Navegando por Autor "Silva, Fábio N."
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Item Brazilian begomovirus populations are highly recombinant, rapidly evolving, and segregated based on geographical location(Journal of Virology, 2013-03-04) Rocha, Carolina S.; Castillo-Urquiza, Gloria P.; Lima, Alison T. M.; Silva, Fábio N.; Xavier, Cesar A. D.; Hora-Júnior, Braz T.; Beserra-Júnior, José E. A.; Malta, Antonio W. O.; Martin, Darren P.; Varsani, Arvind; Alfenas-Zerbini, Poliane; Mizubuti, Eduardo S. G.; Zerbini, F. MuriloThe 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 adap- tation 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 iden- tified 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.Item Complete genome sequence of a novel satellite virus associated with cassava Plants(Genome Anouncements, 2017-04-20) Souza, Adriana N.; Carvalho, Claudine M.; Silva, Fábio N.A novel satellite virus of 1,228 bp in length was found in a single cassava plant. Bioinformatic analyses show that it has two open reading frames (ORFs) in its genome, probably encoding a coat protein of 156 and a putative protein of 90 amino acids.Item The diversification of begomovirus populations is predominantly driven by mutational dynamics(Virus Evolution, 2017-03-02) Lima, Alison T. M.; Silva, Jose ́ C. F.; Silva, Fábio N.; Castillo-Urquiza, Gloria P.; Silva, Fabyano F.; Seah, Yee M.; Mizubuti, Eduardo S. G.; Duffy, Siobain; Zerbini, MuriloBegomoviruses (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.Item Synergism and negative interference during co-infection of tomato and Nicotiana benthamiana with two bipartite begomoviruses(Virology, 2009-03-12) Alves-Júnior, Miguel; Alfenas-Zerbini, Poliane; Andrade, Eduardo C.; Esposito, Débora A.; Silva, Fábio N.; Cruz, Ana Cláudia F. da; Ventrella, Marília C.; Otoni, Wagner C.; Zerbini, F. MuriloIn Brazil, at least eight begomoviruses including Tomato rugose mosaic virus (ToRMV) and Tomato yellow spot virus (ToYSV) infect tomatoes. ToYSV symptoms in tomato and Nicotiana benthamiana appear earlier and are more severe compared to those of ToRMV. We investigated the role of several factors in this differential adaptation. To analyze infection kinetics, a single leaf was inoculated and subsequently detached after different periods of time. Viral DNA accumulation was quantified in plants, viral replication was analyzed in protoplasts, and tissue tropism was determined by in situ hybridization. Results indicate that ToYSV establishes a systemic infection and reaches a higher concentration earlier than ToRMV in both hosts. ToRMV negatively interferes with ToYSV during the initial stages of infection, but once systemic infection is established this interference ceases. In N. benthamiana, ToYSV invades the mesophyll, while ToRMV is phloem-restricted. During dual infection in this host, ToYSV releases ToRMV from the phloem.Item Synonymous site variation due to recombination explains higher genetic variability in begomovirus populations infecting non-cultivated hosts(Journal of General Virology, 2013-02-01) Lima, Alison T. M.; Sobrinho, Roberto R.; González-Aguilera, Jorge; Rocha, Carolina S.; Silva, Sarah J. C.; Xavier, César A. D.; Silva, Fábio N.; Zerbini, F. Murilo; Duffy, SiobainBegomoviruses 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.