Fitopatologia - Artigos
URI permanente para esta coleçãohttps://locus.ufv.br/handle/123456789/11741
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Item Variabilidade genética de isolados de badnavírus infectando inhame (Dioscorea spp.) no Nordeste do Brasil(Tropical Plant Pathology, 2013-07) Lima, Joyce Silva; Lima, Alison T. M.; Castillo- Urquiza, Gloria P.; Silva, Sarah J. C.; Assunção, Iraildes P.; Michereff, Sami J.; Zerbini, F. Murilo; Lima, Gaus S. A.Viroses causadas por vírus do gênero Badnavirus são responsáveis por grandes prejuízos à cultura do inhame no Nordeste brasileiro. O conhecimento da variabilidade destes patógenos pode fornecer informações importantes sobre seu potencial evolutivo, permitindo a elaboração de melhores estratégias de manejo da doença. A análise de 425 amostras foliares de inhame coletadas em três estados do Nordeste brasileiro, em 2010, revelou uma alta incidência (93,3%) de badnaviroses. Para avaliar a variabilidade genética dos badnavírus infectando inhame, um fragmento de 579 nucleotídeos correspondente à região codificante da transcriptase reversa (RT)/RNaseH dos isolados amostrados foi amplificada por PCR e sequenciada. A análise filogenética das sequências de nucleotídeos revelou que os isolados dividem-se em dois grupos. Um é altamente relacionado com Dioscorea bacilliform AL virus (DBALV), enquanto o outro forma um clado altamente divergente dentro do gênero Badnavirus. Os isolados de DBALV apresentam 70-98% de identidade nucleotídica entre si e foram detectados em todas as áreas avaliadas e em D. alata e D. cayennensis, as duas espécies de inhame mais cultivadas no Nordeste. Os isolados do outro grupo compartilham 47-58% de identidade com isolados de DBALV e 78-95% entre si e foram encontrados apenas em D. alata na Paraíba.Item World management of geminiviruses(Annual Review of Phytopathology, 2018) Rojas, Maria R.; Macedo, Monica A.; Maliano, Minor R.; Soto-Aguilar, Maria; Souza, Juliana O.; Briddon, Rob W.; Kenyon, Lawrence; Bustamante, Rafael F. Rivera; Zerbini, F. Murilo; Adkins, Scott; Legg, James P.; Kvarnheden, Anders; Wintermantel, William M.; Sudarshana, Mysore R.; Peterschmitt, Michel; Lapidot, Moshe; Martin, Darren P.; et al.Management of geminiviruses is a worldwide challenge because of the widespread distribution of economically important diseases caused by these viruses. Regardless of the type of agriculture, management is most effective with an integrated pest management (IPM) approach that involves measures before, during, and after the growing season. This includes starting with resistant cultivars and virus- and vector-free transplants and ropagative plants. For high value vegetables, protected culture (e.g., greenhouses and screenhouses) allows for effective management but is limited owing to high cost. Protection of young plants in open fields is provided by row covers, but other measures are typically required. Measures that are used for crops in open fields include roguing infected plants and insect vector management. Application of insecticide to manage vectors (whiteflies and leafhoppers) is the most widely used measure but can cause undesirable environmental and human health issues. For annual crops, these measures can be more effective when combined with host-free periods of two to three months. Finally, given the great diversity of the viruses, their insect vectors, and the crops affected, IPM approaches need to be based on the biology and ecology of the virus and vector and the crop production system. Here, we present the general measures that can be used in an IPM program for geminivirus diseases, specific case studies, and future challenges.Item Taxonomy of the order Mononegavirales: second update 2018(Archives of Virology, 2019-04) Zerbini, F. Murilo; Maes, Piet; Amarasinghe, Gaya K.; Ayllón, María A.; Basler, Christopher F.; Bavari, Sina; Blasdell, Kim R.; Briese, Thomas; Brown, Paul A.; Bukreyev, Alexander; Balkema-Buschmann, Anne; Buchholz, Ursula J.; Chandran, Kartik; Crozier, Ian; Swart, Rik L. de; Dietzgen, Ralf G.; Dolnik, Olga; Domier, Leslie L.In October 2018, the order Mononegavirales was amended by the establishment of three new families and three new genera, abolishment of two genera, and creation of 28 novel species. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).Item Taxonomy of the order Bunyavirales: second update 2018(Archives of Virology, 2019-03) Zerbini, F. Murilo; Maes, Piet; Adkins, Scott; Alkhovsky, Sergey V.; Avšič-Županc, Tatjana; Ballinger, Matthew J.; Bente, Dennis A.; Beer, Martin; Bergeron, Éric; Blair, Carol D.; Briese, Thomas; Buchmeier, Michael J.; Burt, Felicity J.; Calisher, Charles H.; Charrel, Rémi N.; Choi, Il Ryong; Clegg, J. Christopher S.; Torre, Juan Carlos de laIn October 2018, the order Bunyavirales was amended by inclusion of the family renaviridae, abolishment of three families, creation of three new families, 19 new genera, and 14 new species, and renaming of three genera and 22 species. This article presents the updated taxonomy of the order Bunyavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).Item Revisiting the classification of curtoviruses based on genome-wide pairwise identity(Archives of Virology, 2014-01-25) Zerbini, F. Murilo; Varsani, Arvind; Martin, Darren P.; Navas-Castillo, Jesús; Moriones, Enrique; Hernández-Zepeda, Cecilia; Idris, Ali; Brown, Judith K.Members of the genus Curtovirus (family Geminiviridae) are important pathogens of many wild and cultivated plant species. Until recently, relatively few full curtovirus genomes have been characterised. However, with the 19 full genome sequences now available in public databases, we revisit the proposed curtovirus species and strain classification criteria. Using pairwise identities coupled with phylogenetic evidence, revised species and strain demarcation guidelines have been instituted. Specifically, we have established 77 % genome-wide pairwise identity as a species demarcation threshold and 94 % genome-wide pairwise identity as a strain demarcation threshold. Hence, whereas curtovirus sequences with >77 % genome-wide pairwise identity would be classified as belonging to the same species, those sharing >94 % identity would be classified as belonging to the same strain. We provide step-by-step guidelines to facilitate the classification of newly discovered curtovirus full genome sequences and a set of defined criteria for naming new species and strains. The revision yields three curtovirus species: Beet curly top virus (BCTV), Spinach severe surly top virus (SpSCTV) and Horseradish curly top virus (HrCTV).Item Establishment of three new genera in the family Geminiviridae: Becurtovirus, Eragrovirus and Turncurtovirus(Archives of Virology, 2014-03-22) Zerbini, F. Murilo; Varsani, Arvind; Navas-Castillo, Jesús; Moriones, Enrique; Hernández-Zepeda, Cecilia; Idris, Ali; Brown, Judith K.; Martin, Darren P.The family Geminiviridae includes plant-infecting circular single-stranded DNA viruses that have geminate particle morphology. Members of this family infect both monocotyledonous and dicotyledonous plants and have a nearly global distribution. With the advent of new molecular tools and low-cost sequencing, there has been a significant increase in the discovery of new geminiviruses in various cultivated and non-cultivated plants. In this communication, we highlight the establishment of three new genera (Becurtovirus, Eragrovirus and Turncurtovirus) to accommodate various recently discovered geminiviruses that are highly divergent and, in some cases, have unique genome architectures. The genus Becurtovirus has two viral species, Beet curly top Iran virus (28 isolates; leafhopper vector Circulifer haematoceps) and Spinach curly top Arizona virus (1 isolate; unknown vector), whereas the genera Eragrovirus and Turncurtovirus each have a single assigned species: Eragrostis curvula streak virus (6 isolates; unknown vector) and Turnip curly top virus (20 isolates; leafhopper vector Circulifer haematoceps), respectively. Based on analysis of all of the genome sequences available in public databases for each of the three new genera, we provide guidelines and protocols for species and strain classification within these three new genera.Item A genome-wide pairwise-identity-based proposal for the classification of viruses in the genus Mastrevirus (family Geminiviridae)(Archives of Virology, 2013-01-23) Zerbini, F. Murilo; Muhire, Brejnev; Martin, Darren P.; Brown, Judith K.; Navas-Castillo, Jesús; Moriones, Enrique; Rivera-Bustamante, Rafael; Malathi, V. G.; Briddon, Rob W.; Varsani, ArvindRecent advances in the ease with which the genomes of small circular single-stranded DNA viruses can be amplified, cloned, and sequenced have greatly accelerated the rate at which full genome sequences of mastreviruses (family Geminiviridae, genus Mastrevirus) are being deposited in public sequence databases. Although guidelines currently exist for species-level classification of newly determined, complete mastrevirus genome sequences, these are difficult to apply to large sequence datasets and are permissive enough that, effectively, a high degree of leeway exists for the proposal of new species and strains. The lack of a standardised and rigorous method for testing whether a new genome sequence deserves such a classification is resulting in increasing numbers of questionable mastrevirus species proposals. Importantly, the recommended sequence alignment and pairwise identity calculation protocols of the current guidelines could easily be modified to make the classification of newly determined mastrevirus genome sequences significantly more objective. Here, we propose modified versions of these protocols that should substantially minimise the degree of classification inconsistency that is permissible under the current system. To facilitate the objective application of these guidelines for mastrevirus species demarcation, we additionally present a user-friendly computer program, SDT (species demarcation tool), for calculating and graphically displaying pairwise genome identity scores. We apply SDT to the 939 full genome sequences of mastreviruses that were publically available in May 2012, and based on the distribution of pairwise identity scores yielded by our protocol, we propose mastrevirus species and strain demarcation thresholds of >78 % and >94 % identity, respectively.Item Revision of Begomovirus taxonomy based on pairwise sequence comparisons(Archives of Virology, 2015-04-18) Zerbini, F. Murilo; Brown, Judith K.; Navas-Castillo, Jesús; Moriones, Enrique; Ramos-Sobrinho, Roberto; Silva, José C. F.; Fiallo-Olivé, Elvira; Briddon, Rob W.; Hernández-Zepeda, Cecilia; Idris, Ali; Malathi, V. G.; Martin, Darren P.; Rivera-Bustamante, Rafael; Ueda, Shigenori; Varsani, ArvindViruses of the genus Begomovirus (family Geminiviridae) are emergent pathogens of crops throughout the tropical and subtropical regions of the world. By virtue of having a small DNA genome that is easily cloned, and due to the recent innovations in cloning and low-cost sequencing, there has been a dramatic increase in the number of available begomovirus genome sequences. Even so, most of the available sequences have been obtained from cultivated plants and are likely a small and phylogenetically unrepresentative sample of begomovirus diversity, a factor constraining taxonomic decisions such as the establishment of operationally useful species demarcation criteria. In addition, problems in assigning new viruses to established species have highlighted shortcomings in the previously recommended mechanism of species demarcation. Based on the analysis of 3,123 full-length begomovirus genome (or DNA-A component) sequences available in public databases as of December 2012, a set of revised guidelines for the classification and nomenclature of begomoviruses are proposed. The guidelines primarily consider a) genus-level biological characteristics and b) results obtained using a standardized classification tool, Sequence Demarcation Tool, which performs pairwise sequence alignments and identity calculations. These guidelines are consistent with the recently published recommendations for the genera Mastrevirus and Curtovirus of the family Geminiviridae. Genome-wide pairwise identities of 91 % and 94 % are proposed as the demarcation threshold for begomoviruses belonging to different species and strains, respectively. Procedures and guidelines are outlined for resolving conflicts that may arise when assigning species and strains to categories wherever the pairwise identity falls on or very near the demarcation threshold value.Item High genetic variability and recombination in a begomovirus population infecting the ubiquitous weed Cleome affinis in northeastern Brazil(Archives of Virology, 2011-10-18) Silva, Sarah J. C. da; Castillo-Urquiza, Gloria P.; Hora Júnior, Braz T.; Assunção, Iraildes P.; Lima, Gaus S. A.; Pio-Ribeiro, Gilvan; Mizubuti, Eduardo S. G.; Zerbini, F. MuriloDiseases caused by begomoviruses are a serious constraint to crop production in many tropical and subtropical areas of the world, including Brazil. Begomoviruses are whitefly-transmitted, single-stranded DNA viruses that are often associated with weed plants, which may act as natural reservoirs of viruses that cause epidemics in crop plants. Cleome affinis (family Capparaceae) is an annual weed that is frequently associated with leguminous crops in Brazil. Samples of C. affinis were collected in four states in the northeast of Brazil. Analysis of 14 full-length DNA-A components revealed that only one begomovirus was present, with 91-96% identity to cleome leaf crumple virus (ClLCrV). In a phylogenetic tree, ClLCrV forms a basal group relative to all other Brazilian begomoviruses. Evidence of multiple recombination events was detected among the ClLCrV isolates, which also display a high degree of genetic variability. Despite ClLCrV being the only begomovirus found, its phylogenetic placement, high genetic variability and recombinant nature suggest that C. affinis may act as a source of novel viruses for crop plants. Alternatively, ClLCrV could be a genetically isolated begomovirus. Further studies on the biological properties of ClLCrV should help to clarify the role of C. affinis in the epidemiological scenario of Brazilian begomoviruses.Item Analysis of the full-length genome sequence of papaya lethal yellowing virus (PLYV), determined by deep sequencing, confirms its classification in the genus Sobemovirus(Archives of Virology, 2012-06-29) Pereira, Álvaro J.; Alfenas-Zerbini, Poliane; Cascardo, Renan S.; Andrade, Eduardo C.; Zerbini, F. MuriloPapaya lethal yellowing virus (PLYV) causes an economically important disease in papayas in northeastern Brazil. Based on biological and molecular properties, PLYV has been tentatively assigned to the genus Sobemovirus. We report the sequence of the full-length genome of a PLYV isolate from Brazil, determined by deep sequencing. The PLYV genome is 4,145 nt long and contains four ORFs, with an arrangement identical to that of sobemoviruses. The polyprotein and CP display significant sequence identity with the corresponding proteins of other sobemoviruses. Pairwise comparisons and phylogenetic analysis based on complete nucleotide sequences confirm the classification of PLYV in the genus Sobemovirus.