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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.

Há muito tempo, os micro-organismos vêm sendo uma promissora fonte de recursos biotecnológicos com aplicações na agropecuária, como para o controle de fitopatógenos. Desta forma, vários estudos têm sido conduzidos com o intuito de se descobrir micro-organismos, como fungos, com potenciais aplicações na agricultura. Diante disto, objetivou-se por meio deste estudo a prospecção química e atividade antagônica in vitro do fungo endófito Phomopsis sp. contra fungos fitopatogênicos. Foram conduzidos dois experimentos. No primeiro experimento, foram conduzidos ensaios de prospecção química do micélio do fungo supracitado, onde foi avaliada a biomassa micelial, seu crescimento em cinco meios de cultura: Batata Dextrose Agar (BDA), Batata Sacarose Agar (BSA), Cenoura Agar (CA), Czapek (CZA) e Triptona Soja Agar (TSA), e incidência de luz e Ressonância Magnética Nuclear (RMN) dos cristais de carbono obtidos nos extratos miceliais. O segundo experimento compreendeu ao teste de pareamento e formação de halo de inibição contra três fungos fitopatógenos (Rhizoctonia sp., Pestalotiopsis sp. e Colletotrichum sp.), onde foram inoculados em placas contendo meio BDA e avaliados após cinco dias de incubação, onde se verificou a presença de halo de inibição. Por meio da prospecção química foi verificado que o fungo endófito Phomopsis sp. possui melhor crescimento em meio BDA sob luz contínua e presença de ergosterol em suas membranas. O isolado também foi capaz de produzir halo de inibição contra os fitopatógenos testados.

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.

Badnaviruses are plant pararetroviruses that infect economically important crops worldwide, and several badnaviral species have been reported causing significant economic losses in cacao plantations in West Africa. Based on the available full-length genome sequences of cacao swollen shoot disease (CSSD)-associated badnaviruses (n = 66), four primer pairs (CSSD1-CSSD4) were designed to amplify a fragment of the 5′ region of open reading frame (ORF) 3, which comprises the movement protein, by polymerase chain reaction (PCR). Primers were evaluated for their ability to amplify a badnaviral fragment(s) from symptomatic and asymptomatic cacao leaf samples collected in Cote d’Ivoire during 2017–2019. The PCR products obtained by amplification with the CSSD1 primers showed high sequence variability and were phylogenetically related to one of three different badnaviral species, Cacao swollen shoot Togo B virus, Cacao swollen shoot CD virus, and Cacao swollen shoot CE virus, while the CSSD2 and CSSD4 amplicon sequences grouped exclusively with either cacao swollen shoot Togo B virus (CSSTBV) and Cacao swollen shoot Ghana M virus isolates, respectively. The majority of the isolates obtained here were most closely phylogenetically related to CSSTBV, with which they shared 81.0–98.0% nucleotide identity, making the CSSTBV-like isolates the predominant species associated with badnavirus-infected cacao trees tested in Cote d’Ivoire.

Made available in DSpace on 2022-04-28T19:41:35Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-07-01 Background. The necessity of a competent vector for transmission is a primary ecological factor driving the host range expansion of plant arthropod-borne viruses, with vectors playing an essential role in disease emergence. Cassava begomoviruses severely constrain cassava production in Africa. Curiously, begomoviruses have never been reported in cassava in South America, the center of origin for this crop. It has been hypothesized that the absence of a competent vector in cassava is the reason why begomoviruses have not emerged in South America. Methods. We performed a country-wide whitefly diversity study in cassava in Brazil. Adults and/or nymphs of whiteflies were collected from sixty-six cassava fields in the main agroecological zones of the country. A total of 1,385 individuals were genotyped based on mitochondrial cytochrome oxidase I sequences. Results. A high species richness was observed, with five previously described species and two putative new ones. The prevalent species were Tetraleurodes acaciae and Bemisia tuberculata, representing over 75% of the analyzed individuals. Although we detected, for the first time, the presence of Bemisia tabaci Middle East-Asia Minor 1 (BtMEAM1) colonizing cassava in Brazil, it was not prevalent. The species composition varied across regions, with fields in the Northeast region showing a higher diversity. These results expand our knowledge of whitefly diversity in cassava and support the hypothesis that begomovirus epidemics have not occurred in cassava in Brazil due to the absence of competent vector populations. However, they indicate an ongoing adaptation process of BtMEAM1 to cassava, increasing the likelihood of begomovirus emergence in this crop. Dep. de Fitopatologia/BIOAGRO Universidade Federal de Viçosa, MG Dep. de Proteção Vegetal Universidade Estadual Paulista, SP Faculdade de Engenharia Agronômica Universidade Federal do Pará, PA Instituto Federal do Sudeste de Minas Gerais, MG Dep. de Fitotecnia Universidade Federal do Piauí, PI Embrapa Amazônia Oriental, PA Dep. de Fitotecnia e Fitossanidade Universidade Federal do Paraná, PR Centro de Ciências Agroveterinárias Universidade do Estado de Santa Catarina, SC Centro Multidisciplinar do Campus de Barra Universidade Federal do Oeste da Bahia, BA Centro de Ciências Agrárias/Fitossanidade Universidade Federal de Alagoas, AL Embrapa Arroz e Feijão, GO Instituto Capixaba de Pesquisa e Extensão Rural, ES Faculdade de Engenharia Florestal Universidade Federal do Pará, PA Dep. de Proteção Vegetal Universidade Estadual Paulista, SP

Black pod disease, caused by Phytophthora species, is among the main limiting factors of cacao (Theobroma cacao L.) production. High incidence levels of black pod disease have been reported in Brazil, being induced by Phytophthora capsici, Phytophthora citrophthora, Phytophthora heveae, and Phytophthora palmivora. To assess the diversity of Phytophthora species affecting cacao in Brazil, 40 new isolates were obtained from cacao pods exhibiting symptoms of black pod disease collected in different smallholder farms in 2017. Further, ten cacao-infecting isolates morphologically identified as P. citrophthora and P. palmivora were molecularly characterized. The genomic regions beta-tubulin, elongation factor 1 alpha, heat shock protein 90, and internal transcribed spacer, and the mitochondrially encoded cytochrome c oxidase I and II genes were PCR-amplified and Sanger-sequenced from the cacao-infecting Phytophthora isolates. The morphological characterization and evaluation of the mycelial growth rates for the Phytophthora isolates were performed in vitro. Based on the molecular analysis and morphological comparisons, 19 isolates were identified as P. palmivora (clade 4). Interestingly, 31 isolates grouped together in the phylogenetic tree and were placed apart from previously known species in Phytophthora clade 2. Therefore, these isolates are considered as a new species herein referred to as Phytophthora theobromicola sp. nov., which produced papillate, semipapillate, and persistent sporangia on simple sporangiophores. The P. palmivora isolates were identified as A1 mating type by pairing each isolate with known A1 and A2 tester strains of P. capsici, but no oogonia/antheridia were observed when P. theobromicola was paired with the different tester strains. The P. theobromicola and P. citrophthora isolates showed higher mycelial growth rates, when compared to P. palmivora, on different media at 10, 15, and 20°C, but similar values were observed when grown on clarified CA media at 25 and 30°C. The pathogenicity tests carried out on pods of four cacao clones (CCN51, PS1319, Cepec2004, and CP49) showed significant variability among the isolates of both Phytophthora species, with P. theobromicola inducing higher rates of necrotic lesion expansion, when compared to P. palmivora. Here, two Phytophthora species were found associated with black pod disease in the state of Bahia, Brazil, and the previously undescribed P. theobromicola seems to be prevalent in field conditions. This is the first report of P. theobromicola on T. cacao. Also, these findings are crucial to improve the disease control strategies, and for the development of cacao materials genetically resistant to Phytophthora.

Cotton leafroll dwarf virus (CLRDV) was first reported in the United States (US) in 2017 from cotton plants in Alabama (AL) and has become widespread in cotton-growing states of the southern US. To investigate the genomic variability among CLRDV isolates in the US, complete genomes of the virus were obtained from infected cotton plants displaying mild to severe symptoms from AL, Florida, and Texas. Eight CLRDV genomes were determined, ranging in size from 5865 to 5867 bp, and shared highest nucleotide identity with other CLRDV isolates in the US, at 95.9–98.7%. Open reading frame (ORF) 0, encoding the P0 silencing suppressor, was the most variable gene, sharing 88.5–99.6% and 81.2–89.3% amino acid similarity with CLRDV isolates reported in cotton growing states in the US and in Argentina and Brazil in South America, respectively. Based on Bayesian analysis, the complete CLRDV genomes from cotton in the US formed a monophyletic group comprising three relatively divergent sister clades, whereas CLRDV genotypes from South America clustered as closely related sister-groups, separate from US isolates, patterns reminiscent of phylogeographical structuring. The CLRDV isolates exhibited a complex pattern of recombination, with most breakpoints evident in ORFs 2 and 3, and ORF5. Despite extensive nucleotide diversity among all available CLRDV genomes, purifying selection (dN/dS &lt, 1) was implicated as the primary selective force acting on viral protein evolution.

Cacao swollen shoot disease (CSSD) is a damaging disease of Theobroma cacao L. associated with infection by a group of poorly characterized badnaviral species. To establish causality and characterize the symptomatology associated with infection by the badnavirus cacao swollen shoot Ghana M virus (CSSGMV), an infectious clone (1.3-mer) was constructed and used to inoculated cacao “Amelonado” seedlings by biolistic inoculation (BI; n = 18) and agroinoculation (AI; n = 15). Newly expanded leaves of BI (10/18) and AI (12/15) plants developed foliar mosaic and curling symptoms 30-days post inoculation (dpi), with chlorotic mottling and necrotic crinkling being evident by 90 dpi. By 120 dpi, three of 15 AI plants exhibited characteristic stem-swelling. Viral infection was verified by PCR-amplification and sequencing of a 1068 bp fragment of the CSSGMV ORF3 from newly expanding leaves 60 dpi. The PCR results indicated that 14 of 18 and 15 of 15 BI and AI plants, respectively, were systemically infected. The complete CSSGMV genome sequence was determined, by Illumina sequencing, from representative AI and BI plants and shared >99.5% pairwise nucleotide identity with CSSGMV-Nig9 (GenBank Accession No. MH785299). Based on the development of characteristic CSSD symptoms and recovery of partial and complete genome sequences of CSSGMV-Nig9 from systemically infected cacao plants, Koch's postulates have been fulfilled.

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 supported clusters (badnavirus groups 1-4), with clusters 1 and 3 being sister groups comprising predominantly sugarcane- and banana-infecting species. Non-tree-like evolution analysis evidenced putative recombination events among badnaviruses, and at least 23 independent events were detected. High levels of nucleotide diversity were observed for the partial RT/RNaseH region in isolates of 11 badnavirus species. These results showed that mutation and recombination are important mechanisms that acting on badnavirus diversification.

The production of cactus prickly pear (Nopalea cochenillifera) as a foraging plant in the Brazilian Northeastern region is limited by diseases for which knowledge of etiology and diversity of pathogens is scarce. In this work Botryosphaeriaceae fungi isolated from cladode spots of cactus prickly pear were characterized based on morphology and phylogeny using on partial nucleotide sequences of ITS-rDNA, EF1-α e β-tub. Four species were identified, of which three caused a brown spot, Lasiodiplodia theobromae, L. jatrophicola and Neofusicoccum batangarum and one, Neoscytalidium hyalinum, caused a squamous spot firstly reported to occur in N. cochenillifera. We report for the first time worldwide L. jatrophicola and N. hyalinum species causing spots on cactus prickly pear.

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, this isolate was considered a putative new begomovirus species, and the name Gaya yellow mosaic virus (GaYMV) is suggested. The GaYMV isolate grouped with SiMoAV and other begomoviruses infecting Sida spp. from the State of Alagoas, Brazil. This is the first report of a begomovirus infecting G. guerkeana, indicating that this non-cultivated plant can act as a reservoir/source of begomoviruses.

Fungal species belonging to the genus Balansia (Clavicipitaceae) are well known as endophytic and epibiotic species commonly found on grasses or sedges. Among the 36 species of Balansia described worldwide, ten have been reported in Brazil. While most species of balansoid fungi were described on graminaceous plants, only four were characterized on cyperaceous hosts. To correctly identify the species of balansoid fungi associated with Scleria bracteata (Cyperaceae), specimens were collected in the state of Alagoas, Brazil, in 2014 and 2016. Nucleotide partial sequences of the second-largest subunit of RNA polymerase II (RPB2), translation elongation factor 1-α (TEF1), 18S subunit ribosomal DNA (SSU), 28S subunit ribosomal DNA (LSU), and internal transcribed spacers (ITS) were obtained from each balansoid specimen. Based on morphology and molecular data, the specimens were identified as a putative new species of Balansia, herein referred to as Balansia scleriae sp. nov.

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 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.

Plant virus ecology is strongly dependent on that of its vector. The necessity of a competent vector for transmission is a primary ecological factor driving the host range expansion of plant arthropod-borne viruses, with vectors playing an essential role in promoting disease emergence. Cassava begomoviruses severely constrain cassava production in Africa. Curiously, begomoviruses have never been reported in cassava in South America, the center of origin for this crop. It has been hypothesized that the absence of a competent begomoviruses vector that efficiently colonizes cassava is the reason why begomoviruses have not emerged in South America. To test this hypothesis, we performed a country-wide whitefly diversity study in cassava in Brazil. Adults and/or nymphs of whiteflies were collected from sixty-six cassava fields across twelve states representing the main agroecological zones of the country. A total of 1,385 individuals were genotyped based on partial mitochondrial cytochrome oxidase I (mtCOI) sequences. A high species richness was observed, with five previously described species and two putative new ones. The most prevalent species wereTetraleurodes acaciaeandBemisia tuberculata, representing over 75% of the analyzed individuals. Although we detected, for the first time, the presence ofBemisia tabaciMiddle East-Asia Minor 1 (BtMEAM1) colonizing cassava in Brazil, it was not prevalent. The species composition varied across regions, with fields in the Northeast region showing a higher diversity. These results expand our knowledge of whitefly diversity in cassava and support the hypothesis that begomovirus epidemics have not occurred in cassava in Brazil due to the absence of competent vector populations. However, they indicate an ongoing adaptation process ofBtMEAM1 to cassava, increasing the likelihood of begomovirus emergence in this crop in the near future.

Several key evolutionary events marked the evolution of geminiviruses, culminating with the emergence of bipartite genomes represented by viruses classified in the genusBegomovirus. This genus represents the most abundant group of multipartite viruses, contributing significantly to the observed abundance of multipartite species in the virosphere. Although aspects related to virus-host interactions and evolutionary dynamics have been extensively studied, the bipartite nature of these viruses has been little explored in evolutionary studies. We performed a parallel evolutionary analysis of the DNA-A and DNA-B components of New World begomoviruses. A total of 239 full-length DNA-B sequences obtained in this study, combined with 292 DNA-A and 76 DNA-B sequences retrieved from GenBank, were analyzed. The results indicate that the DNA-A and DNA-B respond differentially to evolutionary processes, with the DNA-B being more permissive to variation and more prone to recombination than the DNA-A. Although a clear geographic segregation was observed for both components, differences in the genetic structure between DNA-A and DNA-B were also observed, with cognate components belonging to distinct genetic clusters. DNA-B coding regions evolve under the same selection pressures than DNA-A coding regions. Together, our results indicate an interplay between reassortment and recombination acting at different levels across distinct subpopulations and components.

The incidence of cacao swollen shoot disease (CSSD) in cacao (Theobroma cacao L.) has increased in West Africa since ~2000. To investigate the genomic and species diversity of the CSSD-badnaviruses infecting cacao in C&ocirc, te d&rsquo, Ivoire and Ghana, symptomatic leaves were subjected to high-throughput sequencing. Among the 30 newly determined genomes, three badnaviruses were identified, Cacao swollen shoot Togo B virus (CSSTBV), Cacao swollen shoot CD virus, and Cacao swollen shoot CE virus (CSSCEV). The phylogenetic trees reconstructed for the reverse transcriptase (RT) and ribonuclease H (RNase H) sequences were incongruent with the complete viral genomes, which had the most robust statistical support. Recombination seems to be involved in the CSSD-badnavirus diversification. The genomic diversity varied among different CSSD-badnaviruses, with CSSTBV showing the lowest nucleotide diversity (&pi, = 0.06236), and CSSCEV exhibiting the greatest variability (&pi, = 0.21911). Evidence of strong purifying selection was found in the coding regions of the CSSTBV isolates.

Virus-like disease symptoms consisting of leaf cupping, shortened internodes, and overall stunting were observed in commercial cotton fields in Alabama in 2017 to 2018. To determine the complete genome sequence of the suspected causal polerovirus, symptomatic leaf samples were collected in Macon County, Alabama, and subjected to Illumina RNA sequencing. Based on BLASTn analysis, the Illumina contig of 5,771 nt shared the highest nucleotide identity (approximately 95%) with members of the species Cotton leafroll dwarf virus (CLRDV) (genus Polerovirus; family Luteoviridae) from Argentina and Brazil. The full-length viral genome sequence was verified by reverse transcription (RT)-PCR amplification, cloning, and Sanger sequencing. The complete CLRDV genome of 5,865 nt in length shared 94.8 to 95.2% nucleotide identity with six previously reported CLRDV isolates. The genome of the CLRDV isolate amplified from Alabama samples (CLRDV-AL) has seven predicted open reading frames (ORFs). Viral proteins 1 to 5 (P1 to P5) shared 91.9 to 99.5% amino acid identity with the six CLRDV isolates from Argentina and Brazil. However, P0, the suppressor of host gene silencing, shared 82.4 to 88.5% pairwise amino acid identity with the latter CLRDV isolates. Phylogenetic analysis of the seven full-length CLRDV genomes resolved three sister clades: CLRDV-AL, CLRDV-typical, and CLRDV-atypical, respectively. Three recombination events were detected by the recombination detection program among the seven CLRDV isolates with breakpoints occurring along the genome. Pairwise nucleotide identity comparisons of ORF0 sequences for the three CLRDV-AL field isolates indicated that they were >99% identical, suggesting that this previously unknown CLRDV genotype represents a single introduction to Alabama.

Turnera subulata L. is a plant that belongs to the Turneraceae family and is popularly known in Brazil as “Chanana”; it is used as an alternative medicine. Among all microorganisms, fungi are mostly associated with plants. The aim of this study is to isolate, identify and evaluate the antifungal and antioxidant activity of extracts of Phomopsis sp. isolated from T. subulata. From the leaf fragment obtained from T. subulata, the filamentous endophytic fungus Phomopsis sp was isolated. The fungal isolate had a higher growth in potato dextrose agar (PDA) and potato sucrose agar (PSA) culture medium, as well as in the presence of light. In the antagonism test of the endophytic Phomopsis sp. against human pathogens, there was inhibition zone against Escherichia coli, Staphylococcus aureus, Candida albicans, C. tropicalis and C. glabrata. Concerning the antioxidant activity, it was observed that the chloroform extract was more effective than hexane. On the other hand, all the extracts from the mycelium of Phomopsis sp. and its ethyl acetate extract from the cultured filtrate had low antimicrobial activity against strains of E. coli, S. aureus, C. albicans, C. tropicalis and C. glabrata. Therefore it was concluded that Phomopsis sp. may act as an endophyte of T. subulata. Extracts from Phomopsis sp. promoted inhibition zone of growth when tested against human pathogen. Its hexanic and chloroform extracts showed lower antioxidant activity. Key words: Biological control, endophytic fungus, secondary metabolites, filamentous fungus, fungal extract.

Anthracnose, caused by Colletotrichum spp., is one of the major fungal diseases that affect Capsicum spp. and leads to severe crop losses. The aim of this study was to identify species within Colletotrichum that cause anthracnose in bell and hot pepper using phylogenetic and morphological criteria. Pathogenic isolates were obtained from bell and hot peppers exhibiting anthracnose symptoms and grown in the northeastern region of Brazil. These were initially identified based on the sequences of GAPDH, ACT, CAL, β-TUB genes and the ITS-rDNA region. Mycelial growth, coloration of the colony, size and shape of conidia and appressoria were determined for the selected isolates. It was concluded that five species: C. brevisporum, C. scovillei, C. siamense, C. tropicale and C. truncatum compose the species complex associated with anthracnose of Capsicum spp. in northeastern Brazil.

Begomoviruses are among the most damaging pathogens infecting cultivated hosts worldwide, and are considered an important limiting factor in tomato fields. In the present study, foliar samples of tomato and Sida spp. were collected in Boqueirao, state of Paraiba, Brazil, in May 2014. Viral genomes were amplified, cloned and sequenced. A total of 30 DNA-A components were obtained. Pairwise comparisons indicated the presence of only two begomovirus species: Tomato mottle leaf curl virus (ToMoLCV) from tomato samples and Sida mottle Alagoas virus (SiMoAV) in Sida spp. ToMoLCV and SiMoAV subpopulations showed high genetic variability, with the ToMoLCV Rep gene being the most variable. Recombination events were detected only among ToMoLCV isolates, with recombination breakpoints occurring in the common region and in the Rep gene. Negative or purifying selection seems to be among the most important evolutionary mechanisms acting on the CP and Rep genes in both ToMoLCV and SiMoAV. Our results indicate that ToMoLCV remains as the main tomato-infecting begomovirus in northeastern Brazil, and that Sida spp. do not contribute to ToMoLCV epidemics in tomato.

The emergence of begomoviruses (whitefly-transmitted viruses classified in the genus Begomovirus, family Geminiviridae) in Brazil probably occurred by horizontal transfer from non-cultivated plants after the introduction of Bemisia tabaci MEAM1. The centre of diversity of Euphorbia heterophylla (Euphorbiaceae) is located in Brazil and Paraguay, where it is an invasive species in soybean and other crops. Reports of possible begomovirus infection of E. heterophylla in Brazil date back to the 1950s. In 2011, Euphorbia yellow mosaic virus (EuYMV) was described in symptomatic plants collected in the Brazilian state of Goias. Here we assess the genetic variability and population structure of begomoviruses infecting E. heterophylla in samples collected throughout nine Brazilian states from 2009 to 2014. A total of 158 and 57 haplotypes were compared in DNA-A and DNA-B datasets, respectively. Analysis comparing population structure in a large sampled area enabled us to differentiate two subpopulations. Further, the application of discriminant analysis of principal components allowed the differentiation of six subpopulations according to sampling locations and in agreement with phylogenetic analysis. In general, negative selection was predominant in all six subpopulations. Interestingly, we were able to reconstruct the phylogeny based on the information from the 23 sites that contributed most to the geographical structure proposed, demonstrating that these polymorphisms hold supporting information to discriminate between subpopulations. These sites were mapped in the genome and compared at the level of amino acid changes, providing insights into how genetic drift and selection contribute to maintain the patterns of begomovirus population variability from a geographical structuring point of view. Made available in DSpace on 2021-08-17T18:00:26Z (GMT). No. of bitstreams: 1 1537-vir000784.pdf: 4851397 bytes, checksum: 730af24bd8ded1625075e99bbb40c713 (MD5) Previous issue date: 2017

Okra (Abelmoschus esculentus [L.] Moench) is an important fresh market vegetable crop in southern Texas, U.S.A. In fall 2018, an investigation was conducted to identify the agent(s) of a virus-like disease outbreak on a 4.9-ha okra (cv. Clemson Spineless) farm in Hidalgo Co., Texas. By mid-growing season, disease incidence was 100%, which led to total crop loss. Symptoms—foliar yellow mosaic, bleaching, and vein clearing—were reminiscent of those caused by begomoviruses (Begomovirus, Geminiviridae). Leaves collected from 10 randomly distributed symptomatic plants were subjected to total DNA isolation (Dellaporta et al. 1983) and rolling cycle amplification (RCA) (TempliPhi 100 Amplification Kit, GE Healthcare Biosciences). The RCA product was used as a template for PCR amplification of a diagnostic fragment of the DNA-A (Wyatt and Brown 1996) and DNA-B (Rojas et al. 1993) components and full-length alphasatellites (Bull et al. 2003) and betasatellites (Briddon et al. 2002). The expected-size amplicon corresponding to each of the four targets was obtained from all 10 samples, except the betasatellite, for which half of the expected ∼1,350-bp product resulted. Amplicons were cloned into the pJET1.2 plasmid vector, and inserts of the expected sizes were Sanger sequenced (n ≥ 3 per event). BLASTn searches of GenBank revealed an unexpectedly complex begomovirome, consisting of the monopartite cotton leaf curl Gezira virus (CLCuGV), cotton leaf curl Gezira alphasatellite (CLCuGA; Colecusatellite, Alphasatellitidae), cotton leaf curl Gezira betasatellite (CLCuGB; Betasatellite, Tolecusatellitidae), and the bipartite okra yellow mosaic Mexico virus (OkYMMV). Viral genome-, component-, and satellite-specific abutting primers were designed and used to PCR amplify the corresponding molecule from two RCA products in two different labs, followed by cloning and bidirectional Sanger sequencing of ≥3 clones per event. The complete genome sequences were analyzed comparatively with corresponding GenBank sequences of each genomic DNA segment using SDT1.2 (Muhire et al. 2014). The OkYMMV DNA-A of 2,613 nt (GenBank MN027195 to 96) and DNA-B of 2,594 nt (MN027197 to 98), each shared 99.5 and 99.7% maximum identity, respectively, with the DNA-A (HM035059) and -B (HM035060) of OkYMMV-[US:TX:09] from okra plants in Texas (Hernandez-Zepeda et al. 2010). The complete monopartite genome sequence of the CLCuGV okra isolates (MN027199 to 202) was 2,764 nt and shared 99.5 to 99.6% maximum identity with an isolate of CLCuGV from hollyhock plants in Jordan (CLCuGV-[JO:Hol:09]: GU945265). The closest relative of the CLCuGA okra isolate, of 1,354 nt (MN027203 to 05), was CLCuGA-[IL:IsSq-C171:11] (KT099176) from whiteflies collected from squash plants in Israel, at 99% identity. Several approaches by two independent laboratories to clone and sequence a full-length CLCuGB, involving restriction digestion from total DNA or RCA (n = 2) and/or PCR amplification with abutting primers designed based on the full-length CLCuGB sequences (AF397217, KT099178), yielded only “defective-sized” CLCuGB molecules of 676 to 730 nt (MN027206 to 220). The betasatellite half-mers lacked the βC1 coding region while sharing 96 to 99% identity with CLCuGB-[EG:OK03:02] (AF397217) from okra plants in Egypt and CLCuGB-[IL:IsSq-C9:11] (KT099178) from whiteflies. This is the first U.S. report of CLCuGV and its associated alphasatellite and betasatellite, which are endemic to Africa (Idris and Brown 2000). More recently, members of the CLCuGV-satellite complex have been reported in the African Sahel, Arabian Peninsula and Middle East, and Pakistan (Idris et al. 2014; Tahir et al. 2011; Tiendrebeogo et al. 2010). The source of this Old World CLCuGV-satellite complex into New World okra plants is unknown, but its introduction via infected plants or viruliferous whiteflies transported into southern Texas, with its intensive cotton and vegetable production, is plausible. Spread of this complex poses a serious threat because U.S. cotton and vegetable varieties harbor no resistance to CLCuGV.

Badnaviruses are dsDNA plant viruses that cause diseases in economically important crops in most tropical and subtropical regions of the world. In northeastern Brazil, badnaviruses are a serious constraint to yam crops. We assessed the genetic variability of badnaviruses infecting yam crops in northeastern Brazil, based on the sequence of the RT/RNAseH domain of 96 badnavirus isolates obtained between 2011 and 2012. Phylogenetic analysis revealed that Dioscorea bacilliform AL virus (DBALV) is the only badnavirus species infecting yam in the Brazilian northeast part. No evidence of recombination was found among DBALV isolates. Genetic variability of the DBALV population is high, with a mutation frequency on the order of 10−4, similar to those found for RNA viruses. We conclude that several mechanisms, including purifying selection and adaptation of the virus to the dioscorea species cultivation system, are important evolutionary processes in the genetic diversification of the DBALV population.

The family Caulimoviridae comprises virus species that replicate by reverse transcription, and is composed by seven genera. Viruses classified within the genus Badnavirus are pathogens in economically important crops worldwide, and previous studies suggest a high genetic diversity in badnaviruses infecting cultivated hosts. To assess the genetic diversity of sugarcane-infecting badnaviruses, samples were obtained from a germplasm collection in Brazil in 2013. A total of 300 samples were collected, and PCR-analysis showed a badnavirus incidence level of 36 %. Partial sequences comprising the RT/RNaseH genomic region were obtained for 37 isolates. Sequence analysis showed the presence of at least six badnavirus species, with one being novel. The phylogenetic analysis showed that some sugarcane isolates are closely related to badnaviruses infecting banana (Musa spp.).

The soil microbiota is associated with the formation and maintenance of the stability of aggregates for the production of proteins and extracellular polysaccharides, and can be a determining factor in controlling the diversity of vegetable and other organisms that live aboveground. Arbuscular mycorrhizal (AM) fungi have yet to be fully utilized in agriculture, because certain aspects of their symbiotic nature (e.g., biogeography, ecology) are not fully understood. This symbiosis is an association formed between the roots of plant species and members of soil fungi belonging to the phylum Glomeromycota. Species of this phylum are obligate biotrophs, which, during symbiosis, establish a source sink for plant photosynthates. In exchange, the symbiont provides, through the hyphae, uptake of inorganic nutrients and water from the soil solution and their translocation to the host plant. Establishment of this symbiosis implies changes in the host plant’s primary and secondary metabolism. This reprogramming transcriptome induced by the symbiont results in mycorrhizal plant acclimatization to environmental stresses. This chapter attempts to highlight the contribution that AM symbiosis can play as an ecosystem service provider to guarantee host plant nutrition under abiotic stress conditions, and discusses briefly the exploitation of arbuscular mycorrhiza in sustainable agriculture.

Background The Geminiviridae family encompasses a group of single-stranded DNA viruses with twinned and quasi-isometric virions, which infect a wide range of dicotyledonous and monocotyledonous plants and are responsible for significant economic losses worldwide. Geminiviruses are divided into nine genera, according to their insect vector, host range, genome organization, and phylogeny reconstruction. Using rolling-circle amplification approaches along with high-throughput sequencing technologies, thousands of full-length geminivirus and satellite genome sequences were amplified and have become available in public databases. As a consequence, many important challenges have emerged, namely, how to classify, store, and analyze massive datasets as well as how to extract information or new knowledge. Data mining approaches, mainly supported by machine learning (ML) techniques, are a natural means for high-throughput data analysis in the context of genomics, transcriptomics, proteomics, and metabolomics. Results Here, we describe the development of a data warehouse enriched with ML approaches, designated geminivirus.org. We implemented search modules, bioinformatics tools, and ML methods to retrieve high precision information, demarcate species, and create classifiers for genera and open reading frames (ORFs) of geminivirus genomes. Conclusions The use of data mining techniques such as ETL (Extract, Transform, Load) to feed our database, as well as algorithms based on machine learning for knowledge extraction, allowed us to obtain a database with quality data and suitable tools for bioinformatics analysis. The Geminivirus Data Warehouse (geminivirus.org) offers a simple and user-friendly environment for information retrieval and knowledge discovery related to geminiviruses. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1646-4) contains supplementary material, which is available to authorized users.

Begomoviruses have been detected infecting the weed Cnidoscolus urens (family Euphorbiaceae) since 2004, but the viral species to which these viruses belonged was not known. Here, we report for the first time the complete genome sequence of a bipartite begomovirus obtained from C. urens collected in the state of Alagoas, Brazil. This isolate met the criteria to be classified as a member of a new begomovirus species, and the tentative name cnidoscolus mosaic leaf deformation virus (CnMLDV) is proposed. Pairwise sequence comparisons and phylogenetic analysis showed that the DNA-A genomic component of CnMLDV is most closely related to that of passionfruit severe leaf distortion virus, with 86.3 % nucleotide sequence identity.

Begomoviruses are whitefly-transmitted single-stranded DNA viruses of great economic importance in the tropics and subtropics. Several begomovirus species have been reported in tomatoes in Brazil, but only a few predominate in the field, for unknown reasons. In this study begomovirus-infected tomato samples were collected in Vicosa, State of Minas Gerais, in Nov/2009 and Dec/2010. Viral genomes were amplified, cloned and sequenced. A total of 36 DNA-A components were obtained. Sequence comparisons indicated the presence of a single begomovirus, Tomato severe rugose virus (ToSRV), with pairwise identities between isolates ranging from 97.3 to 100%. Subdivision tests indicated the existence of a single population. The analysis of variability descriptors indicated that the ToSRV population has a genetic variability similar to other begomovirus populations described in Brazil infecting tomato. Neutrality tests suggested the occurrence of purifying selection acting upon the population. Recombination analysis identified recombination events with begomoviruses from the weed species Sida micrantha. The wide distribution of ToSRV in the field and the detection of recombination indicate that continuous monitoring of viral populations in the field will be required to enable an efficient resistance-based control strategy for begomoviruses.

Begomoviruses are whitefly-transmitted, single-stranded DNA viruses that are often associated with weed plants. The aim of this study was to further characterize the diversity of begomoviruses infecting weeds (mostly Sida spp.) in Brazil. Total DNA was extracted from weed samples collected in Viçosa (Minas Gerais state) and in some municipalities of Alagoas state in 2009 and 2010. Viral genomes were amplified by RCA, cloned and sequenced. A total of 26 DNA-A clones were obtained. Sequence analysis indicated the presence of 10 begomoviruses. All viral isolates from Blainvillea rhomboidea belonged to the same species, Blainvillea yellow spot virus (BlYSV ), thereby suggesting that BlYSV may be the only begomovirus present in this weed species. Four isolates represent new species, for which the following names are proposed: Sida yellow blotch virus (SiYBV), Sida yellow net virus (SiYNV), Sida mottle Alagoas virus (SiMoAV) and Sida yellow mosaic Alagoas virus (SiYMAV). Recombination events were detected among the SiYBV isolates and in the SiYNV isolate. These results constitute further evidence of the high species diversity of begomoviruses in Sida spp. However, the role of this weed species as a source of begomoviruses infecting crop plants remains to be determined.

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.

Viruses 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.

Begomoviruses are whitefly-transmitted, ssDNA plant viruses and are among the most damaging pathogens causing epidemics in economically important crops worldwide. Wild/non-cultivated plants play a crucial epidemiological role, acting as begomovirus reservoirs and as ‘mixing vessels' where recombination can occur. Previous work suggests a higher degree of genetic variability in begomovirus populations from non-cultivated hosts compared with cultivated hosts. To assess this supposed host effect on the genetic variability of begomovirus populations, cultivated (common bean, Phaseolus vulgaris, and lima bean, Phaseolus lunatus) and non-cultivated (Macroptilium lathyroides) legume hosts were sampled from two regions of Brazil. A total of 212 full-length DNA-A genome segments were sequenced from samples collected between 2005 and 2012, and populations of the begomoviruses Bean golden mosaic virus (BGMV) and Macroptilium yellow spot virus (MaYSV) were obtained. We found, for each begomovirus species, similar genetic variation between populations infecting cultivated and non-cultivated hosts, indicating that the presumed genetic variability of the host did not a priori affect viral variability. We observed a higher degree of genetic variation in isolates from MaYSV populations than BGMV populations, which was explained by numerous recombination events in MaYSV. MaYSV and BGMV showed distinct distributions of genetic variation, with the BGMV population (but not MaYSV) being structured by both host and geography.

Ninety-five tomato accessions belonging to the Vegetable Crops Germplasm Bank of the Federal University of Vicosa (BGH-UFV) were evaluated in a protected environment (biolistic inoculation under greenhouse conditions) and in the field (natural infection) for resistance to bipartite begomoviruses present in Brazil. Plants were assessed by the visual evaluation of symptoms, and viral infection was confirmed by non-radioactive molecular hybridization. Univariate statistical analyses and correlations were made between the traits. High and significant correlations were found between the percentages of visual symptoms and of viral replication, with values of 0.67 in the protected environment and 0.60 in the field. We concluded that under the protected environment, the accessions BGH-2144, BGH-2150, BGH-6878 and BGH-6881 displayed resistance to infection. Under field conditions with natural infection, the best results were obtained for the accessions BGH-2080 and BGH-6881. Only the BGH-6881 (Solanum peruvianum L.) accession excelled in both conditions; this resistance was attributed to the presence of the Ty-2 and Ty-3 resistance gene alleles in heterozygosity. In general, all of the accessions selected in both experimental conditions can serve as sources for the development of cultivars tolerant or resistant to the bipartite begomoviruses present in Brazil.

Begomoviruses 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-infectingMacroptilium yellow spot virus(MaYSV) or the crop-infectingTomato 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.