Title:	Diversidade do complexo de Sida micrantha mosaic virus e caracterização de novos begomovírus em Malvaceae no Brasil
Authors:	Ferreira, Marcos Silva de Queiroz
Orientador(es)::	Carvalho, Rita de Cássia Pereira
Assunto::	Vírus de plantas Tomate - doenças e pragas Brasil
Issue Date:	24-Jul-2024
Data de defesa::	28-Feb-2023
Citation:	FERREIRA, Marcos Silva de Queiroz. Diversidade do complexo de Sida micrantha mosaic virus e caracterização de novos begomovírus em Malvaceae no Brasil. 2023. 67 f., il. Dissertação (Mestrado em Fitopatologia) — Universidade de Brasília, Brasília, 2023.
Abstract:	Begomovirus (family Geminiviridae) corresponds to the largest genus of plant viruses, encompassing viral species that have one or two single-stranded circular DNA molecules, separately encapsidated in 18-30 nanometer particles. Isolates with a bipartite genome (with DNA-A and DNA-B components) predominate in tomato in the New World. Begomoviruses are transmitted with great efficiency by the Bemisia tabaci Middle East Asian Minor 1 (MEAM-1 = biotype B) vector, which is widely distributed, with a polyphagous feeding habit and high adaptability to different environmental conditions. The introduction of B. tabaci MEAM 1 in the early 1990s was the triggering factor for begomovirus epidemics in tomato in Brazil, with a subsequent increase in the number of new viral species. Furthermore, distinct patterns of diversity and dynamics of viral subpopulations were observed in different environments. In this scenario, weeds play an important role as they function as natural reservoirs of begomovirus. New viral species have been reported in weeds, including areas in and around commercial tomato fields. Some weed begomoviruses have been identified and biologically characterized, however it is believed that these studies have not been extensive enough to estimate the actual diversity of new species in weeds. In the country, four begomoviruses were reported concomitantly infecting tomato and weeds. Globally, more than 40 begomoviruses have been described in Malvaceae species, and some of these have been detected originally infecting Solanaceae species. The small and bipartite genome, together with the transmission efficiency and polyphagy of the vector, provide favorable conditions for the occurrence of mixed infections and recombination and pseudorecombination events between begomoviruses, thus contributing to the frequent alteration of the genetic structure of viral populations in our conditions. Different strategies have been employed to analyze the evolutionary processes capable of shaping the genetic-molecular structure of begomoviruses. The main strategy is to obtain the complete viral genome (DNA-A and DNA-B) for further analysis using different programs and evolutionary models. The metagenomics combined with High Throughput Sequencing (HTS) has allowed to determine a great viral diversity present in Brazil. A high frequency of mixed infections has been detected with many of them involving potential new species capable of inducing severe symptoms in plants. In the present work, four contigs obtained from HTS of Malvaceae leaf samples were selected for study and characterization, in according to the methodology carried out by the LVV-Fito team and summarized below. Initially foliar samples of weeds showing typical symptoms of begomovirus (generalized chlorosis, mosaics, and golden spots) were collected in tomato production areas and/or areas close to tomato cultivation, in the five regions of the country. Samplings were carried out from 2001 to 2020, with a total of 78 leaf samples from plants of the Malvaceae family analyzed (selected using the year/place of collection as criteria). Total DNA was extracted via CTAB and organic solvents and stored at -20°C. The initial confirmation of the presence of begomovirus infection in the samples was made through PCR (polymerase chain reaction) assays using degenerate primers ‘PAR1c496’ and ‘PAL1v1978’. Viral circular DNA were enriched in positive samples via rolling circle amplification (RCA). HighThroughput Sequencing (HTS) was performed on an Illumina NovaSeq 6000 platform. The viral contigs were annotated and the reads were mapped back to the annotated genome using the ‘Map to reference’ tool available in the Geneious 11.1.5 program. About 7,391,728 million readings were obtained from the pool of 78 samples. After assembly, using the CLC Genomics Workbench 11 program, 10,679 contigs were obtained. Four contigs were selected. Three of these contigs corresponded to complete DNA-A and exhibited identity levels below 91%, consistent with the current taxonomic criteria for defining new species within the genus Begomovirus. The DNA-A component of potencial new species #1 showed 79% identity with Sidastrum golden leaf spot virus (HM357458), new species #2 showed 81% identity with Oxalis yellow vein virus (KM887907), while new #3 showed 78% identity with Sida yellow mosaic Alagoas virus (JX871383), confirming the occurrence of three new species of begomovirus in weeds. Sequences of DNAB components were obtained and analyzes performed, including confirmation of cognates species. The fourth contig showed 98,24% identity with Sida micranta mosaic virus (SiMMV) (AJ557451). After using specific primers, already available, a result of 41 positive samples for SiMMV was obtained. The characterization of these three species, as well as the occurrence and distribution of Sida micranta mosaic virus in five Brazilian regions, and the reassessment of the diversity of the Sida micrantha mosaic virus (SiMMV) and Sida mottle virus (SiMoV) complex involving species status, host range and geographic distribution regions will be presented in this dissertation.
metadata.dc.description.unidade:	Instituto de Ciências Biológicas (IB) Departamento de Fitopatologia (IB FIT)
Description:	Dissertação (mestrado) — Universidade de Brasília, Instituto de Ciências Biológicas, Departamento de Fitopatologia, 2023.
metadata.dc.description.ppg:	Programa de Pós-Graduação em Fitopatologia
Licença::	A concessão da licença deste item refere-se ao termo de autorização impresso assinado pelo autor com as seguintes condições: Na qualidade de titular dos direitos de autor da publicação, autorizo a Universidade de Brasília e o IBICT a disponibilizar por meio dos sites www.bce.unb.br, www.ibict.br, http://hercules.vtls.com/cgi-bin/ndltd/chameleon?lng=pt&skin=ndltd sem ressarcimento dos direitos autorais, de acordo com a Lei nº 9610/98, o texto integral da obra disponibilizada, conforme permissões assinaladas, para fins de leitura, impressão e/ou download, a título de divulgação da produção científica brasileira, a partir desta data.
Agência financiadora:	Fundação de Apoio à Pesquisa do Distrito Federal (FAPDF).
Appears in Collections:	Teses, dissertações e produtos pós-doutorado

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