species from Guatemala, Puerto Rico, and Spain. This begomovirus survey extends the known diversity of these highly damaging plant viruses. However, the new genomes described here and in the recent literature appear to reflect the outcome of interactions between closely-related species, often resulting from recombination, instead of unique, highly divergent species.
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Affiliation(s)
- Karyna Rosario
- College of Marine Science, University of South Florida, Saint Petersburg, FL 33701, USA.
| | - Yee Mey Seah
- Microbiology and Molecular Genetics, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.
| | - Christian Marr
- College of Marine Science, University of South Florida, Saint Petersburg, FL 33701, USA.
| | - Arvind Varsani
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Ilam, Christchurch 8041, New Zealand.
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA.
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Rondebosch, Cape Town 7701, South Africa.
| | - Simona Kraberger
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Ilam, Christchurch 8041, New Zealand.
| | - Daisy Stainton
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Ilam, Christchurch 8041, New Zealand.
| | - Enrique Moriones
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Estación Experimental "La Mayora", Algarrobo-Costa, Málaga 29750, Spain.
| | - Jane E Polston
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA.
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.
| | - Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, FL 33701, USA.
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67
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Kumar RV, Singh AK, Singh AK, Yadav T, Basu S, Kushwaha N, Chattopadhyay B, Chakraborty S. Complexity of begomovirus and betasatellite populations associated with chilli leaf curl disease in India. J Gen Virol 2015; 96:3143-3158. [PMID: 26251220 DOI: 10.1099/jgv.0.000254] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
Chilli, which encompasses several species in the genus Capsicum, is widely consumed throughout the world. In the Indian subcontinent, production of chilli is constrained due to chilli leaf curl disease (ChiLCD) caused by begomoviruses. Despite the considerable economic consequences of ChiLCD on chilli cultivation in India, there have been scant studies of the genetic diversity and structure of the begomoviruses that cause this disease. Here we report on a comprehensive survey across major chilli-growing regions in India. Analysis of samples collected in the survey indicates that ChiLCD-infected plants are associated with a complex of begomoviruses (including one previously unreported species) with a diverse group of betasatellites found in crops and weeds. The associated betasatellites neither enhanced the accumulation of the begomovirus components nor reduced the incubation period in Nicotiana benthamiana. The ChiLCD-associated begomoviruses induced mild symptoms on Capsicum spp., but both the level of helper virus that accumulated and the severity of symptoms were increased in the presence of cognate betasatellites. Interestingly, most of the begomoviruses were found to be intra-species recombinants. The betasatellites possess high nucleotide variability, and recombination among them was also evident. The nucleotide substitution rates were determined for the AV1 gene of begomoviruses (2.60 × 10- 3 substitutions site- 1 year- 1) and the βC1 gene of betasatellites [chilli leaf curl betasatellite (ChiLCB), 2.57 × 10- 4 substitution site- 1 year- 1; tomato leaf curl Bangladesh betasatellite (ToLCBDB), 5.22 × 10- 4 substitution site- 1 year- 1]. This study underscores the current understanding of Indian ChiLCD-associated begomoviruses and also demonstrates the crucial role of betasatellites in severe disease development in Capsicum spp.
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Affiliation(s)
- R Vinoth Kumar
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi- 110 067, India
| | - Achuit Kumar Singh
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi- 110 067, India
| | - Ashish Kumar Singh
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi- 110 067, India
| | - Tribhuwan Yadav
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi- 110 067, India
- Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, USA
| | - Saumik Basu
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi- 110 067, India
- Department of Entomology, University of Nebraska, Lincoln, USA
| | - Nirbhay Kushwaha
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi- 110 067, India
| | - Brotati Chattopadhyay
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi- 110 067, India
| | - Supriya Chakraborty
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi- 110 067, India
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68
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Murray GGR, Wang F, Harrison EM, Paterson GK, Mather AE, Harris SR, Holmes MA, Rambaut A, Welch JJ. The effect of genetic structure on molecular dating and tests for temporal signal. Methods Ecol Evol 2015; 7:80-89. [PMID: 27110344 PMCID: PMC4832290 DOI: 10.1111/2041-210x.12466] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/23/2015] [Indexed: 12/23/2022]
Abstract
‘Dated‐tip’ methods of molecular dating use DNA sequences sampled at different times, to estimate the age of their most recent common ancestor. Several tests of ‘temporal signal’ are available to determine whether data sets are suitable for such analysis. However, it remains unclear whether these tests are reliable. We investigate the performance of several tests of temporal signal, including some recently suggested modifications. We use simulated data (where the true evolutionary history is known), and whole genomes of methicillin‐resistant Staphylococcus aureus (to show how particular problems arise with real‐world data sets). We show that all of the standard tests of temporal signal are seriously misleading for data where temporal and genetic structures are confounded (i.e. where closely related sequences are more likely to have been sampled at similar times). This is not an artefact of genetic structure or tree shape per se, and can arise even when sequences have measurably evolved during the sampling period. More positively, we show that a ‘clustered permutation’ approach introduced by Duchêne et al. (Molecular Biology and Evolution, 32, 2015, 1895) can successfully correct for this artefact in all cases and introduce techniques for implementing this method with real data sets. The confounding of temporal and genetic structures may be difficult to avoid in practice, particularly for outbreaks of infectious disease, or when using ancient DNA. Therefore, we recommend the use of ‘clustered permutation’ for all analyses. The failure of the standard tests may explain why different methods of dating pathogen origins have reached such wildly different conclusions.
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Affiliation(s)
- Gemma G R Murray
- Department of Genetics University of Cambridge Downing Street Cambridge CB2 3EH UK
| | - Fang Wang
- Department of Genetics University of Cambridge Downing Street Cambridge CB2 3EH UK
| | - Ewan M Harrison
- Department of Veterinary Medicine University of Cambridge Madingley Road Cambridge CB3 0ES UK
| | - Gavin K Paterson
- Department of Veterinary Medicine University of Cambridge Madingley Road Cambridge CB3 0ESUK; School of Biological, Biomedical and Environmental Sciences University of Hull Cottingham Road Hull HU6 7RX UK
| | - Alison E Mather
- Department of Veterinary Medicine University of Cambridge Madingley Road Cambridge CB3 0ESUK; Wellcome Trust Sanger Institute Hinxton CB10 1SA UK
| | | | - Mark A Holmes
- Department of Veterinary Medicine University of Cambridge Madingley Road Cambridge CB3 0ES UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology University of Edinburgh King's Buildings Edinburgh EH9 3FL UK
| | - John J Welch
- Department of Genetics University of Cambridge Downing Street Cambridge CB2 3EH UK
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69
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George B, Alam CM, Kumar RV, Gnanasekaran P, Chakraborty S. Potential linkage between compound microsatellites and recombination in geminiviruses: Evidence from comparative analysis. Virology 2015; 482:41-50. [DOI: 10.1016/j.virol.2015.03.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 02/16/2015] [Accepted: 03/05/2015] [Indexed: 01/10/2023]
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70
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Rosario K, Schenck RO, Harbeitner RC, Lawler SN, Breitbart M. Novel circular single-stranded DNA viruses identified in marine invertebrates reveal high sequence diversity and consistent predicted intrinsic disorder patterns within putative structural proteins. Front Microbiol 2015. [PMID: 26217327 PMCID: PMC4498126 DOI: 10.3389/fmicb.2015.00696] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Viral metagenomics has recently revealed the ubiquitous and diverse nature of single-stranded DNA (ssDNA) viruses that encode a conserved replication initiator protein (Rep) in the marine environment. Although eukaryotic circular Rep-encoding ssDNA (CRESS-DNA) viruses were originally thought to only infect plants and vertebrates, recent studies have identified these viruses in a number of invertebrates. To further explore CRESS-DNA viruses in the marine environment, this study surveyed CRESS-DNA viruses in various marine invertebrate species. A total of 27 novel CRESS-DNA genomes, with Reps that share less than 60.1% identity with previously reported viruses, were recovered from 21 invertebrate species, mainly crustaceans. Phylogenetic analysis based on the Rep revealed a novel clade of CRESS-DNA viruses that included approximately one third of the marine invertebrate associated viruses identified here and whose members may represent a novel family. Investigation of putative capsid proteins (Cap) encoded within the eukaryotic CRESS-DNA viral genomes from this study and those in GenBank demonstrated conserved patterns of predicted intrinsically disordered regions (IDRs), which can be used to complement similarity-based searches to identify divergent structural proteins within novel genomes. Overall, this study expands our knowledge of CRESS-DNA viruses associated with invertebrates and explores a new tool to evaluate divergent structural proteins encoded by these viruses.
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Affiliation(s)
- Karyna Rosario
- College of Marine Science, University of South Florida St. Petersburg, FL, USA
| | - Ryan O Schenck
- College of Marine Science, University of South Florida St. Petersburg, FL, USA
| | - Rachel C Harbeitner
- College of Marine Science, University of South Florida St. Petersburg, FL, USA
| | - Stephanie N Lawler
- College of Marine Science, University of South Florida St. Petersburg, FL, USA
| | - Mya Breitbart
- College of Marine Science, University of South Florida St. Petersburg, FL, USA
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71
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Krupovic M, Zhi N, Li J, Hu G, Koonin EV, Wong S, Shevchenko S, Zhao K, Young NS. Multiple layers of chimerism in a single-stranded DNA virus discovered by deep sequencing. Genome Biol Evol 2015; 7:993-1001. [PMID: 25840414 PMCID: PMC4419787 DOI: 10.1093/gbe/evv034] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Viruses with single-stranded (ss) DNA genomes infect hosts in all three domains of life and include many medically, ecologically, and economically important pathogens. Recently, a new group of ssDNA viruses with chimeric genomes has been discovered through viral metagenomics. These chimeric viruses combine capsid protein genes and replicative protein genes that, respectively, appear to have been inherited from viruses with positive-strand RNA genomes, such as tombusviruses, and ssDNA genomes, such as circoviruses, nanoviruses or geminiviruses. Here, we describe the genome sequence of a new representative of this virus group and reveal an additional layer of chimerism among ssDNA viruses. We show that not only do these viruses encompass genes for capsid proteins and replicative proteins that have distinct evolutionary histories, but also the replicative genes themselves are chimeras of functional domains inherited from viruses of different families. Our results underscore the importance of horizontal gene transfer in the evolution of ssDNA viruses and the role of genetic recombination in the emergence of novel virus groups.
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Affiliation(s)
- Mart Krupovic
- Department of Microbiology, Institut Pasteur, Paris, France
| | - Ning Zhi
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Jungang Li
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Gangqing Hu
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD
| | - Susan Wong
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Sofiya Shevchenko
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Keji Zhao
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Neal S Young
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
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72
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Duchêne S, Duchêne D, Holmes EC, Ho SYW. The Performance of the Date-Randomization Test in Phylogenetic Analyses of Time-Structured Virus Data. Mol Biol Evol 2015; 32:1895-906. [PMID: 25771196 DOI: 10.1093/molbev/msv056] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Rates and timescales of viral evolution can be estimated using phylogenetic analyses of time-structured molecular sequences. This involves the use of molecular-clock methods, calibrated by the sampling times of the viral sequences. However, the spread of these sampling times is not always sufficient to allow the substitution rate to be estimated accurately. We conducted Bayesian phylogenetic analyses of simulated virus data to evaluate the performance of the date-randomization test, which is sometimes used to investigate whether time-structured data sets have temporal signal. An estimate of the substitution rate passes this test if its mean does not fall within the 95% credible intervals of rate estimates obtained using replicate data sets in which the sampling times have been randomized. We find that the test sometimes fails to detect rate estimates from data with no temporal signal. This error can be minimized by using a more conservative criterion, whereby the 95% credible interval of the estimate with correct sampling times should not overlap with those obtained with randomized sampling times. We also investigated the behavior of the test when the sampling times are not uniformly distributed throughout the tree, which sometimes occurs in empirical data sets. The test performs poorly in these circumstances, such that a modification to the randomization scheme is needed. Finally, we illustrate the behavior of the test in analyses of nucleotide sequences of cereal yellow dwarf virus. Our results validate the use of the date-randomization test and allow us to propose guidelines for interpretation of its results.
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Affiliation(s)
- Sebastián Duchêne
- School of Biological Sciences, University of Sydney, Sydney, NSW, Australia
| | - David Duchêne
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Edward C Holmes
- School of Biological Sciences, University of Sydney, Sydney, NSW, Australia Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Simon Y W Ho
- School of Biological Sciences, University of Sydney, Sydney, NSW, Australia
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73
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Pérez-Losada M, Arenas M, Galán JC, Palero F, González-Candelas F. Recombination in viruses: mechanisms, methods of study, and evolutionary consequences. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2015; 30:296-307. [PMID: 25541518 PMCID: PMC7106159 DOI: 10.1016/j.meegid.2014.12.022] [Citation(s) in RCA: 198] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Revised: 12/15/2014] [Accepted: 12/17/2014] [Indexed: 02/08/2023]
Abstract
Recombination is a pervasive process generating diversity in most viruses. It joins variants that arise independently within the same molecule, creating new opportunities for viruses to overcome selective pressures and to adapt to new environments and hosts. Consequently, the analysis of viral recombination attracts the interest of clinicians, epidemiologists, molecular biologists and evolutionary biologists. In this review we present an overview of three major areas related to viral recombination: (i) the molecular mechanisms that underlie recombination in model viruses, including DNA-viruses (Herpesvirus) and RNA-viruses (Human Influenza Virus and Human Immunodeficiency Virus), (ii) the analytical procedures to detect recombination in viral sequences and to determine the recombination breakpoints, along with the conceptual and methodological tools currently used and a brief overview of the impact of new sequencing technologies on the detection of recombination, and (iii) the major areas in the evolutionary analysis of viral populations on which recombination has an impact. These include the evaluation of selective pressures acting on viral populations, the application of evolutionary reconstructions in the characterization of centralized genes for vaccine design, and the evaluation of linkage disequilibrium and population structure.
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Affiliation(s)
- Marcos Pérez-Losada
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Portugal; Computational Biology Institute, George Washington University, Ashburn, VA 20147, USA
| | - Miguel Arenas
- Centre for Molecular Biology "Severo Ochoa", Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Juan Carlos Galán
- Servicio de Microbiología, Hospital Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; CIBER en Epidemiología y Salud Pública, Spain
| | - Ferran Palero
- CIBER en Epidemiología y Salud Pública, Spain; Unidad Mixta Infección y Salud Pública, FISABIO-Universitat de València, Valencia, Spain
| | - Fernando González-Candelas
- CIBER en Epidemiología y Salud Pública, Spain; Unidad Mixta Infección y Salud Pública, FISABIO-Universitat de València, Valencia, Spain.
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Bioinformatic analysis reveals genome size reduction and the emergence of tyrosine phosphorylation site in the movement protein of New World bipartite begomoviruses. PLoS One 2014; 9:e111957. [PMID: 25383632 PMCID: PMC4226511 DOI: 10.1371/journal.pone.0111957] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 10/09/2014] [Indexed: 11/19/2022] Open
Abstract
Begomovirus (genus Begomovirus, family Geminiviridae) infection is devastating to a wide variety of agricultural crops including tomato, squash, and cassava. Thus, understanding the replication and adaptation of begomoviruses has important translational value in alleviating substantial economic loss, particularly in developing countries. The bipartite genome of begomoviruses prevalent in the New World and their counterparts in the Old World share a high degree of genome homology except for a partially overlapping reading frame encoding the pre-coat protein (PCP, or AV2). PCP contributes to the essential functions of intercellular movement and suppression of host RNA silencing, but it is only present in the Old World viruses. In this study, we analyzed a set of non-redundant bipartite begomovirus genomes originating from the Old World (N = 28) and the New World (N = 65). Our bioinformatic analysis suggests ∼ 120 nucleotides were deleted from PCP's proximal promoter region that may have contributed to its loss in the New World viruses. Consequently, genomes of the New World viruses are smaller than the Old World counterparts, possibly compensating for the loss of the intercellular movement functions of PCP. Additionally, we detected substantial purifying selection on a portion of the New World DNA-B movement protein (MP, or BC1). Further analysis of the New World MP gene revealed the emergence of a putative tyrosine phosphorylation site, which likely explains the increased purifying selection in that region. These findings provide important information about the strategies adopted by bipartite begomoviruses in adapting to new environment and suggest future in planta experiments.
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75
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Evolution of cocirculating varicella-zoster virus genotypes during a chickenpox outbreak in Guinea-Bissau. J Virol 2014; 88:13936-46. [PMID: 25275123 PMCID: PMC4249134 DOI: 10.1128/jvi.02337-14] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Varicella-zoster virus (VZV), a double-stranded DNA alphaherpesvirus, is associated with seasonal outbreaks of varicella in nonimmunized populations. Little is known about whether these outbreaks are associated with a single or multiple viral genotypes and whether new mutations rapidly accumulate during transmission. Here, we take advantage of a well-characterized population cohort in Guinea-Bissau and produce a unique set of 23 full-length genome sequences, collected over 7 months from eight households. Comparative sequence analysis reveals that four distinct genotypes cocirculated among the population, three of which were present during the first week of the outbreak, although no patients were coinfected, which indicates that exposure to infectious virus from multiple sources is common during VZV outbreaks. Transmission of VZV was associated with length polymorphisms in the R1 repeat region and the origin of DNA replication. In two cases, these were associated with the formation of distinct lineages and point to the possible coevolution of these loci, despite the lack of any known functional link in VZV or related herpesviruses. We show that these and all other sequenced clade 5 viruses possess a distinct R1 repeat motif that increases the acidity of an ORF11p protein domain and postulate that this has either arisen or been lost following divergence of the major clades. Thus, sequencing of whole VZV genomes collected during an outbreak has provided novel insights into VZV biology, transmission patterns, and (recent) natural history. IMPORTANCE VZV is a highly infectious virus and the causative agent of chickenpox and shingles, the latter being particularly associated with the risk of painful complications. Seasonal outbreaks of chickenpox are very common among young children, yet little is known about the dynamics of the virus during person-to-person to transmission or whether multiple distinct viruses seed and/or cocirculate during an outbreak. In this study, we have sequenced chickenpox viruses from an outbreak in Guinea-Bissau that are supported by detailed epidemiological data. Our data show that multiple different virus strains seeded and were maintained throughout the 6-month outbreak period and that viruses transmitted between individuals accumulated new mutations in specific genomic regions. Of particular interest is the potential coevolution of two distinct parts of the genomes and our calculations of the rate of viral mutation, both of which increase our understanding of how VZV evolves over short periods of time in human populations.
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76
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High-resolution mapping of resistance to cassava mosaic geminiviruses in cassava using genotyping-by-sequencing and its implications for breeding. Virus Res 2014; 186:87-96. [DOI: 10.1016/j.virusres.2013.12.028] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 12/18/2013] [Accepted: 12/20/2013] [Indexed: 11/20/2022]
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77
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Varsani A, Kraberger S, Jennings S, Porzig EL, Julian L, Massaro M, Pollard A, Ballard G, Ainley DG. A novel papillomavirus in Adélie penguin (Pygoscelis adeliae) faeces sampled at the Cape Crozier colony, Antarctica. J Gen Virol 2014; 95:1352-1365. [PMID: 24686913 DOI: 10.1099/vir.0.064436-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Papillomaviruses are epitheliotropic viruses that have circular dsDNA genomes encapsidated in non-enveloped virions. They have been found to infect a variety of mammals, reptiles and birds, but so far they have not been found in amphibians. Using a next-generation sequencing de novo assembly contig-informed recovery, we cloned and Sanger sequenced the complete genome of a novel papillomavirus from the faecal matter of Adélie penguins (Pygoscelis adeliae) nesting on Ross Island, Antarctica. The genome had all the usual features of a papillomavirus and an E9 ORF encoding a protein of unknown function that is found in all avian papillomaviruses to date. This novel papillomavirus genome shared ~60 % pairwise identity with the genomes of the other three known avian papillomaviruses: Fringilla coelebs papillomavirus 1 (FcPV1), Francolinus leucoscepus papillomavirus 1 (FlPV1) and Psittacus erithacus papillomavirus 1. Pairwise identity analysis and phylogenetic analysis of the major capsid protein gene clearly indicated that it represents a novel species, which we named Pygoscelis adeliae papillomavirus 1 (PaCV1). No evidence of recombination was detected in the genome of PaCV1, but we did detect a recombinant region (119 nt) in the E6 gene of FlPV1 with the recombinant region being derived from ancestral FcPV1-like sequences. Previously only paramyxoviruses, orthomyxoviruses and avian pox viruses have been genetically identified in penguins; however, the majority of penguin viral identifications have been based on serology or histology. This is the first report, to our knowledge, of a papillomavirus associated with a penguin species.
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Affiliation(s)
- Arvind Varsani
- Electron Microscope Unit, Division of Medical Biochemistry, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, 7700, South Africa.,Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA.,School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Simona Kraberger
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Scott Jennings
- Department of Fisheries and Wildlife, Oregon Cooperative Fish and Wildlife Research Unit, US Geological Survey, Oregon State University, Corvallis, OR, USA
| | | | - Laurel Julian
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Melanie Massaro
- School of Environmental Sciences, Charles Sturt University, Albury, NSW 2640, Australia
| | | | - Grant Ballard
- Point Blue Conservation Science, Petaluma, CA 94954, USA
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78
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Stenzel T, Piasecki T, Chrząstek K, Julian L, Muhire BM, Golden M, Martin DP, Varsani A. Pigeon circoviruses display patterns of recombination, genomic secondary structure and selection similar to those of beak and feather disease viruses. J Gen Virol 2014; 95:1338-1351. [PMID: 24639400 DOI: 10.1099/vir.0.063917-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Pigeon circovirus (PiCV) has a ~2 kb genome circular ssDNA genome. All but one of the known PiCV isolates have been found infecting pigeons in various parts of the world. In this study, we screened 324 swab and tissue samples from Polish pigeons and recovered 30 complete genomes, 16 of which came from birds displaying no obvious pathology. Together with 17 other publicly available PiCV complete genomes sampled throughout the Northern Hemisphere and Australia, we find that PiCV displays a similar degree of genetic diversity to that of the related psittacine-infecting circovirus species, beak and feather disease virus (BFDV). We show that, as is the case with its pathology and epidemiology, PiCV also displays patterns of recombination, genomic secondary structure and natural selection that are generally very similar to those of BFDV. It is likely that breeding facilities play a significant role in the emergence of new recombinant PiCV variants and given that ~50 % of the domestic pigeon population is infected subclinically, all pigeon breeding stocks should be screened routinely for this virus.
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Affiliation(s)
- Tomasz Stenzel
- Department of Avian Diseases, Faculty of Veterinary Medicine, University of Warmia and Mazury, ul. Oczapowskiego 13, 10-719 Olsztyn, Poland
| | - Tomasz Piasecki
- Department of Epizootiology with Clinic of Birds and Exotic Animals, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, 50-360 Wrocław, Poland
| | - Klaudia Chrząstek
- Department of Epizootiology with Clinic of Birds and Exotic Animals, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, 50-360 Wrocław, Poland
| | - Laurel Julian
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Brejnev M Muhire
- Institute of Infectious Diseases and Molecular Medicine, Computational Biology Group, University of Cape Town, South Africa
| | - Michael Golden
- Institute of Infectious Diseases and Molecular Medicine, Computational Biology Group, University of Cape Town, South Africa
| | - Darren P Martin
- Institute of Infectious Diseases and Molecular Medicine, Computational Biology Group, University of Cape Town, South Africa
| | - Arvind Varsani
- Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA.,Electron Microscope Unit, Division of Medical Biochemistry, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory 7700, South Africa.,School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand.,Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand
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79
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Abstract
Studying phage codon adaptation is important not only for understanding the process of translation elongation, but also for reengineering phages for medical and industrial purposes. To evaluate the effect of mutation and selection on phage codon usage, we developed an index to measure selection imposed by host translation machinery, based on the difference in codon usage between all host genes and highly expressed host genes. We developed linear and nonlinear models to estimate the C→T mutation bias in different phage lineages and to evaluate the relative effect of mutation and host selection on phage codon usage. C→T-biased mutations occur more frequently in single-stranded DNA (ssDNA) phages than in double-stranded DNA (dsDNA) phages and affect not only synonymous codon usage, but also nonsynonymous substitutions at second codon positions, especially in ssDNA phages. The host translation machinery affects codon adaptation in both dsDNA and ssDNA phages, with a stronger effect on dsDNA phages than on ssDNA phages. Strand asymmetry with the associated local variation in mutation bias can significantly interfere with codon adaptation in both dsDNA and ssDNA phages.
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80
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De novo reconstruction of consensus master genomes of plant RNA and DNA viruses from siRNAs. PLoS One 2014; 9:e88513. [PMID: 24523907 PMCID: PMC3921208 DOI: 10.1371/journal.pone.0088513] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 01/06/2014] [Indexed: 11/19/2022] Open
Abstract
Virus-infected plants accumulate abundant, 21-24 nucleotide viral siRNAs which are generated by the evolutionary conserved RNA interference (RNAi) machinery that regulates gene expression and defends against invasive nucleic acids. Here we show that, similar to RNA viruses, the entire genome sequences of DNA viruses are densely covered with siRNAs in both sense and antisense orientations. This implies pervasive transcription of both coding and non-coding viral DNA in the nucleus, which generates double-stranded RNA precursors of viral siRNAs. Consistent with our finding and hypothesis, we demonstrate that the complete genomes of DNA viruses from Caulimoviridae and Geminiviridae families can be reconstructed by deep sequencing and de novo assembly of viral siRNAs using bioinformatics tools. Furthermore, we prove that this 'siRNA omics' approach can be used for reliable identification of the consensus master genome and its microvariants in viral quasispecies. Finally, we utilized this approach to reconstruct an emerging DNA virus and two viroids associated with economically-important red blotch disease of grapevine, and to rapidly generate a biologically-active clone representing the wild type master genome of Oilseed rape mosaic virus. Our findings show that deep siRNA sequencing allows for de novo reconstruction of any DNA or RNA virus genome and its microvariants, making it suitable for universal characterization of evolving viral quasispecies as well as for studying the mechanisms of siRNA biogenesis and RNAi-based antiviral defense.
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81
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Smith O, Clapham A, Rose P, Liu Y, Wang J, Allaby RG. A complete ancient RNA genome: identification, reconstruction and evolutionary history of archaeological Barley Stripe Mosaic Virus. Sci Rep 2014; 4:4003. [PMID: 24499968 PMCID: PMC3915304 DOI: 10.1038/srep04003] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 01/20/2014] [Indexed: 01/12/2023] Open
Abstract
The origins of many plant diseases appear to be recent and associated with the rise of domestication, the spread of agriculture or recent global movements of crops. Distinguishing between these possibilities is problematic because of the difficulty of determining rates of molecular evolution over short time frames. Heterochronous approaches using recent and historical samples show that plant viruses exhibit highly variable and often rapid rates of molecular evolution. The accuracy of estimated evolution rates and age of origin can be greatly improved with the inclusion of older molecular data from archaeological material. Here we present the first reconstruction of an archaeological RNA genome, which is of Barley Stripe Mosaic Virus (BSMV) isolated from barley grain ~750 years of age. Phylogenetic analysis of BSMV that includes this genome indicates the divergence of BSMV and its closest relative prior to this time, most likely around 2000 years ago. However, exclusion of the archaeological data results in an apparently much more recent origin of the virus that postdates even the archaeological sample. We conclude that this viral lineage originated in the Near East or North Africa, and spread to North America and East Asia with their hosts along historical trade routes.
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Affiliation(s)
- Oliver Smith
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry CV4 7AL
| | - Alan Clapham
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry CV4 7AL
| | - Pam Rose
- The Austrian Archaeological Institute; Cairo Branch, Zamalek, Sharia Ismail Muhammed, Apt 62/72, Cairo, Egypt
| | - Yuan Liu
- BGI-Europe-UK, 9 Devonshire Square, London, EC2M 4YF, UK
| | - Jun Wang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Robin G Allaby
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry CV4 7AL
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82
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Yang XL, Zhou MN, Qian YJ, Xie Y, Zhou XP. Molecular variability and evolution of a natural population of tomato yellow leaf curl virus in Shanghai, China. J Zhejiang Univ Sci B 2014; 15:133-42. [PMID: 24510706 PMCID: PMC3924389 DOI: 10.1631/jzus.b1300110] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 08/21/2013] [Indexed: 11/11/2022]
Abstract
Tomato yellow leaf curl virus (TYLCV), belonging to the genus Begomovirus of the family Geminiviridae, is emerging as the most destructive pathogen of tomato plants. Since the first report of TYLCV in Shanghai, China in 2006, TYLCV has spread rapidly to 13 provinces or autonomous regions of China. In this study, the molecular variability and evolution of TYLCV were monitored in Shanghai from its first upsurge in 2006 until 2010. Full-length genomic sequences of 26 isolates were obtained by rolling circle amplification. Sequence analysis showed that the intergenic region was the most variable, with a mean mutation rate of 4.81×10(-3) nucleotide substitutions per site per year. Genetic differentiation was found within isolates obtained from 2006, 2009, and 2010, though a linear increase in genetic diversity over time was not evident. Whilst significant parts of TYLCV genes were under negative selection, the C4 gene embedded entirely within the C1 gene had a tendency to undergo positive selection. Our results indicate that a mechanism of independent evolution of overlapping regions could apply to the natural population of TYLCV in Shanghai, China.
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83
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Cell tropism predicts long-term nucleotide substitution rates of mammalian RNA viruses. PLoS Pathog 2014; 10:e1003838. [PMID: 24415935 PMCID: PMC3887100 DOI: 10.1371/journal.ppat.1003838] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 11/04/2013] [Indexed: 02/05/2023] Open
Abstract
The high rates of RNA virus evolution are generally attributed to replication with error-prone RNA-dependent RNA polymerases. However, these long-term nucleotide substitution rates span three orders of magnitude and do not correlate well with mutation rates or selection pressures. This substitution rate variation may be explained by differences in virus ecology or intrinsic genomic properties. We generated nucleotide substitution rate estimates for mammalian RNA viruses and compiled comparable published rates, yielding a dataset of 118 substitution rates of structural genes from 51 different species, as well as 40 rates of non-structural genes from 28 species. Through ANCOVA analyses, we evaluated the relationships between these rates and four ecological factors: target cell, transmission route, host range, infection duration; and three genomic properties: genome length, genome sense, genome segmentation. Of these seven factors, we found target cells to be the only significant predictors of viral substitution rates, with tropisms for epithelial cells or neurons (P<0.0001) as the most significant predictors. Further, one-tailed t-tests showed that viruses primarily infecting epithelial cells evolve significantly faster than neurotropic viruses (P<0.0001 and P<0.001 for the structural genes and non-structural genes, respectively). These results provide strong evidence that the fastest evolving mammalian RNA viruses infect cells with the highest turnover rates: the highly proliferative epithelial cells. Estimated viral generation times suggest that epithelial-infecting viruses replicate more quickly than viruses with different cell tropisms. Our results indicate that cell tropism is a key factor in viral evolvability. RNA viruses are the fastest evolving human pathogens, making their treatment and control difficult. Compared to DNA viruses, RNA viruses replicate with much lower fidelity, which can explain why RNA viruses evolve significantly faster than most DNA viruses. However, there is tremendous variation among the evolutionary rates of different RNA viruses, which is not explained by variation in mutation rates. Here we present a survey of mammalian RNA virus rates of evolution, and a comprehensive comparison of these rates to different properties of virus genomic architecture and ecology. We found that cell tropism is the most significant predictor of long-term rates of mammalian RNA virus evolution. For instance, viruses targeting epithelial cells evolve significantly faster than viruses that target neurons. Our results provide mechanistic insight into why viruses that infect respiratory and gastrointestinal epithelia have been difficult to control.
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84
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Sarker S, Patterson EI, Peters A, Baker GB, Forwood JK, Ghorashi SA, Holdsworth M, Baker R, Murray N, Raidal SR. Mutability dynamics of an emergent single stranded DNA virus in a naïve host. PLoS One 2014; 9:e85370. [PMID: 24416396 PMCID: PMC3885698 DOI: 10.1371/journal.pone.0085370] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 11/26/2013] [Indexed: 01/21/2023] Open
Abstract
Quasispecies variants and recombination were studied longitudinally in an emergent outbreak of beak and feather disease virus (BFDV) infection in the orange-bellied parrot (Neophema chrysogaster). Detailed health monitoring and the small population size (<300 individuals) of this critically endangered bird provided an opportunity to longitudinally track viral replication and mutation events occurring in a circular, single-stranded DNA virus over a period of four years within a novel bottleneck population. Optimized PCR was used with different combinations of primers, primer walking, direct amplicon sequencing and sequencing of cloned amplicons to analyze BFDV genome variants. Analysis of complete viral genomes (n = 16) and Rep gene sequences (n = 35) revealed that the outbreak was associated with mutations in functionally important regions of the normally conserved Rep gene and immunogenic capsid (Cap) gene with a high evolutionary rate (3.41×10−3 subs/site/year) approaching that for RNA viruses; simultaneously we observed significant evidence of recombination hotspots between two distinct progenitor genotypes within orange-bellied parrots indicating early cross-transmission of BFDV in the population. Multiple quasispecies variants were also demonstrated with at least 13 genotypic variants identified in four different individual birds, with one containing up to seven genetic variants. Preferential PCR amplification of variants was also detected. Our findings suggest that the high degree of genetic variation within the BFDV species as a whole is reflected in evolutionary dynamics within individually infected birds as quasispecies variation, particularly when BFDV jumps from one host species to another.
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Affiliation(s)
- Subir Sarker
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
- Graham Centre for Agricultural Innovation (NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga, New South Wales, Australia
| | - Edward I. Patterson
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
- Graham Centre for Agricultural Innovation (NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga, New South Wales, Australia
| | - Andrew Peters
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
- Graham Centre for Agricultural Innovation (NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga, New South Wales, Australia
| | - G. Barry Baker
- Institute of Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Jade K. Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
- Graham Centre for Agricultural Innovation (NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga, New South Wales, Australia
| | - Seyed A. Ghorashi
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
- Graham Centre for Agricultural Innovation (NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga, New South Wales, Australia
| | - Mark Holdsworth
- Biodiversity Conservation Branch, Department of Primary Industries, Parks, Water and Environment, Hobart, Tasmania, Australia
| | - Rupert Baker
- Healesville Sanctuary, Zoos Victoria, Healesville, Victoria, Australia
| | - Neil Murray
- Department of Genetics, La Trobe University, Bundoora, Victoria, Australia
| | - Shane R. Raidal
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
- Graham Centre for Agricultural Innovation (NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga, New South Wales, Australia
- * E-mail:
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85
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Rocha CS, Castillo-Urquiza GP, Lima ATM, Silva FN, Xavier CAD, Hora-Júnior BT, Beserra-Júnior JEA, Malta AWO, Martin DP, Varsani A, Alfenas-Zerbini P, Mizubuti ESG, Zerbini FM. Brazilian begomovirus populations are highly recombinant, rapidly evolving, and segregated based on geographical location. J Virol 2013; 87:5784-99. [PMID: 23487451 PMCID: PMC3648162 DOI: 10.1128/jvi.00155-13] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 03/04/2013] [Indexed: 01/21/2023] Open
Abstract
The incidence of begomovirus infections in crop plants sharply increased in Brazil during the 1990s following the introduction of the invasive B biotype of the whitefly vector, Bemisia tabaci. It is believed that this biotype transmitted begomoviruses from noncultivated plants to crop species with greater efficiency than indigenous B. tabaci biotypes. Either through rapid host adaptation or selection pressure in genetically diverse populations of noncultivated hosts, over the past 20 years various previously unknown begomovirus species have became progressively more prevalent in cultivated species such as tomato. Here we assess the genetic structure of begomovirus populations infecting tomatoes and noncultivated hosts in southeastern Brazil. Between 2005 and 2010, we sampled and sequenced 126 DNA-A and 58 DNA-B full-length begomovirus components. We detected nine begomovirus species in tomatoes and eight in the noncultivated host samples, with four species common to both tomatoes and noncultivated hosts. Like many begomoviruses, most species are obvious interspecies recombinants. Furthermore, species identified in tomato have probable parental viruses from noncultivated hosts. While the population structures of five well-sampled viral species all displayed geographical subdivision, a noncultivated host-infecting virus was more genetically variable than the four predominantly tomato-infecting viruses.
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Affiliation(s)
- Carolina S. Rocha
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Gloria P. Castillo-Urquiza
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Alison T. M. Lima
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Fábio N. Silva
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Cesar A. D. Xavier
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Braz T. Hora-Júnior
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - José E. A. Beserra-Júnior
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Antonio W. O. Malta
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Darren P. Martin
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, Cape Town, South Africa
| | - Arvind Varsani
- Electron Microscope Unit, University of Cape Town, Rondebosch, Cape Town, South Africa
- School of Biological Sciences, University of Canterbury, Ilam, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Ilam, Christchurch, New Zealand
| | - Poliane Alfenas-Zerbini
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Eduardo S. G. Mizubuti
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - F. Murilo Zerbini
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
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86
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Sánchez-Campos S, Martínez-Ayala A, Márquez-Martín B, Aragón-Caballero L, Navas-Castillo J, Moriones E. Fulfilling Koch's postulates confirms the monopartite nature of tomato leaf deformation virus: a begomovirus native to the New World. Virus Res 2013; 173:286-93. [PMID: 23415858 DOI: 10.1016/j.virusres.2013.02.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Revised: 01/25/2013] [Accepted: 02/05/2013] [Indexed: 10/27/2022]
Abstract
The monopartite nature of the begomovirus tomato leaf deformation virus (ToLDeV) reported in Peru is demonstrated here. The DNA molecule cloned from an infected plant was shown to be fully infectious in tomatoes inducing leaf curling and stunted growth similar to that observed in field-infected plants. The viral DNA was reisolated from systemically infected tissues of inoculated plants, thus fulfilling Koch's postulates. ToLDeV was demonstrated, therefore, as the causal agent of the disease syndrome widespread in tomato crops in Peru. This virus was shown to be present throughout the major tomato-growing regions of this country, both in tomatoes and wild plants. Analyses of the sequences of 51 ToLDeV isolates revealed a significant genetic diversity with three major genetic types co-circulating in the population. A geographical segregation was observed which should be taken into account for virus control. Constraints to genetic divergence found for the C4 gene of ToLDeV isolates suggest a relevant function for this protein. The results obtained confirm ToLDeV as a monopartite begomovirus native to the New World, which is a significant finding for this region.
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Affiliation(s)
- S Sánchez-Campos
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Estación Experimental La Mayora, 29750 Algarrobo-Costa, Málaga, Spain
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87
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Rodelo-Urrego M, Pagán I, González-Jara P, Betancourt M, Moreno-Letelier A, Ayllón MA, Fraile A, Piñero D, García-Arenal F. Landscape heterogeneity shapes host-parasite interactions and results in apparent plant-virus codivergence. Mol Ecol 2013; 22:2325-40. [DOI: 10.1111/mec.12232] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 12/12/2012] [Accepted: 12/20/2012] [Indexed: 12/22/2022]
Affiliation(s)
- M. Rodelo-Urrego
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and E.T.S.I. Agrónomos; Campus de Montegancedo; Universidad Politécnica de Madrid; Pozuelo de Alarcón Madrid 28223 Spain
| | - I. Pagán
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and E.T.S.I. Agrónomos; Campus de Montegancedo; Universidad Politécnica de Madrid; Pozuelo de Alarcón Madrid 28223 Spain
| | - P. González-Jara
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and E.T.S.I. Agrónomos; Campus de Montegancedo; Universidad Politécnica de Madrid; Pozuelo de Alarcón Madrid 28223 Spain
| | - M. Betancourt
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and E.T.S.I. Agrónomos; Campus de Montegancedo; Universidad Politécnica de Madrid; Pozuelo de Alarcón Madrid 28223 Spain
| | - A. Moreno-Letelier
- Departamento de Ecología Evolutiva; Instituto de Ecología; Universidad Nacional Autónoma de México; Apartado Postal 70-275 México DF 04510 México
| | - M. A. Ayllón
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and E.T.S.I. Agrónomos; Campus de Montegancedo; Universidad Politécnica de Madrid; Pozuelo de Alarcón Madrid 28223 Spain
| | - A. Fraile
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and E.T.S.I. Agrónomos; Campus de Montegancedo; Universidad Politécnica de Madrid; Pozuelo de Alarcón Madrid 28223 Spain
| | - D. Piñero
- Departamento de Ecología Evolutiva; Instituto de Ecología; Universidad Nacional Autónoma de México; Apartado Postal 70-275 México DF 04510 México
| | - F. García-Arenal
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and E.T.S.I. Agrónomos; Campus de Montegancedo; Universidad Politécnica de Madrid; Pozuelo de Alarcón Madrid 28223 Spain
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88
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Lima ATM, Sobrinho RR, González-Aguilera J, Rocha CS, Silva SJC, Xavier CAD, Silva FN, Duffy S, Zerbini FM. Synonymous site variation due to recombination explains higher genetic variability in begomovirus populations infecting non-cultivated hosts. J Gen Virol 2013; 94:418-431. [DOI: 10.1099/vir.0.047241-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Begomoviruses are ssDNA plant viruses that cause serious epidemics in economically important crops worldwide. Non-cultivated plants also harbour many begomoviruses, and it is believed that these hosts may act as reservoirs and as mixing vessels where recombination may occur. Begomoviruses are notoriously recombination-prone, and also display nucleotide substitution rates equivalent to those of RNA viruses. In Brazil, several indigenous begomoviruses have been described infecting tomatoes following the introduction of a novel biotype of the whitefly vector in the mid-1990s. More recently, a number of viruses from non-cultivated hosts have also been described. Previous work has suggested that viruses infecting non-cultivated hosts have a higher degree of genetic variability compared with crop-infecting viruses. We intensively sampled cultivated and non-cultivated plants in similarly sized geographical areas known to harbour either the weed-infecting Macroptilium yellow spot virus (MaYSV) or the crop-infecting Tomato severe rugose virus (ToSRV), and compared the molecular evolution and population genetics of these two distantly related begomoviruses. The results reinforce the assertion that infection of non-cultivated plant species leads to higher levels of standing genetic variability, and indicate that recombination, not adaptive selection, explains the higher begomovirus variability in non-cultivated hosts.
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Affiliation(s)
- Alison T. M. Lima
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
| | - Roberto R. Sobrinho
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
| | - Jorge González-Aguilera
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
| | - Carolina S. Rocha
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
| | - Sarah J. C. Silva
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
| | - César A. D. Xavier
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
| | - Fábio N. Silva
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - F. Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
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89
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Cardinale DJ, DeRosa K, Duffy S. Base composition and translational selection are insufficient to explain codon usage bias in plant viruses. Viruses 2013; 5:162-81. [PMID: 23322170 PMCID: PMC3564115 DOI: 10.3390/v5010162] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 01/09/2013] [Accepted: 01/11/2013] [Indexed: 02/06/2023] Open
Abstract
Viral codon usage bias may be the product of a number of synergistic or antagonistic factors, including genomic nucleotide composition, translational selection, genomic architecture, and mutational or repair biases. Most studies of viral codon bias evaluate only the relative importance of genomic base composition and translational selection, ignoring other possible factors. We analyzed the codon preferences of ssRNA (luteoviruses and potyviruses) and ssDNA (geminiviruses) plant viruses that infect translationally distinct monocot and dicot hosts. We found that neither genomic base composition nor translational selection satisfactorily explains their codon usage biases. Furthermore, we observed a strong relationship between the codon preferences of viruses in the same family or genus, regardless of host or genomic nucleotide content. Our results suggest that analyzing codon bias as either due to base composition or translational selection is a false dichotomy that obscures the role of other factors. Constraints such as genomic architecture and secondary structure can and do influence codon usage in plant viruses, and likely in viruses of other hosts.
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Affiliation(s)
- Daniel J Cardinale
- Department of Ecology, Evolution, and Natural Resources, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.
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90
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Monjane AL, Pande D, Lakay F, Shepherd DN, van der Walt E, Lefeuvre P, Lett JM, Varsani A, Rybicki EP, Martin DP. Adaptive evolution by recombination is not associated with increased mutation rates in Maize streak virus. BMC Evol Biol 2012; 12:252. [PMID: 23268599 PMCID: PMC3556111 DOI: 10.1186/1471-2148-12-252] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Accepted: 12/12/2012] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Single-stranded (ss) DNA viruses in the family Geminiviridae are proving to be very useful in real-time evolution studies. The high mutation rate of geminiviruses and other ssDNA viruses is somewhat mysterious in that their DNA genomes are replicated in host nuclei by high fidelity host polymerases. Although strand specific mutation biases observed in virus species from the geminivirus genus Mastrevirus indicate that the high mutation rates in viruses in this genus may be due to mutational processes that operate specifically on ssDNA, it is currently unknown whether viruses from other genera display similar strand specific mutation biases. Also, geminivirus genomes frequently recombine with one another and an alternative cause of their high mutation rates could be that the recombination process is either directly mutagenic or produces a selective environment in which the survival of mutants is favoured. To investigate whether there is an association between recombination and increased basal mutation rates or increased degrees of selection favoring the survival of mutations, we compared the mutation dynamics of the MSV-MatA and MSV-VW field isolates of Maize streak virus (MSV; Mastrevirus), with both a laboratory constructed MSV recombinant, and MSV recombinants closely resembling MSV-MatA. To determine whether strand specific mutation biases are a general characteristic of geminivirus evolution we compared mutation spectra arising during these MSV experiments with those arising during similar experiments involving the geminivirus Tomato yellow leaf curl virus (Begomovirus genus). RESULTS Although both the genomic distribution of mutations and the occurrence of various convergent mutations at specific genomic sites indicated that either mutation hotspots or selection for adaptive mutations might elevate observed mutation rates in MSV, we found no association between recombination and mutation rates. Importantly, when comparing the mutation spectra of MSV and TYLCV we observed similar strand specific mutation biases arising predominantly from imbalances in the complementary mutations G → T: C → A. CONCLUSIONS While our results suggest that recombination does not strongly influence mutation rates in MSV, they indicate that high geminivirus mutation rates are at least partially attributable to increased susceptibility of all geminivirus genomes to oxidative damage while in a single stranded state.
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Affiliation(s)
- Adérito L Monjane
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
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91
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De Bruyn A, Villemot J, Lefeuvre P, Villar E, Hoareau M, Harimalala M, Abdoul-Karime AL, Abdou-Chakour C, Reynaud B, Harkins GW, Varsani A, Martin DP, Lett JM. East African cassava mosaic-like viruses from Africa to Indian ocean islands: molecular diversity, evolutionary history and geographical dissemination of a bipartite begomovirus. BMC Evol Biol 2012. [PMID: 23186303 PMCID: PMC3560262 DOI: 10.1186/1471-2148-12-228] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Cassava (Manihot esculenta) is a major food source for over 200 million sub-Saharan Africans. Unfortunately, its cultivation is severely hampered by cassava mosaic disease (CMD). Caused by a complex of bipartite cassava mosaic geminiviruses (CMG) species (Family: Geminivirideae; Genus: Begomovirus) CMD has been widely described throughout Africa and it is apparent that CMG's are expanding their geographical distribution. Determining where and when CMG movements have occurred could help curtail its spread and reveal the ecological and anthropic factors associated with similar viral invasions. We applied Bayesian phylogeographic inference and recombination analyses to available and newly described CMG sequences to reconstruct a plausible history of CMG diversification and migration between Africa and South West Indian Ocean (SWIO) islands. RESULTS The isolation and analysis of 114 DNA-A and 41 DNA-B sequences demonstrated the presence of three CMG species circulating in the Comoros and Seychelles archipelagos (East African cassava mosaic virus, EACMV; East African cassava mosaic Kenya virus, EACMKV; and East African cassava mosaic Cameroon virus, EACMCV). Phylogeographic analyses suggest that CMG's presence on these SWIO islands is probably the result of at least four independent introduction events from mainland Africa occurring between 1988 and 2009. Amongst the islands of the Comoros archipelago, two major migration pathways were inferred: One from Grande Comore to Mohéli and the second from Mayotte to Anjouan. While only two recombination events characteristic of SWIO islands isolates were identified, numerous re-assortments events were detected between EACMV and EACMKV, which seem to almost freely interchange their genome components. CONCLUSIONS Rapid and extensive virus spread within the SWIO islands was demonstrated for three CMG complex species. Strong evolutionary or ecological interaction between CMG species may explain both their propensity to exchange components and the absence of recombination with non-CMG begomoviruses. Our results suggest an important role of anthropic factors in CMGs spread as the principal axes of viral migration correspond with major routes of human movement and commercial trade. Finer-scale temporal analyses of CMGs to precisely scale the relative contributions of human and insect transmission to their movement dynamics will require further extensive sampling in the SWIO region.
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Affiliation(s)
- Alexandre De Bruyn
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, Saint-Pierre, Ile de La Réunion 97410, France
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92
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Nawaz-ul-Rehman MS, Briddon RW, Fauquet CM. A melting pot of Old World begomoviruses and their satellites infecting a collection of Gossypium species in Pakistan. PLoS One 2012; 7:e40050. [PMID: 22899988 PMCID: PMC3416816 DOI: 10.1371/journal.pone.0040050] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 05/31/2012] [Indexed: 11/19/2022] Open
Abstract
CLCuD in southern Asia is caused by a complex of multiple begomoviruses (whitefly transmitted, single-stranded [ss]DNA viruses) in association with a specific ssDNA satellite; Cotton leaf curl Multan betasatellite (CLCuMuB). A further single ssDNA molecule, for which the collective name alphasatellites has been proposed, is also frequently associated with begomovirus-betasatellite complexes. Multan is in the center of the cotton growing area of Pakistan and has seen some of the worst problems caused by CLCuD. An exhaustive analysis of the diversity of begomoviruses and their satellites occurring in 15 Gossypium species (including G. hirsutum, the mainstay of Pakistan's cotton production) that are maintained in an orchard in the vicinity of Multan has been conducted using φ29 DNA polymerase-mediated rolling-circle amplification, cloning and sequence analysis. The non-cultivated Gossypium species, including non-symptomatic plants, were found to harbor a much greater diversity of begomoviruses and satellites than found in the cultivated G. hirsutum. Furthermore an African cassava mosaic virus (a virus previously only identified in Africa) DNA-A component and a Jatropha curcas mosaic virus (a virus occurring only in southern India) DNA-B component were identified. Consistent with earlier studies of cotton in southern Asia, only a single species of betasatellite, CLCuMuB, was identified. The diversity of alphasatellites was much greater, with many previously unknown species, in the non-cultivated cotton species than in G. hirsutum. Inoculation of newly identified components showed them to be competent for symptomatic infection of Nicotiana benthamiana plants. The significance of the findings with respect to our understanding of the role of host selection in virus diversity in crops and the geographical spread of viruses by human activity are discussed.
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Affiliation(s)
| | - Rob W. Briddon
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Jhang Road, Faisalabad, Pakistan
| | - Claude M. Fauquet
- Danforth Plant Science Center, St. Louis, Missouri, United States of America
- * E-mail:
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93
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Hicks AL, Duffy S. One misdated sequence of rabbit hemorrhagic disease virus prevents accurate estimation of its nucleotide substitution rate. BMC Evol Biol 2012; 12:74. [PMID: 22646287 PMCID: PMC3426481 DOI: 10.1186/1471-2148-12-74] [Citation(s) in RCA: 15] [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: 03/13/2012] [Accepted: 05/30/2012] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The literature is ripe with phylogenetic estimates of nucleotide substitution rates, especially of measurably evolving species such as RNA viruses. However, it is not known how robust these rate estimates are to inaccuracies in the data, particularly in sampling dates that are used for molecular clock calibration. Here we report on the rate of evolution of the emerging pathogen Rabbit hemorrhagic disease virus (RHDV), which has significantly different rates of evolution for the same outer capsid (VP60) gene published in the literature. In an attempt to reconcile the conflicting data and further elucidate details of RHDV 's evolutionary history, we undertook fresh Bayesian analyses and employed jackknife control methods to produce robust substitution rate and time to most recent common ancestor (TMRCA) estimates for RHDV based on the VP60 and RNA-dependent RNA polymerase genes. RESULTS Through these control methods, we were able to identify a single misdated taxon, a passaged lab strain used for vaccine production, which was responsible for depressing the RHDV capsid gene's rate of evolution by 65%. Without this isolate, the polymerase and the capsid protein genes had nearly identical rates of evolution: 1.90x10-3 nucleotide substitutions/site/year, ns/s/y, (95% highest probability density (HPD) 1.25x10-3-2.55x10-3) and 1.91x10-3 ns/s/y (95% HPD 1.50x10-3-2.34x10-3), respectively. CONCLUSIONS After excluding the misdated taxon, both genes support a significantly higher substitution rate as well as a relatively recent emergence of RHDV, and obviate the need for previously hypothesized decades of unobserved diversification of the virus. The control methods show that using even one misdated taxon in a large dataset can significantly skew estimates of evolutionary parameters and suggest that it is better practice to use smaller datasets composed of taxa with unequivocal isolation dates. These jackknife controls would be useful for future tip-calibrated rate analyses that include taxa with ambiguous dates of isolation.
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Affiliation(s)
- Allison L Hicks
- Department of Ecology, Evolution, and Natural Resources, School of Environmental and Biological Sciences Rutgers, The State University of New Jersey, 14 College Farm Rd, New Brunswick, NJ, 08901, USA
| | - Siobain Duffy
- Department of Ecology, Evolution, and Natural Resources, School of Environmental and Biological Sciences Rutgers, The State University of New Jersey, 14 College Farm Rd, New Brunswick, NJ, 08901, USA
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94
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Taylor NJ, Halsey M, Gaitán-Solís E, Anderson P, Gichuki S, Miano D, Bua A, Alicai T, Fauquet CM. The VIRCA Project: virus resistant cassava for Africa. GM CROPS & FOOD 2012; 3:93-103. [PMID: 22572842 DOI: 10.4161/gmcr.19144] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The VIRCA (Virus Resistant Cassava for Africa) project is a collaborative program between the Donald Danforth Plant Science Center, USA the National Crops Resources Research Institute, Uganda and the Kenya Agricultural Research Institute, Kenya. VIRCA is structured to include all aspects of the intellectual property, technology, regulatory, biosafety, quality control, communication and distribution components required for a GM crop development and delivery process. VIRCA's goal is to improve cassava for resistance to the viral diseases cassava brown streak disease (CBSD) and cassava mosaic disease (CMD) using pathogen-derived RNAi technology, and to field test, obtain regulatory approval for and deliver these products to small landholder farmers. During Phase I of the project, proof of concept was achieved by production and testing of virus resistant plants under greenhouse and confined field trials in East Africa. In VIRCA Phase II, two farmer-preferred varieties will be modified for resistance to CBSD and CMD, and lead events identified after molecular and field screening. In addition to delivery of royalty-free improved planting materials for farmers, VIRCA capacity building activities are enhancing indigenous capability for crop biotechnology in East Africa.
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Affiliation(s)
- Nigel J Taylor
- Donald Danforth Plant Science Center, St. Louis, MO, USA
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95
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Tracking viral evolution during a disease outbreak: the rapid and complete selective sweep of a circovirus in the endangered Echo parakeet. J Virol 2012; 86:5221-9. [PMID: 22345474 DOI: 10.1128/jvi.06504-11] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Circoviruses are among the smallest and simplest of all viruses, but they are relatively poorly characterized. Here, we intensively sampled two sympatric parrot populations from Mauritius over a period of 11 years and screened for the circovirus Beak and feather disease virus (BFDV). During the sampling period, a severe outbreak of psittacine beak and feather disease, which is caused by BFDV, occurred in Echo parakeets. Consequently, this data set presents an ideal system for studying the evolution of a pathogen in a natural population and to understand the adaptive changes that cause outbreaks. Unexpectedly, we discovered that the outbreak was most likely caused by changes in functionally important regions of the normally conserved replication-associated protein gene and not the immunogenic capsid. Moreover, these mutations were completely fixed in the Echo parakeet host population very shortly after the outbreak. Several capsid alleles were linked to the replication-associated protein outbreak allele, suggesting that whereas the key changes occurred in the latter, the scope of the outbreak and the selective sweep may have been influenced by positive selection in the capsid. We found evidence for viral transmission between the two host populations though evidence for the invasive species as the source of the outbreak was equivocal. Finally, the high evolutionary rate that we estimated shows how rapidly new variation can arise in BFDV and is consistent with recent results from other small single-stranded DNA viruses.
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96
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Delaney NF, Balenger S, Bonneaud C, Marx CJ, Hill GE, Ferguson-Noel N, Tsai P, Rodrigo A, Edwards SV. Ultrafast evolution and loss of CRISPRs following a host shift in a novel wildlife pathogen, Mycoplasma gallisepticum. PLoS Genet 2012; 8:e1002511. [PMID: 22346765 PMCID: PMC3276549 DOI: 10.1371/journal.pgen.1002511] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2011] [Accepted: 12/09/2011] [Indexed: 12/19/2022] Open
Abstract
Measureable rates of genome evolution are well documented in human pathogens but are less well understood in bacterial pathogens in the wild, particularly during and after host switches. Mycoplasma gallisepticum (MG) is a pathogenic bacterium that has evolved predominantly in poultry and recently jumped to wild house finches (Carpodacus mexicanus), a common North American songbird. For the first time we characterize the genome and measure rates of genome evolution in House Finch isolates of MG, as well as in poultry outgroups. Using whole-genome sequences of 12 House Finch isolates across a 13-year serial sample and an additional four newly sequenced poultry strains, we estimate a nucleotide diversity in House Finch isolates of only ∼2% of ancestral poultry strains and a nucleotide substitution rate of 0.8-1.2×10(-5) per site per year both in poultry and in House Finches, an exceptionally fast rate rivaling some of the highest estimates reported thus far for bacteria. We also found high diversity and complete turnover of CRISPR arrays in poultry MG strains prior to the switch to the House Finch host, but after the invasion of House Finches there is progressive loss of CRISPR repeat diversity, and recruitment of novel CRISPR repeats ceases. Recent (2007) House Finch MG strains retain only ∼50% of the CRISPR repertoire founding (1994-95) strains and have lost the CRISPR-associated genes required for CRISPR function. Our results suggest that genome evolution in bacterial pathogens of wild birds can be extremely rapid and in this case is accompanied by apparent functional loss of CRISPRs.
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Affiliation(s)
- Nigel F. Delaney
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Susan Balenger
- Department of Biological Sciences, Auburn University, Auburn, Alabama, United States of America
| | - Camille Bonneaud
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Christopher J. Marx
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Geoffrey E. Hill
- Department of Biological Sciences, Auburn University, Auburn, Alabama, United States of America
| | - Naola Ferguson-Noel
- Poultry Diagnostic and Research Center, University of Georgia, Athens, Georgia, United States of America
| | - Peter Tsai
- Bioinformatics Institute, University of Auckland, Auckland, New Zealand
| | - Allen Rodrigo
- Bioinformatics Institute, University of Auckland, Auckland, New Zealand
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
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97
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Stainton D, Kraberger S, Walters M, Wiltshire EJ, Rosario K, Halafihi M, Lolohea S, Katoa I, Faitua TH, Aholelei W, Taufa L, Thomas JE, Collings DA, Martin DP, Varsani A. Evidence of inter-component recombination, intra-component recombination and reassortment in banana bunchy top virus. J Gen Virol 2012; 93:1103-1119. [PMID: 22278830 DOI: 10.1099/vir.0.040337-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Banana bunchy top virus (BBTV; family Nanoviridae, genus Babuvirus) is a multi-component, ssDNA virus, which causes widespread banana crop losses throughout tropical Africa and Australasia. We determined the full genome sequences of 12 BBTV isolates from the Kingdom of Tonga and analysed these together with previously determined BBTV sequences to show that reassortment and both inter- and intra-component recombination have all been relatively frequent occurrences during BBTV evolution. We found that whereas DNA-U3 components display evidence of complex inter- and intra-component recombination, all of the South Pacific DNA-R components have a common intra-component recombinant origin spanning the replication-associated protein gene. Altogether, the DNA-U3 and DNA-M components display a greater degree of inter-component recombination than the DNA-R, -S, -C and -M components. The breakpoint distribution of the inter-component recombination events reveals a primary recombination hotspot around the 5' side of the common region major and, in accordance with recombination hotspots detectable in related ssDNA viruses, a secondary recombination hotspot near the origin of virion-strand replication.
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Affiliation(s)
- Daisy Stainton
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Simona Kraberger
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Matthew Walters
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Elizabeth J Wiltshire
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Karyna Rosario
- College of Marine Science, University of South Florida, St Petersburg, FL 33701, USA
| | - Mana'ia Halafihi
- Ministry of Agriculture and Food, Forests and Fisheries, Nuku'alofa, Tongatapu, Kingdom of Tonga
| | | | - Ika Katoa
- Ministry of Agriculture and Food, Forests and Fisheries, Nuku'alofa, Tongatapu, Kingdom of Tonga
| | | | - Waikato Aholelei
- Ministry of Agriculture and Food, Forests and Fisheries, Nuku'alofa, Tongatapu, Kingdom of Tonga
| | - Luseane Taufa
- Ministry of Agriculture and Food, Forests and Fisheries, Nuku'alofa, Tongatapu, Kingdom of Tonga
| | - John E Thomas
- The University of Queensland, Centre for Plant Science, Queensland Alliance for Agriculture and Food Innovation, Ecosciences Precinct, PO Box 46, Brisbane QLD 4001, Australia
| | - David A Collings
- Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand.,School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Darren P Martin
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Arvind Varsani
- Electron Microscope Unit, University of Cape Town, Rondebosch 7701, Cape Town, South Africa.,Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand.,School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
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98
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Monjane AL, van der Walt E, Varsani A, Rybicki EP, Martin DP. Recombination hotspots and host susceptibility modulate the adaptive value of recombination during maize streak virus evolution. BMC Evol Biol 2011; 11:350. [PMID: 22136133 PMCID: PMC3280948 DOI: 10.1186/1471-2148-11-350] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Accepted: 12/02/2011] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Maize streak virus -strain A (MSV-A; Genus Mastrevirus, Family Geminiviridae), the maize-adapted strain of MSV that causes maize streak disease throughout sub-Saharan Africa, probably arose between 100 and 200 years ago via homologous recombination between two MSV strains adapted to wild grasses. MSV recombination experiments and analyses of natural MSV recombination patterns have revealed that this recombination event entailed the exchange of the movement protein - coat protein gene cassette, bounded by the two genomic regions most prone to recombination in mastrevirus genomes; the first surrounding the virion-strand origin of replication, and the second around the interface between the coat protein gene and the short intergenic region. Therefore, aside from the likely adaptive advantages presented by a modular exchange of this cassette, these specific breakpoints may have been largely predetermined by the underlying mechanisms of mastrevirus recombination. To investigate this hypothesis, we constructed artificial, low-fitness, reciprocal chimaeric MSV genomes using alternating genomic segments from two MSV strains; a grass-adapted MSV-B, and a maize-adapted MSV-A. Between them, each pair of reciprocal chimaeric genomes represented all of the genetic material required to reconstruct - via recombination - the highly maize-adapted MSV-A genotype, MSV-MatA. We then co-infected a selection of differentially MSV-resistant maize genotypes with pairs of reciprocal chimaeras to determine the efficiency with which recombination would give rise to high-fitness progeny genomes resembling MSV-MatA. RESULTS Recombinants resembling MSV-MatA invariably arose in all of our experiments. However, the accuracy and efficiency with which the MSV-MatA genotype was recovered across all replicates of each experiment depended on the MSV susceptibility of the maize genotypes used and the precise positions - in relation to known recombination hotspots - of the breakpoints required to re-create MSV-MatA. Although the MSV-sensitive maize genotype gave rise to the greatest variety of recombinants, the measured fitness of each of these recombinants correlated with their similarity to MSV-MatA. CONCLUSIONS The mechanistic predispositions of different MSV genomic regions to recombination can strongly influence the accessibility of high-fitness MSV recombinants. The frequency with which the fittest recombinant MSV genomes arise also correlates directly with the escalating selection pressures imposed by increasingly MSV-resistant maize hosts.
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Affiliation(s)
- Adérito L Monjane
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
| | | | - Arvind Varsani
- Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
- Electron Microscope Unit, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
| | - Edward P Rybicki
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
- Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, 7925, Cape Town, South Africa
| | - Darren P Martin
- Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, 7925, Cape Town, South Africa
- Centre for High-Performance Computing, Rosebank, Cape Town, South Africa
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99
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Silva G, Marques N, Nolasco G. The evolutionary rate of citrus tristeza virus ranks among the rates of the slowest RNA viruses. J Gen Virol 2011; 93:419-429. [PMID: 22071513 DOI: 10.1099/vir.0.036574-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Citrus tristeza virus (CTV) has been studied intensively at the molecular level. However, knowledge regarding the dynamics of its evolution is practically non-existent. In the past, diverse authors have referred to CTV as a highly variable virus, implying rapid evolution. Others have, in recent times, referred to CTV as an exceptionally slowly evolving virus. In this work, we used the capsid protein (CP) gene to estimate the rate of evolution. This was obtained from a large set of heterochronous CP gene sequences using a bayesian coalescent approach. The best-fitting evolutionary and population models pointed to an evolutionary rate of 1.58×10(-4) nt per site year(-1) (95 % highest posterior density, 1.73×10(-5)-3.16×10(-4) nt per site year(-1)). For an unbiased comparison with other plant and animal viruses, the evolutionary rate of synonymous substitutions was considered. In a series of 88 synonymous evolutionary rates, ranging from 5.2×10(-6) to 6.2×10(-2) nt per site year(-1), CTV ranks in the 10th percentile, embedded among the slowest animal RNA viruses. At the time of citrus dissemination to Europe and the New World, the major clades that led to the current phylogenetic groups were already defined, which may explain the absence nowadays of geographical speciation.
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Affiliation(s)
- Gonçalo Silva
- Plant Virology Laboratory, Center for Biodiversity, Functional and Integrative Genomics (BioFig), Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Natália Marques
- Plant Virology Laboratory, Center for Biodiversity, Functional and Integrative Genomics (BioFig), Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Gustavo Nolasco
- Plant Virology Laboratory, Center for Biodiversity, Functional and Integrative Genomics (BioFig), Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
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100
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Acosta-Leal R, Duffy S, Xiong Z, Hammond RW, Elena SF. Advances in plant virus evolution: translating evolutionary insights into better disease management. PHYTOPATHOLOGY 2011; 101:1136-48. [PMID: 21554186 DOI: 10.1094/phyto-01-11-0017] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Recent studies in plant virus evolution are revealing that genetic structure and behavior of virus and viroid populations can explain important pathogenic properties of these agents, such as host resistance breakdown, disease severity, and host shifting, among others. Genetic variation is essential for the survival of organisms. The exploration of how these subcellular parasites generate and maintain a certain frequency of mutations at the intra- and inter-host levels is revealing novel molecular virus-plant interactions. They emphasize the role of host environment in the dynamic genetic composition of virus populations. Functional genomics has identified host factors that are transcriptionally altered after virus infections. The analyses of these data by means of systems biology approaches are uncovering critical plant genes specifically targeted by viruses during host adaptation. Also, a next-generation resequencing approach of a whole virus genome is opening new avenues to study virus recombination and the relationships between intra-host virus composition and pathogenesis. Altogether, the analyzed data indicate that systematic disruption of some specific parameters of evolving virus populations could lead to more efficient ways of disease prevention, eradication, or tolerable virus-plant coexistence.
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