Title:	Metagenomic analysis of the begomovirus diversity in tomatoes in Central Brazil and impact of the Ty-1 tolerance gene on viral evolutionary dynamics
Authors:	Reis, Luciane de Nazaré Almeida dos
Orientador(es)::	Carvalho, Rita de Cássia Pereira
Coorientador(es)::	Boiteux, Leonardo Silva
Assunto::	Begomovírus Diversidade biológica Solanum lycopersicum Tomate - doenças e pragas Tomate - resistência a doenças e pragas
Issue Date:	24-Sep-2020
Data de defesa::	23-Jun-2020
Citation:	REIS, Luciane de Nazaré Almeida dos. Metagenomic analysis of the begomovirus diversity in tomatoes in Central Brazil and impact of the Ty-1 tolerance gene on viral evolutionary dynamics. 2020. 205 f., il. Tese (Doutorado em Fitopatologia)—Universidade de Brasília, Brasília, 2020.
Abstract:	Tomato (Solanum lycopersicum L.) is one of the main vegetable crops cultivated in Brazil. Until the early 1990s, the occurrence of diseases caused by Begomovirus species (family Geminiviridae) was sporadic in the country. However, from this period on, an extremely diverse complex of begomoviruses emerged in tomato fields, coinciding with the wide geographical dispersion of the Bemisia tabaci MEAM 1 (Middle East-Asian Minor 1 = biotype B). Most begomoviruses have a bipartite genome and have varying levels of transmission efficiency by the vector. The more intense use of resistant/tolerant hybrids (mainly with the Ty–1 gene) is a potentical factor in the evolution process of this group of viruses in Brazil. Metagenomics combined with Next-Generation Sequencing (NGS) is one of the most efficient tools for large scale analysis of the diversity of viral populations in different environmental conditions. In this context, the general objective of the present work was to conduct metagenomics studies on the diversity of begomoviruses in tomatoes in Brazil. The specific objectives were: (a) to carry out comparative studies of the begomovirus diversity infecting tomato plants with and without the Ty– 1 gene and (b) to catalog the predominant viral species and/or new begomoviruses occurring in tomato plants with and without the Ty–1 gene. For this, 107 samples were collected in production fields in Goiás (n = 56), Distrito Federal (n = 27) and Minas Gerais (n = 24) between the years 2002 and 2016. The total DNA of the samples was extracted and submitted to PCR using primers to detect begomovirus and also with primers for the genomic region linked to the Ty–1 gene. Subsequently, the samples were subjected to enrichment via RCA (Rolling Circle Amplification) and divided into two pools: tomatoes without the Ty–1 gene (n = 64) and with the Ty–1 gene (n = 43). The two pools were sequenced on an Illumina HiSeq 2500 platform. The obtained sequences were assembled using the CLC Genomics Workbench 11.0 program and analyzed in Geneious 10.1. The sequences were then compared to viral sequences present on GenBank using the BLASTn algorithm. Specific primer pairs were designed to recover the complete genome and confirm the presence of viruses in individual samples within each pool. The results of these analyzes are described in Chapter 2. A greater diversity of viral species (n = 14) was observed in the sample pool without the Ty – 1 gene compared to those obtained from plants with the Ty – 1 gene (n = 6). It was observed an apparent filtering effect among viral species detected in the two pools. A high frequency of mixed infections was also observed in the samples, with cases of the simultaneous occurrence of up to five species in a single sample. Three potential new species were detected, two in samples without the Ty–1 gene (MG-378 and GO-169) and one in samples containing the Ty–1 gene (DF-640). In addition, a species of the genus Gemycircularvirus and a new alpha-satellite were detected. Tomato golden vein virus (TGVV) was one of the species widely detected in these analyzes. Studies conducted in Chapter 3 have shown that TGVV and Tomato yellow vein streak virus (ToYVSV) are closely related as indicated by analyzes using Sequence Demarcation Tool (SDT) and MUSCLE alignment. Two well-defined clusters were identified, consistent with the current criteria for demarcation of Begomovirus species. In addition, a distinct set of genomic, biological and ecological characteristics specific to each viral species was identified. A reassessment of the TGVV and ToYVSV isolates available on GenBank showed that a large fraction of them is erroneously classified at the species level. Bean golden mosaic virus (BGMV) was also detected in association with tomato in the analyzes carried out in Chapter 1. In Chapter 4 the diversity of 161 isolates classified as BGMV was cataloged by comparing their complete sequences with the DNA–A and DNA–B components of reference isolate. Phylogenetic and SDT analyzes indicated that the isolates collectively described as BGMV actually comprise two distinct species: one that encompasses isolates of BGMV from Phaseolus vulgaris and from a wide range of hosts (including tomato) and a closely related species (with identity ranging from 89 to 91% compared to the reference BGMV isolate), which were mainly associated with lima beans (P. lunatus). Chapter 5 describes the molecular characterization of a Gemycircularvirus (2,189 nucleotides) identified in association with tomato in Central Brazil. The analyzes showed that the gemycircularvirus shared 99% of identity with a virus tentatively named as Plant-associated genomovirus 12 of Larrea tridentata. Chapter 6 describes two new Begomovirus species that were identified in samples from Minas Gerais and Goiás states. The complete viral genomes were cloned, sequenced via Sanger and tentatively named as Tomato golden net virus – ToGNV (2,649 nucleotides) and Tomato yellow net virus – ToYNV (2,636 nucleotides). Both viruses exhibited DNA–A organization with typical features of the New World begomovirus species. However, no cognate components of DNA–B were found, indicating that ToGNV and ToYNV might comprise a peculiar group of monopartite neotropical begomoviruses.
metadata.dc.description.unidade:	Instituto de Ciências Biológicas (IB) Departamento de Fitopatologia (IB FIT)
Description:	Tese (doutorado)—Univesidade de Brasília, Instituto de Ciências Biológicas, Departamento de Fitopatologia, 2020.
metadata.dc.description.ppg:	Programa de Pós-Graduação em Fitopatologia
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Agência financiadora:	Conselho Nacional de Desenvolvimento Científico e Tecnológico e Fundação de Apoio a Pesquisa do Distrito Federal (FAP/DF).
Appears in Collections:	Teses, dissertações e produtos pós-doutorado

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