A novel bipartite begomovirus infecting Cnidoscolus urens (Euphorbiaceae) from Pernambuco State, ... more A novel bipartite begomovirus infecting Cnidoscolus urens (Euphorbiaceae) from Pernambuco State, Brazil, has been characterized. The complete DNA-A (2657 nt) and DNA-B (2622 nt) components of the viral isolates show the typical genome organization of New World bipartite begomoviruses. DNA-A of the isolates had the highest percentage of nucleotide sequence identity (88.6-88.9%) to cnidoscolus mosaic leaf deformation virus. Based on the current classification criteria for the genus Begomovirus, the virus infecting C. urens should be considered a new member of the genus, and the name "cnidoscolus mild mosaic virus" is proposed for the virus, and the name "Begomovirus caboniensis" is proposed for its species.
Badnaviruses (family Caulimoviridae) have semicircular dsDNA genomes encapsidated into bacillifor... more Badnaviruses (family Caulimoviridae) have semicircular dsDNA genomes encapsidated into bacilliform particles. Dioscorea bacilliform virus (DBV) is an important Badnavirus infecting several species of Dioscorea (yam) in the southern hemisphere. In this study, 235 yam leaf samples were collected from different germplasm banks maintained by "Luiz de Queiroz" College of Agriculture (ESALQ/USP), Federal University of Viçosa (UFV) and Federal University of Recôncavo da Bahia (UFRB). The average incidence of badnavirus in the evaluated samples was 75.3%. Molecular and phylogenetic analyses, carried out from 42 nucleotide sequences, of the badnavirus RT/RNaseH region, revealed the occurrence of Dioscorea bacilliform AL virus (DBALV) and Dioscorea bacilliform SN virus (DBSNV) in different yam species. So far, only DBALV has been reported in yams in Brazil, being restricted to the Northeast region. Therefore, this is the first report of DBSNV infecting yam crop in the country. In ad...
Begomoviruses have circular, single-stranded DNA genomes encapsidated into twinned quasi-icosahed... more Begomoviruses have circular, single-stranded DNA genomes encapsidated into twinned quasi-icosahedral particles and are transmitted by whiteflies of the Bemisia tabaci sibling group. Begomoviruses infect cultivated and non-cultivated plants, causing great losses in economically important crops worldwide. To better understand the genetic diversity of begomoviruses infecting the non-cultivated host Cnidoscolus urens, leaf samples exhibiting virus-like symptoms were collected in different localities in the state of Alagoas, Brazil, during 2015 and 2016. Forty-two complete DNA-A sequences were cloned and sequenced by the Sanger method. Based on nucleotide sequence comparisons, the 42 new isolates were identified as the bipartite begomovirus cnidoscolus mosaic leaf deformation virus (CnMLDV). The CnMLDV isolates were clustered in two phylogenetic groups (clusters I and II) corresponding to their sampling areas, and the high value of Wright's F fixation index observed for the DNA-A sequences suggests population structuring. At least seven independent intraspecies recombination events were predicted among CnMLDV isolates, with recombination breakpoints located in the common region (CR) and in the CP and Rep genes. Also, a high per site nucleotide diversity (π) was observed for CnMLDV isolates, with CP being significantly more variable than Rep. Despite the high genetic variability, strong negative or purifying selection was identified as the main selective force acting upon CP and Rep.
To analyze the DNA virome associated with cacao (Theobroma cacao L.) trees showing virus-like sym... more To analyze the DNA virome associated with cacao (Theobroma cacao L.) trees showing virus-like symptoms in Brazil (BR) and Puerto Rico (PR) during 2018-2019, total DNA was isolated from symptomatic leaves and subjected to high-throughput Illumina sequencing. The assembled complete badnaviral genome sequences were verified by PCR amplification, cloning, and DNA sequencing. Based on pairwise distances and phylogenetic analysis, three badnaviral genomes were identified, and these viruses were found to be isolates of the previously described cacao mild mosaic virus (CaMMV). The three genomes were 7,520, 7,524, and 7,514 bp in size for the isolates CaMMV-BR321, CaMMV-BR322, and CaMMV-PR3, respectively. Each genome contained four predicted open reading frames: ORFs 1-3 and ORFY. The CaMMV-PR3 isolate was identified as a probable recombinant, with a CaMMV-BR-like virus as the major parent.
ABSTRACT: Brazil is one of the main global producers of pineapple (Ananas comosus L. Merril), wit... more ABSTRACT: Brazil is one of the main global producers of pineapple (Ananas comosus L. Merril), with emphasis in the Northeastern region of the country. Pineapple is exposed to several phytosanitary problems, including viruses. Pineapple badnaviruses are caused by two distinct species: Pineapple bacilliform CO virus (PBCoV) and Pineapple bacilliform ER virus (PBErV). The present study aimed to detect possible species of the genus Badnavirus in pineapple samples in Northeastern Brazil, via PCR and sequencing of the RT/RNaseH region. Leaf samples of pineapples were collected in the states of Alagoas, Maranhão, Paraiba and Pernambuco, and subsequently subjected to total DNA extraction and amplification via PCR. Badnavirus positive samples were selected for sequencing. Analysis of pairwise comparisons revealed that all sequences obtained in this work showed an identity greater than 80% with the sequence of the species PBCoV (EU377664), from Australia, fully corroborating with phylogenetic...
RESUMO Os badnavírus (família Caulimoviridae) possuem genoma de dsDNA semicircular encapsidado em... more RESUMO Os badnavírus (família Caulimoviridae) possuem genoma de dsDNA semicircular encapsidado em partículas baciliformes. Dioscorea bacilliform virus (DBV) é um importante Badnavirus infectando várias espécies de Dioscorea (inhame) no hemisfério sul. No presente estudo, 235 amostras foliares de inhame foram coletadas em diferentes bancos de germoplasma mantidos pela Escola Superior de Agricultura Luiz (ESALQ/USP), Universidade Federal de Viçosa (UFV) e Universidade Federal do Recôncavo Baiano (UFRB). A incidência média de badnavírus nas amostras avaliadas foi de 75,3%. As análises moleculares e filogenéticas, realizadas a partir de 42 sequências nucleotídicas, da região da RT/RNaseH de badnavírus, revelaram a ocorrência do Dioscorea bacilliform AL virus (DBALV) e Dioscorea bacilliform SN virus (DBSNV) em diferentes espécies de inhame. Até o momento, somente o DBALV havia sido relatado em inhame no Brasil, estando restrito à região Nordeste. Portanto, este é o primeiro relato do DBS...
Badnaviruses (family Caulimoviridae) have semicircular dsDNA genomes encapsidated into bacillifor... more Badnaviruses (family Caulimoviridae) have semicircular dsDNA genomes encapsidated into bacilliform particles. The genus Badnavirus is the most important due to its high number of species reported infecting cultivated plants worldwide. This study aimed to evaluate the phylogenetic positioning and population genetic variability into Badnavirus. Data sets comprising the badnavirus complete genome and partial sequences of the RT and RNaseH genes were obtained from the GenBank database. Multiple nucleotide sequence alignments from complete genome, ORFIII, complete genomic domain RT/RNaseH (1020pb) and partial (579pb) were performed. A total of 127 genomes were obtained, representing 53 species of badnavirus. Nucleotide sequence comparisons for the RT/RNaseH domain showed only a few isolates reported as distinct species shared ≥80% identity, the current threshold used for species demarcation into this genus. Phylogenetic trees for the complete genome and for ORFIII showed four well suppor...
The genus Begomovirus (family Geminirvidae) comprises circular single-stranded DNA viruses that i... more The genus Begomovirus (family Geminirvidae) comprises circular single-stranded DNA viruses that infect both cultivated and non-cultivated hosts, being transmitted by the insect vector Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae). This study aimed to conduct the molecular characterization of a novel begomovirus infecting the non-cultivated plant Gaya guerkeana K. Schum. (Malvaceae). A leaf sample of G. guerkeana was collected in the State of Pernambuco, Brazil, in 2010. Viral genomic components were amplified via RCA, cloned, and commercially sequenced. The full-length DNA-A sequence was used for phylogenetic analysis and pairwise comparisons with other previously reported begomoviruses. The begomovirus DNA-A from G. guerkeana was most closely related to the Sida mottle Alagoas virus (SiMoAV, JX871386), having 84.8% nucleotide identity. Using the ≥ 91% identity criteria for DNA-A established by the Geminivirus Study Group of the International Committee on Taxonomy of Viruses, ...
Begomoviruses are single-strand DNA plant viruses that infect economically important crops worldw... more Begomoviruses are single-strand DNA plant viruses that infect economically important crops worldwide, exhibiting high genetic variability and species diversity. Based on the current taxonomic criteria established for the genus Begomovirus, a new member of this genus infecting a malvaceous weed is reported here. The name triumfetta yellow mosaic virus is proposed. At least one recombination event was detected in this new begomovirus, with putative parents being begomoviruses from tomato and Centrosema.
A novel bipartite begomovirus infecting Cnidoscolus urens (Euphorbiaceae) from Pernambuco State, ... more A novel bipartite begomovirus infecting Cnidoscolus urens (Euphorbiaceae) from Pernambuco State, Brazil has been characterized. The complete DNA-A (2657 to 2692 nt) and DNA-B (2622 nt) components of the viral isolates showed a typical genome organization of New World bipartite begomoviruses. DNA-A of the isolates had the highest percentage of nucleotide identity (88.6–88.9%) with the Cnidoscolus mosaic leaf deformation virus (NC_038982). Based on the current classification criteria for the genus Begomovirus, a new member infecting C. urens was reported, and the name Begomovirus caboniensis was proposed for these viruses, adopting the standardized binomial system.
A novel bipartite begomovirus infecting Cnidoscolus urens (Euphorbiaceae) from Pernambuco State, ... more A novel bipartite begomovirus infecting Cnidoscolus urens (Euphorbiaceae) from Pernambuco State, Brazil, has been characterized. The complete DNA-A (2657 nt) and DNA-B (2622 nt) components of the viral isolates show the typical genome organization of New World bipartite begomoviruses. DNA-A of the isolates had the highest percentage of nucleotide sequence identity (88.6-88.9%) to cnidoscolus mosaic leaf deformation virus. Based on the current classification criteria for the genus Begomovirus, the virus infecting C. urens should be considered a new member of the genus, and the name "cnidoscolus mild mosaic virus" is proposed for the virus, and the name "Begomovirus caboniensis" is proposed for its species.
Badnaviruses (family Caulimoviridae) have semicircular dsDNA genomes encapsidated into bacillifor... more Badnaviruses (family Caulimoviridae) have semicircular dsDNA genomes encapsidated into bacilliform particles. Dioscorea bacilliform virus (DBV) is an important Badnavirus infecting several species of Dioscorea (yam) in the southern hemisphere. In this study, 235 yam leaf samples were collected from different germplasm banks maintained by "Luiz de Queiroz" College of Agriculture (ESALQ/USP), Federal University of Viçosa (UFV) and Federal University of Recôncavo da Bahia (UFRB). The average incidence of badnavirus in the evaluated samples was 75.3%. Molecular and phylogenetic analyses, carried out from 42 nucleotide sequences, of the badnavirus RT/RNaseH region, revealed the occurrence of Dioscorea bacilliform AL virus (DBALV) and Dioscorea bacilliform SN virus (DBSNV) in different yam species. So far, only DBALV has been reported in yams in Brazil, being restricted to the Northeast region. Therefore, this is the first report of DBSNV infecting yam crop in the country. In ad...
Begomoviruses have circular, single-stranded DNA genomes encapsidated into twinned quasi-icosahed... more Begomoviruses have circular, single-stranded DNA genomes encapsidated into twinned quasi-icosahedral particles and are transmitted by whiteflies of the Bemisia tabaci sibling group. Begomoviruses infect cultivated and non-cultivated plants, causing great losses in economically important crops worldwide. To better understand the genetic diversity of begomoviruses infecting the non-cultivated host Cnidoscolus urens, leaf samples exhibiting virus-like symptoms were collected in different localities in the state of Alagoas, Brazil, during 2015 and 2016. Forty-two complete DNA-A sequences were cloned and sequenced by the Sanger method. Based on nucleotide sequence comparisons, the 42 new isolates were identified as the bipartite begomovirus cnidoscolus mosaic leaf deformation virus (CnMLDV). The CnMLDV isolates were clustered in two phylogenetic groups (clusters I and II) corresponding to their sampling areas, and the high value of Wright's F fixation index observed for the DNA-A sequences suggests population structuring. At least seven independent intraspecies recombination events were predicted among CnMLDV isolates, with recombination breakpoints located in the common region (CR) and in the CP and Rep genes. Also, a high per site nucleotide diversity (π) was observed for CnMLDV isolates, with CP being significantly more variable than Rep. Despite the high genetic variability, strong negative or purifying selection was identified as the main selective force acting upon CP and Rep.
To analyze the DNA virome associated with cacao (Theobroma cacao L.) trees showing virus-like sym... more To analyze the DNA virome associated with cacao (Theobroma cacao L.) trees showing virus-like symptoms in Brazil (BR) and Puerto Rico (PR) during 2018-2019, total DNA was isolated from symptomatic leaves and subjected to high-throughput Illumina sequencing. The assembled complete badnaviral genome sequences were verified by PCR amplification, cloning, and DNA sequencing. Based on pairwise distances and phylogenetic analysis, three badnaviral genomes were identified, and these viruses were found to be isolates of the previously described cacao mild mosaic virus (CaMMV). The three genomes were 7,520, 7,524, and 7,514 bp in size for the isolates CaMMV-BR321, CaMMV-BR322, and CaMMV-PR3, respectively. Each genome contained four predicted open reading frames: ORFs 1-3 and ORFY. The CaMMV-PR3 isolate was identified as a probable recombinant, with a CaMMV-BR-like virus as the major parent.
ABSTRACT: Brazil is one of the main global producers of pineapple (Ananas comosus L. Merril), wit... more ABSTRACT: Brazil is one of the main global producers of pineapple (Ananas comosus L. Merril), with emphasis in the Northeastern region of the country. Pineapple is exposed to several phytosanitary problems, including viruses. Pineapple badnaviruses are caused by two distinct species: Pineapple bacilliform CO virus (PBCoV) and Pineapple bacilliform ER virus (PBErV). The present study aimed to detect possible species of the genus Badnavirus in pineapple samples in Northeastern Brazil, via PCR and sequencing of the RT/RNaseH region. Leaf samples of pineapples were collected in the states of Alagoas, Maranhão, Paraiba and Pernambuco, and subsequently subjected to total DNA extraction and amplification via PCR. Badnavirus positive samples were selected for sequencing. Analysis of pairwise comparisons revealed that all sequences obtained in this work showed an identity greater than 80% with the sequence of the species PBCoV (EU377664), from Australia, fully corroborating with phylogenetic...
RESUMO Os badnavírus (família Caulimoviridae) possuem genoma de dsDNA semicircular encapsidado em... more RESUMO Os badnavírus (família Caulimoviridae) possuem genoma de dsDNA semicircular encapsidado em partículas baciliformes. Dioscorea bacilliform virus (DBV) é um importante Badnavirus infectando várias espécies de Dioscorea (inhame) no hemisfério sul. No presente estudo, 235 amostras foliares de inhame foram coletadas em diferentes bancos de germoplasma mantidos pela Escola Superior de Agricultura Luiz (ESALQ/USP), Universidade Federal de Viçosa (UFV) e Universidade Federal do Recôncavo Baiano (UFRB). A incidência média de badnavírus nas amostras avaliadas foi de 75,3%. As análises moleculares e filogenéticas, realizadas a partir de 42 sequências nucleotídicas, da região da RT/RNaseH de badnavírus, revelaram a ocorrência do Dioscorea bacilliform AL virus (DBALV) e Dioscorea bacilliform SN virus (DBSNV) em diferentes espécies de inhame. Até o momento, somente o DBALV havia sido relatado em inhame no Brasil, estando restrito à região Nordeste. Portanto, este é o primeiro relato do DBS...
Badnaviruses (family Caulimoviridae) have semicircular dsDNA genomes encapsidated into bacillifor... more Badnaviruses (family Caulimoviridae) have semicircular dsDNA genomes encapsidated into bacilliform particles. The genus Badnavirus is the most important due to its high number of species reported infecting cultivated plants worldwide. This study aimed to evaluate the phylogenetic positioning and population genetic variability into Badnavirus. Data sets comprising the badnavirus complete genome and partial sequences of the RT and RNaseH genes were obtained from the GenBank database. Multiple nucleotide sequence alignments from complete genome, ORFIII, complete genomic domain RT/RNaseH (1020pb) and partial (579pb) were performed. A total of 127 genomes were obtained, representing 53 species of badnavirus. Nucleotide sequence comparisons for the RT/RNaseH domain showed only a few isolates reported as distinct species shared ≥80% identity, the current threshold used for species demarcation into this genus. Phylogenetic trees for the complete genome and for ORFIII showed four well suppor...
The genus Begomovirus (family Geminirvidae) comprises circular single-stranded DNA viruses that i... more The genus Begomovirus (family Geminirvidae) comprises circular single-stranded DNA viruses that infect both cultivated and non-cultivated hosts, being transmitted by the insect vector Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae). This study aimed to conduct the molecular characterization of a novel begomovirus infecting the non-cultivated plant Gaya guerkeana K. Schum. (Malvaceae). A leaf sample of G. guerkeana was collected in the State of Pernambuco, Brazil, in 2010. Viral genomic components were amplified via RCA, cloned, and commercially sequenced. The full-length DNA-A sequence was used for phylogenetic analysis and pairwise comparisons with other previously reported begomoviruses. The begomovirus DNA-A from G. guerkeana was most closely related to the Sida mottle Alagoas virus (SiMoAV, JX871386), having 84.8% nucleotide identity. Using the ≥ 91% identity criteria for DNA-A established by the Geminivirus Study Group of the International Committee on Taxonomy of Viruses, ...
Begomoviruses are single-strand DNA plant viruses that infect economically important crops worldw... more Begomoviruses are single-strand DNA plant viruses that infect economically important crops worldwide, exhibiting high genetic variability and species diversity. Based on the current taxonomic criteria established for the genus Begomovirus, a new member of this genus infecting a malvaceous weed is reported here. The name triumfetta yellow mosaic virus is proposed. At least one recombination event was detected in this new begomovirus, with putative parents being begomoviruses from tomato and Centrosema.
A novel bipartite begomovirus infecting Cnidoscolus urens (Euphorbiaceae) from Pernambuco State, ... more A novel bipartite begomovirus infecting Cnidoscolus urens (Euphorbiaceae) from Pernambuco State, Brazil has been characterized. The complete DNA-A (2657 to 2692 nt) and DNA-B (2622 nt) components of the viral isolates showed a typical genome organization of New World bipartite begomoviruses. DNA-A of the isolates had the highest percentage of nucleotide identity (88.6–88.9%) with the Cnidoscolus mosaic leaf deformation virus (NC_038982). Based on the current classification criteria for the genus Begomovirus, a new member infecting C. urens was reported, and the name Begomovirus caboniensis was proposed for these viruses, adopting the standardized binomial system.
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