Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 64
Filter
Add more filters











Publication year range
1.
Viruses ; 16(6)2024 Jun 01.
Article in English | MEDLINE | ID: mdl-38932191

ABSTRACT

The diversity of Geminiviridae and Alphasatellitidae species in tomatoes was assessed via high-throughput sequencing of 154 symptomatic foliar samples collected from 2002 to 2017 across seven Brazilian biomes. The first pool (BP1) comprised 73 samples from the North (13), Northeast (36), and South (24) regions. Sixteen begomoviruses and one Topilevirus were detected in BP1. Four begomovirus-like contigs were identified as putative novel species (NS). NS#1 was reported in the semi-arid (Northeast) region and NS#2 and NS#4 in mild subtropical climates (South region), whereas NS#3 was detected in the warm and humid (North) region. The second pool (BP2) comprised 81 samples from Southeast (39) and Central-West (42) regions. Fourteen viruses and subviral agents were detected in BP2, including two topileviruses, a putative novel begomovirus (NS#5), and two alphasatellites occurring in continental highland areas. The five putative novel begomoviruses displayed strict endemic distributions. Conversely, tomato mottle leaf curl virus (a monopartite species) displayed the most widespread distribution occurring across the seven sampled biomes. The overall diversity and frequency of mixed infections were higher in susceptible (16 viruses + alphasatellites) in comparison to tolerant (carrying the Ty-1 or Ty-3 introgressions) samples, which displayed 9 viruses. This complex panorama reinforces the notion that the tomato-associated Geminiviridae diversity is yet underestimated in Neotropical regions.


Subject(s)
Geminiviridae , Metagenomics , Phylogeny , Plant Diseases , Solanum lycopersicum , Solanum lycopersicum/virology , Brazil , Plant Diseases/virology , Geminiviridae/genetics , Geminiviridae/classification , Geminiviridae/isolation & purification , Animals , Genetic Variation , Genome, Viral , Begomovirus/genetics , Begomovirus/classification , High-Throughput Nucleotide Sequencing
2.
Environ Entomol ; 53(1): 11-17, 2024 Feb 20.
Article in English | MEDLINE | ID: mdl-37478402

ABSTRACT

The beet leafhopper, Circulifer tenellus (Baker 1896), is the sole vector of beet curly top virus (BCTV). Both the virus and the vector have very wide host ranges, including many crops and weeds. Industrial hemp (Cannabis sativa L.) has been reported as a host for both the virus and leafhopper in the past few years with the legal cultivation of the crop in the United States. This research assessed the interactions of the beet leafhopper and hemp in New Mexico by determining the natural infection of hemp with BCTV in 3 field plots in 2021 and 2022 and monitoring the numbers of leafhoppers using yellow sticky traps. The relative preference of beet leafhopper for hemp types and varieties of hemp was assessed using cafeteria-style choice tests. Higher numbers of beet leafhoppers were trapped in and around hemp fields in 2022 than in 2021 in all 3 locations. BCTV was found to infect all 3 types of hemp (cannabidiol or CBD, fiber, and grain) in 2022 in 1 location and only a single CBD variety of hemp in the other 2 locations. Two BCTV strains were identified in CBD hemp, while an additional BCTV strain was found infecting chile pepper grown at the same location.


Subject(s)
Beta vulgaris , Cannabis , Geminiviridae , Hemiptera , Animals , New Mexico , Plant Diseases
3.
Arch Virol ; 168(9): 223, 2023 Aug 10.
Article in English | MEDLINE | ID: mdl-37561218

ABSTRACT

The phylum Cressdnaviricota comprises viruses with single-stranded, circular DNA genomes that encode an HUH-type endonuclease (known as Rep). The phylum includes two classes, eight orders, and 11 families. Here, we report the creation of a twelfth family in the order Mulpavirales, class Arfiviricetes of the phylum Cressdnaviricota. The family Amesuviridae comprises viruses that infect plants and is divided into two genera: Temfrudevirus, including the species Temfrudevirus temperatum (with temperate fruit decay-associated virus as a member), and Yermavirus, including the species Yermavirus ilicis (with yerba mate-associated circular DNA virus as a member). Both viruses encode Rep proteins with HUH endonuclease and SH3 superfamily helicase domains. Phylogenetic analysis indicates that the replicative module of amesuviruses constitutes a well-supported monophyletic clade related to Rep proteins from viruses in the order Mulpavirales. Furthermore, both viruses encode a single capsid protein (CP) related to geminivirus CPs. Phylogenetic incongruence between the replicative and structural modules of amesuviruses suggests a chimeric origin resulting from remote recombination events between ancestral mulpavirales and geminivirids. The creation of the family Amesuviridae has been ratified by the International Committee on Taxonomy of Viruses (ICTV).


Subject(s)
DNA Viruses , Plant Viruses , DNA Viruses/classification , DNA Viruses/isolation & purification , DNA, Circular/genetics , DNA, Single-Stranded/genetics , Endonucleases/genetics , Geminiviridae/genetics , Genome, Viral/genetics , Phylogeny , Plant Viruses/genetics
4.
Plant Dis ; 106(5): 1330-1333, 2022 May.
Article in English | MEDLINE | ID: mdl-34854758

ABSTRACT

Maize striate mosaic virus (MSMV; genus Mastrevirus) was recently reported in maize plants in Brazil and also detected by metagenomic analyses in the corn leafhopper, Dalbulus maidis (DeLong & Wolcott). Although these findings suggested that D. maidis is a potential vector, no transmission studies have been performed. Here, we tested the transmission of MSMV by D. maidis from field-collected infected plants and plants infected with MSMV via leafhopper-mediated transmission in the laboratory; all plants were confirmed positive for MSMV by PCR. In each one of three transmission replicates, aviruliferous D. maidis nymphs and adults were confined together on a source plant during a 4-day acquisition access period (AAP) and subsequently transferred to healthy maize seedlings (10 individuals per test plant) in a series of 4-day inoculation access periods (IAPs). We also tested transmission by the corn aphid, Rhopalosiphum maidis (Fitch) and by mechanical inoculation of healthy maize seedlings. Only D. maidis transmitted MSMV, with overall transmission rates of 29.4 and 39.5% on field-collected infected plants and 18.5% on infected plants in laboratory. D. maidis transmitted MSMV until the third (8 to 12 days after the AAP) or fourth successive IAP (12 to 16 days), with gradual loss in transmission efficiency and rate of viruliferous insects over time, suggesting a persistent but nonpropagative mode of transmission. Infected test plants showed mottling symptoms with mild chlorotic streaks and height reduction. This is the first report of transmission of a mastrevirus by D. maidis, facilitating the completion of Koch's postulate for MSMV.


Subject(s)
Aphids , Geminiviridae , Animals , Brazil , Metagenomics , Zea mays
5.
Viruses ; 13(5)2021 05 06.
Article in English | MEDLINE | ID: mdl-34066372

ABSTRACT

In plant-virus interactions, the plant immune system and virulence strategies are under constant pressure for dominance, and the balance of these opposing selection pressures can result in disease or resistance. The naturally evolving plant antiviral immune defense consists of a multilayered perception system represented by pattern recognition receptors (PRR) and resistance (R) proteins similarly to the nonviral pathogen innate defenses. Another layer of antiviral immunity, signaling via a cell surface receptor-like kinase to inhibit host and viral mRNA translation, has been identified as a virulence target of the geminivirus nuclear shuttle protein. The Geminiviridae family comprises broad-host range viruses that cause devastating plant diseases in a large variety of relevant crops and vegetables and hence have evolved a repertoire of immune-suppressing functions. In this review, we discuss the primary layers of the receptor-mediated antiviral immune system, focusing on the mechanisms developed by geminiviruses to overcome plant immunity.


Subject(s)
Geminiviridae/immunology , Geminiviridae/pathogenicity , Host-Pathogen Interactions/immunology , Plant Diseases/virology , Plant Immunity , Receptors, Pattern Recognition/immunology , Crops, Agricultural/virology , Geminiviridae/genetics , Genome, Viral , Plant Immunity/genetics , Plant Immunity/immunology , Signal Transduction
6.
Viruses ; 12(4)2020 04 03.
Article in English | MEDLINE | ID: mdl-32260283

ABSTRACT

Cactaceae comprise a diverse and iconic group of flowering plants which are almost exclusively indigenous to the New World. The wide variety of growth forms found amongst the cacti have led to the trafficking of many species throughout the world as ornamentals. Despite the evolution and physiological properties of these plants having been extensively studied, little research has focused on cactus-associated viral communities. While only single-stranded RNA viruses had ever been reported in cacti, here we report the discovery of cactus-infecting single-stranded DNA viruses. These viruses all apparently belong to a single divergent species of the family Geminiviridae and have been tentatively named Opuntia virus 1 (OpV1). A total of 79 apparently complete OpV1 genomes were recovered from 31 different cactus plants (belonging to 20 different cactus species from both the Cactoideae and Opuntioideae clades) and from nine cactus-feeding cochineal insects (Dactylopius sp.) sampled in the USA and Mexico. These 79 OpV1 genomes all share > 78.4% nucleotide identity with one another and < 64.9% identity with previously characterized geminiviruses. Collectively, the OpV1 genomes display evidence of frequent recombination, with some genomes displaying up to five recombinant regions. In one case, recombinant regions span ~40% of the genome. We demonstrate that an infectious clone of an OpV1 genome can replicate in Nicotiana benthamiana and Opuntia microdasys. In addition to expanding the inventory of viruses that are known to infect cacti, the OpV1 group is so distantly related to other known geminiviruses that it likely represents a new geminivirus genus. It remains to be determined whether, like its cactus hosts, its geographical distribution spans the globe.


Subject(s)
Cactaceae/virology , Geminiviridae/genetics , Genome, Viral , Phylogeny , Plant Diseases/virology , Animals , Geminiviridae/classification , Geminiviridae/isolation & purification , Hemiptera/virology , Mexico , Recombination, Genetic , Nicotiana/virology , United States
7.
Plant Sci ; 292: 110410, 2020 Mar.
Article in English | MEDLINE | ID: mdl-32005374

ABSTRACT

The Geminiviridae family is one of the most successful and largest families of plant viruses that infect a large variety of important dicotyledonous and monocotyledonous crops and cause significant yield losses worldwide. This broad spectrum of host range is only possible because geminiviruses have evolved sophisticated strategies to overcome the arsenal of antiviral defenses in such diverse plant species. In addition, geminiviruses evolve rapidly through recombination and pseudo-recombination to naturally create a great diversity of virus species with divergent genome sequences giving the virus an advantage over the host recognition system. Therefore, it is not surprising that efficient molecular strategies to combat geminivirus infection under open field conditions have not been fully addressed. In this review, we present the anti-geminiviral arsenal of plant defenses, the evolved virulence strategies of geminiviruses to overcome these plant defenses and the most recent strategies that have been engineered for transgenic resistance. Although, the in vitro reactivation of suppressed natural defenses as well as the use of RNAi and CRISPR/Cas systems hold the potential for achieving broad-range resistance and/or immunity, potential drawbacks have been associated with each case.


Subject(s)
CRISPR-Cas Systems , Geminiviridae/physiology , Host-Pathogen Interactions , Plant Diseases/immunology , Plant Immunity/genetics , RNA Interference , Crops, Agricultural/genetics , Crops, Agricultural/immunology , Disease Resistance/genetics , Genetic Engineering , Plant Diseases/genetics , Plants, Genetically Modified/genetics , Plants, Genetically Modified/immunology
8.
Arch Virol ; 164(5): 1453-1457, 2019 May.
Article in English | MEDLINE | ID: mdl-30895404

ABSTRACT

Grapevine red blotch virus (GRBV) is an emerging virus of significant viticultural importance throughout North America. Here, we report the development of a simple protocol for point-of-use detection of GRBV. Extraction of nucleic acids is not required; instead, the whole intact plant can simply be pricked with a sterile pipette tip, which is then incubated in sterile distilled water to provide the sample template in a loop-mediated isothermal amplification (LAMP) reaction. This method is 10,000 times more sensitive than conventional PCR, costs under a dollar per sample, and can be completed from sampling to readout in just over half an hour.


Subject(s)
DNA, Viral/analysis , Geminiviridae/isolation & purification , Nucleic Acid Amplification Techniques , Plant Diseases/virology , Vitis/virology , Farms , Geminiviridae/classification , Geminiviridae/genetics , Plant Leaves/virology , Polymerase Chain Reaction , Sensitivity and Specificity
9.
Viruses ; 10(4)2018 04 02.
Article in English | MEDLINE | ID: mdl-29614801

ABSTRACT

Brazil is one of the major passion fruit producers worldwide. Viral diseases are among the most important constraints for passion fruit production. Here we identify and characterize a new passion fruit infecting-virus belonging to the family Geminiviridae: passion fruit chlorotic mottle virus (PCMoV). PCMoV is a divergent geminivirus unlike previously characterized passion fruit-infecting geminiviruses that belonged to the genus Begomovirus. Among the presently known geminiviruses, it is most closely related to, and shares ~62% genome-wide identity with citrus chlorotic dwarf associated virus (CCDaV) and camelia chlorotic dwarf associated virus (CaCDaV). The 3743 nt PCMoV genome encodes a capsid protein (CP) and replication-associated protein (Rep) that respectively share 56 and 60% amino acid identity with those encoded by CaCDaV. The CPs of PCMoV, CCDaV, and CaCDaV cluster with those of begomovirus whereas their Reps with those of becurtoviruses. Hence, these viruses likely represent a lineage of recombinant begomo-like and becurto-like ancestral viruses. Furthermore, PCMoV, CCDaV, and CaCDaV genomes are ~12-30% larger than monopartite geminiviruses and this is primarily due to the encoded movement protein (MP; 891-921 nt) and this MP is most closely related to that encoded by the DNA-B component of bipartite begomoviruses. Hence, PCMoV, CCDaV, and CaCDaV lineage of viruses may represent molecules in an intermediary step in the evolution of bipartite begomoviruses (~5.3 kb) from monopartite geminiviruses (~2.7-3 kb). An infectious clone of PCMoV systemically infected Nicotiana benthamina, Arabidopsis thaliana, and Passiflora edulis.


Subject(s)
Begomovirus/classification , Begomovirus/genetics , Passiflora/virology , Brazil , Computational Biology/methods , Geminiviridae/classification , Geminiviridae/genetics , Genome, Viral , High-Throughput Nucleotide Sequencing , Open Reading Frames , Phylogeny , Plant Diseases/virology , Sequence Analysis, DNA
10.
Food Res Int ; 106: 870-877, 2018 04.
Article in English | MEDLINE | ID: mdl-29579998

ABSTRACT

Beet mild curly top virus (BMCTV) is associated with an outbreak of curly top in chili pepper, tomato and other Solanaceae species, which can cause severe crop losses. The aim of this work was to obtain the 1H NMR metabolomic profiling of both healthy chili peppers (cv. mirasol) and infected chili peppers with BMCTV in order to find chemical markers associated to the infection process. Significant differences were found between the two groups, according to principal component analysis and orthogonal projections to latent structure discriminant analysis. Compared to the asymptomatic peppers, the symptomatic fruits had higher relative abundance of fructose, isoleucine, histidine, phenylalanine and tryptophan. Contrarily, the asymptomatic samples showed greater amounts of malonate and isobutyrate. These results suggest that in diseased chili peppers there are metabolic changes related to the viral acquisition of energy for replication and capsid assembly. This is the first study describing the chemical profiling of a polar extract obtained from Capsicum annuum infected by BMCTV under open field conditions.


Subject(s)
Capsicum/virology , Geminiviridae/isolation & purification , Magnetic Resonance Spectroscopy , Metabolomics , Capsicum/chemistry , Food Contamination , Food Microbiology , Fruit/chemistry , Fruit/virology , Geminiviridae/metabolism , Plant Diseases/virology , Principal Component Analysis
11.
Arch Virol ; 163(3): 799-803, 2018 Mar.
Article in English | MEDLINE | ID: mdl-29209812

ABSTRACT

We investigated the molecular characteristics of an Argentinean isolate of alfalfa leaf curl virus (ALCV-Arg), a virus of the genus Capulavirus in the family Geminiviridae that was isolated from alfalfa plants showing dwarfism. The genome was found to be 2,750 nucleotides in length. In pairwise comparisons, this ALCV isolate shared 83.2% to 92.6% sequence identity with European ALCV isolates. Sequence comparisons and phylogenetic analysis showed that this isolate combines features of strains A and B of ALCV. Recombination analysis showed that ALCV-Arg is a recombinant isolate that was generated by intraspecific recombination between ALCV strains A and B. The results of this study not only show that ALCV-Arg is unique because it combines features of strains A and B but also show that ALCV naturally infects this forage crop on the American continent.


Subject(s)
DNA, Viral/genetics , Geminiviridae/genetics , Genome, Viral , Medicago sativa/virology , Phylogeny , Plant Leaves/virology , Argentina , Base Sequence , Geminiviridae/classification , Geminiviridae/isolation & purification , High-Throughput Nucleotide Sequencing , Plant Diseases/virology , Recombination, Genetic , Sequence Analysis, DNA , Sequence Homology, Nucleic Acid
12.
Arch Virol ; 163(1): 263-267, 2018 Jan.
Article in English | MEDLINE | ID: mdl-28956174

ABSTRACT

The genus Mastrevirus (family Geminiviridae) is composed of single-stranded DNA viruses that infect mono- and dicotyledonous plants and are transmitted by leafhoppers. In South America, there have been only two previous reports of mastreviruses, both identified in sweet potatoes (from Peru and Uruguay). As part of a general viral surveillance program, we used a vector-enabled metagenomics (VEM) approach and sampled leafhoppers (Dalbulus maidis) in Itumbiara (State of Goiás), Brazil. High-throughput sequencing of viral DNA purified from the leafhopper sample revealed mastrevirus-like contigs. Using a set of abutting primers, a 2746-nt circular genome was recovered. The circular genome has a typical mastrevirus genome organization and shares <63% pairwise identity with other mastrevirus isolates from around the world. Therefore, the new mastrevirus was tentatively named "maize striate mosaic virus". Seventeen maize leaf samples were collected in the same field as the leafhoppers, and ten samples were found to be positive for this mastrevirus. Furthermore, the ten genomes recovered from the maize samples share >99% pairwise identity with the one from the leafhopper. This is the first report of a maize-infecting mastrevirus in the Americas, the first identified in a non-vegetatively propagated mastrevirus host in South America, and the first mastrevirus to be identified in Brazil.


Subject(s)
Geminiviridae/genetics , Metagenomics/methods , Zea mays/virology , Americas , Genome, Viral , Phylogeny
13.
Plant Dis ; 102(1): 146-153, 2018 Jan.
Article in English | MEDLINE | ID: mdl-30673459

ABSTRACT

In fall 2014, 5 to 75% percent of chili and bell pepper (Capsicum annuum L.) in commercial fields located in the Mexican states of Durango, Zacatecas, and Michoacán had symptoms of deformed, small, mosaic, curled, and chlorotic leaves; shortened internodes; plant dwarfing; or phyllody and rosetting leaf tips. At the same time, leafhoppers and psyllids were observed in the fields, and more than 50 beet leafhoppers (Circulifer tenellus) and nearly 300 potato psyllids (Bactericera cockerelli) were collected from the pepper plants and adjacent weeds. Based on the insect pressure and observed symptoms, nearly 400 pepper samples were collected across this region of Mexico and tested for the presence of leafhopper- and psyllid-associated pathogens. In all, 76% of the pepper samples were found to be infected with 'Candidatus Liberibacter solanacearum', beet leafhopper-transmitted virescence agent (BLTVA) phytoplasma, a strain of a curtovirus, or a combination of any two or three of these pathogens. Additionally, 77% of the collected leafhoppers and 40% of the psyllids were infected with one or more of these pathogens, in addition to Spiroplasma citri. Specifically, the leafhoppers were infected with BLTVA phytoplasma, S. citri, or a strain of curtovirus. Of particular interest, potato psyllids were not only infected with 'Ca. L. solanacearum' but also with phytoplasmas that belong to the groups 16SrVI subgroup A and 16SrI subgroup A. The presence of mixed infections in pepper plants and the insect vectors highlights the need for growers to effectively control both leafhoppers and potato psyllids from solanaceous crops in this region of Mexico in order to prevent the spread of these bacterial and viral pathogens.


Subject(s)
Capsicum/microbiology , Geminiviridae/isolation & purification , Hemiptera/microbiology , Phytoplasma/isolation & purification , Plant Diseases/microbiology , Rhizobiaceae/isolation & purification , Animals , Hemiptera/virology , Insect Vectors/microbiology , Insect Vectors/virology , Mexico , Plant Diseases/virology
14.
BMC Bioinformatics ; 18(1): 431, 2017 Sep 30.
Article in English | MEDLINE | ID: mdl-28964254

ABSTRACT

BACKGROUND: Geminiviruses infect a broad range of cultivated and non-cultivated plants, causing significant economic losses worldwide. The studies of the diversity of species, taxonomy, mechanisms of evolution, geographic distribution, and mechanisms of interaction of these pathogens with the host have greatly increased in recent years. Furthermore, the use of rolling circle amplification (RCA) and advanced metagenomics approaches have enabled the elucidation of viromes and the identification of many viral agents in a large number of plant species. As a result, determining the nomenclature and taxonomically classifying geminiviruses turned into complex tasks. In addition, the gene responsible for viral replication (particularly, the viruses belonging to the genus Mastrevirus) may be spliced due to the use of the transcriptional/splicing machinery in the host cells. However, the current tools have limitations concerning the identification of introns. RESULTS: This study proposes a new method, designated Fangorn Forest (F2), based on machine learning approaches to classify genera using an ab initio approach, i.e., using only the genomic sequence, as well as to predict and classify genes in the family Geminiviridae. In this investigation, nine genera of the family Geminiviridae and their related satellite DNAs were selected. We obtained two training sets, one for genus classification, containing attributes extracted from the complete genome of geminiviruses, while the other was made up to classify geminivirus genes, containing attributes extracted from ORFs taken from the complete genomes cited above. Three ML algorithms were applied on those datasets to build the predictive models: support vector machines, using the sequential minimal optimization training approach, random forest (RF), and multilayer perceptron. RF demonstrated a very high predictive power, achieving 0.966, 0.964, and 0.995 of precision, recall, and area under the curve (AUC), respectively, for genus classification. For gene classification, RF could reach 0.983, 0.983, and 0.998 of precision, recall, and AUC, respectively. CONCLUSIONS: Therefore, Fangorn Forest is proven to be an efficient method for classifying genera of the family Geminiviridae with high precision and effective gene prediction and classification. The method is freely accessible at www.geminivirus.org:8080/geminivirusdw/discoveryGeminivirus.jsp .


Subject(s)
Geminiviridae/genetics , Machine Learning , Area Under Curve , DNA, Satellite/classification , DNA, Satellite/genetics , Geminiviridae/classification , Internet , Open Reading Frames/genetics , Plants/virology , ROC Curve , User-Computer Interface
15.
Virus Res ; 240: 175-179, 2017 08 15.
Article in English | MEDLINE | ID: mdl-28843502

ABSTRACT

Viruses in the family Geminiviridae have single-stranded DNA genomes encapsulated in geminate icosahedral particles. High throughput sequencing (HTS) for metagenomic approaches are being extensively used for the identification of known and novel viruses. Using a HTS approach, we identified a novel geminivirus in a tomato (Solanum lycopersicum) sample and a Cleome sp. sample collected in the midwest region of Brazil. The genomes from the two samples share 99.96% identity and ∼61-63% to genomes in the genus Capulavirus. The novel virus has been tentatively named tomato associated geminivirus 1 (TaGV1). No visual symptoms were observed in the field tomato plant or in the inoculated Nicotiana benthamiana where the virus established a systemic infection. The replication associated protein of TaGV1 is most similar to that encoded by capulaviruses (sharing 62-70% identity), whereas the CP is most similar to that of tomato pseudo curly top virus (sharing ∼31% identity). In the TaGV1 positive Cleome sp. sample, begomovirus DNA A and B components were also detected sharing 96% and 90% sequence identity to cleome leaf crumple virus DNA A and B components, respectively. Using a HTS approach, we identified TaGV1 in tomato and Cleome sp. samples and this is the first report of a geminivirus that is non-begomovirus in Brazil.


Subject(s)
Cleome/virology , Geminiviridae/isolation & purification , Plant Diseases/virology , Solanum lycopersicum/virology , Brazil , Geminiviridae/classification , Geminiviridae/genetics , Phylogeny , Plant Leaves/virology , Sequence Analysis, DNA
16.
Virol J ; 14(1): 146, 2017 07 28.
Article in English | MEDLINE | ID: mdl-28754134

ABSTRACT

BACKGROUND: In Africa and Asia, sugarcane is the host of at least seven different virus species in the genus Mastrevirus of the family Geminiviridae. However, with the exception of Sugarcane white streak virus in Barbados, no other sugarcane-infecting mastrevirus has been reported in the New World. Conservation and exchange of sugarcane germplasm using stalk cuttings facilitates the spread of sugarcane-infecting viruses. METHODS: A virion-associated nucleic acids (VANA)-based metagenomics approach was used to detect mastrevirus sequences in 717 sugarcane samples from Florida (USA), Guadeloupe (French West Indies), and Réunion (Mascarene Islands). Contig assembly was performed using CAP3 and sequence searches using BLASTn and BLASTx. Mastrevirus full genomes were enriched from total DNA by rolling circle amplification, cloned and sequenced. Nucleotide and amino acid sequence identities were determined using SDT v1.2. Phylogenetic analyses were conducted using MEGA6 and PHYML3. RESULTS: We identified a new sugarcane-infecting mastrevirus in six plants sampled from germplasm collections in Florida and Guadeloupe. Full genome sequences were determined and analyzed for three virus isolates from Florida, and three from Guadeloupe. These six genomes share >88% genome-wide pairwise identity with one another and between 89 and 97% identity with a recently identified mastrevirus (KR150789) from a sugarcane plant sampled in China. Sequences similar to these were also identified in sugarcane plants in Réunion. CONCLUSIONS: As these virus isolates share <64% genome-wide identity with all other known mastreviruses, we propose classifying them within a new mastrevirus species named Sugarcane striate virus. This is the first report of sugarcane striate virus (SCStV) in the Western Hemisphere, a virus that most likely originated in Asia. The distribution, vector, and impact of SCStV on sugarcane production remains to be determined.


Subject(s)
Geminiviridae/classification , Geminiviridae/isolation & purification , Saccharum/virology , Cloning, Molecular , Cluster Analysis , DNA, Viral/chemistry , DNA, Viral/genetics , DNA, Viral/isolation & purification , Florida , Guadeloupe , Phylogeny , Reunion , Sequence Analysis, DNA , Sequence Homology , Whole Genome Sequencing
17.
BMC Bioinformatics ; 18(1): 240, 2017 May 05.
Article in English | MEDLINE | ID: mdl-28476106

ABSTRACT

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.


Subject(s)
Computational Biology/methods , Databases, Genetic , Geminiviridae/genetics , Machine Learning , Algorithms , DNA, Single-Stranded/genetics , DNA, Viral/genetics , Open Reading Frames/genetics , Phylogeny , Plants/virology
18.
J Gen Virol ; 98(2): 131-133, 2017 02.
Article in English | MEDLINE | ID: mdl-28284245

ABSTRACT

The geminiviruses are a family of small, non-enveloped viruses with single-stranded, circular DNA genomes of 2500-5200 bases. Geminiviruses are transmitted by various types of insect (whiteflies, leafhoppers, treehoppers and aphids). Members of the genus Begomovirus are transmitted by whiteflies, those in the genera Becurtovirus, Curtovirus, Grablovirus, Mastrevirus and Turncurtovirus are transmitted by specific leafhoppers, the single member of the genus Topocuvirus is transmitted by a treehopper and one member of the genus Capulavirus is transmitted by an aphid. Geminiviruses are plant pathogens causing economically important diseases in most tropical and subtropical regions of the world. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Geminiviridae which is available at www.ictv.global/report/geminiviridae.


Subject(s)
Geminiviridae/classification , Plant Diseases/virology , Animals , Cryoelectron Microscopy , DNA, Single-Stranded/chemistry , DNA, Single-Stranded/genetics , DNA, Viral/chemistry , DNA, Viral/genetics , Geminiviridae/genetics , Geminiviridae/physiology , Geminiviridae/ultrastructure , Gene Order , Genome, Viral , Insecta/virology , Virion/chemistry , Virion/genetics , Virion/ultrastructure , Virus Replication , Zea mays/virology
19.
Biosci. j. (Online) ; 32(1): 73-80, jan./fev. 2016. ilus, tab
Article in English | LILACS | ID: biblio-965242

ABSTRACT

The common bean (Phaseolus vulgaris L.) is a herbal annual plant, which belongs to Fabaceae family, it is grown by small and large farmers alike, in several production systems. It has much economic and social importance. However, the plant is a host to uncounTable fungal, bacterial and viral diseases. Among the viral pathologies there is one known as Bean golden mosaic virus (BGMV), currently spread to virtually every bean production region in Brazil and over the world, causing huge losses season after season. This research's aim was to evaluate the resistance degree presented by fifteen different bean genotypes as to symptomology shown due to infection by the virus on the plants. The experimental design was randomized blocks, with 15 treatments and a witness, Carioca-Pérola cultivar, and compound by four repetitions. Each parcel was compound by four lines of 3,0 meters in length and 0,5m apart, accounting for a total of 60 parcels of 6,0m². The analyzed characteristics were: Emergency, incidence, severity, thousand-bean weight, productivity, and chlorophyll content in the leaves. For characteristic incidence, at both 28 and 38 DAS, the genotypes did not prove to be resistant to the disease. For severity the strains PL 38, from the breeding between IAPAR 57 and IAPAR 72, and 93, from the breeding between ESAL-589 e IAPAR 57, stood out with superior results. For a thousand-bean weight, the genotype UFU Roxo 12, IAPAR 57 X ESAL 589 - PL 48, followed for ESAL 589 X IAPAR 57 - PL 148-1, UFU Preto 29, ESAL 589 X IAPAR 57 - PL 93, IAPAR 57 X IAPAR 72 - PL 25, IAPAR 57 X IAPAR 65 - PL194, CARIOCA PÉROLA-WITNESS, UFU Carioca 14 and ESAL 589 X IAPAR 72 - PL 129 was the one that showed the best result. The highest productivity per hectare was from the genotype IAPAR57 x ESAL 589 ­ PL48 from carioca group. Concerning the parameter chlorophyll content at 28 DAS, the genotypes ESAL 589 X IAPAR 57 - PL 93, ESAL 589 X IAPAR 72 - PL 129, IAPAR 72 X ESAL 589 ­PL49, UFU Roxo 12, ESAL 589 X IAPAR 57 - PL 28, CARIOCA PÉROLA-Witness, UFU Carioca 14 showed less infected area and the highest chlorophyll content, and at 38 DAS there was no significant difference among the genotypes.


O feijão comum (Phaseolus vulgaris L.) é uma planta anual que pertence à família Fabaceae, é cultivado por pequenos e grandes agricultores em diversos sistemas de produção no Brasil. Ele tem muita importância econômica e social. No entanto, a planta é um hospedeiro para muitas doenças fúngicas, bacterianas e virais. Entre as patologias virais tem-se vírus do mosaico dourado do feijoeiro (VMDF-BGMV), que atualmente se encontra em todas as regiões de produção de feijoeiro no Brasil e no mundo. A doença causa enormes prejuízos em todas estações de cultivo, notadamente no outono- inverno. Objetivo deste trabalho foi avaliar o grau de resistência apresentado por quinze diferentes genótipos de feijoeiro quanto à infecção (incidência be severidade) pelo vírus nas plantas. O delineamento experimental foi em blocos casualizados, com 15 tratamentos e uma testemunha, cultivar Carioca-Pérola, e composto por quatro repetições. Cada parcela foi composto por quatro linhas de 3,0 metros de comprimento e 0,5m de distância, correspondendo a um total de 60 parcelas de 6,0m². As características analisadas foram: emergência, incidência, severida de sintomas, peso de mil de mil grãos, produtividade e teor de clorofila nas folhas (índice SPAD). A incidência não se mostrou como variável inadequada para avaliar a resistência aos 28 e 38 dias após a semeadura (DAS). Para severidade a linhagem PL 38 se destacou e foi obtida apartir do cruzamento IAPAR 57 e IAPAR 72. Também apresentou menor severidade a linhagem 93, obtida do cruzamento entre ESAL-589 e IAPAR 57. Para peso de mil grãos, destacaram-se os genótipos UFU Roxo 12 (IAPAR 57 X ESAL 589 - PL 48), seguido por ESAL 589 X IAPAR 57 - PL 148-1, UFU Preto 29 (ESAL 589 X IAPAR 57 - PL 93), IAPAR 57 X IAPAR 72 - PL 25, IAPAR 57 X IAPAR 65 - PL194, CARIOCA PÉROLA-testemunha, UFU Carioca 14 e ESAL 589 X IAPAR 72 - PL 129. A maior produtividade por hectare foi do genótipo IAPAR57 x ESAL 589 - PL48 do grupo carioca. Quanto ao índice SPAD (clorofila aos 28 DAS), os genótipos ESAL 589 X IAPAR 57 - PL 93, ESAL 589 X IAPAR 72 - PL 129, IAPAR 72 X ESAL 589 -PL49, UFU Roxo 12, ESAL 589 X IAPAR 57 - PL 28, CARIOCA PÉROLA, UFU Carioca 14 apresentaram maior teor de clorofila aos 38 DAS (maior média numérica), más não houve diferença significativa entre os genótipos pelo teste de Scott & Knott a 5 % de probabilidade.


Subject(s)
Geminiviridae , Fungi , Genotype , Fabaceae
20.
Viruses ; 7(12): 6141-51, 2015 Nov 25.
Article in English | MEDLINE | ID: mdl-26610554

ABSTRACT

Germin-like proteins (GLPs) are encoded by a family of genes found in all plants, and in terms of function, the GLPs are implicated in the response of plants to biotic and abiotic stresses. CchGLP is a gene encoding a GLP identified in a geminivirus-resistant Capsicum chinense Jacq accession named BG-3821, and it is important in geminivirus resistance when transferred to susceptible tobacco in transgenic experiments. To characterize the role of this GLP in geminivirus resistance in the original accession from which this gene was identified, this work aimed at demonstrating the possible role of CchGLP in resistance to geminiviruses in Capsicum chinense Jacq. BG-3821. Virus-induced gene silencing studies using a geminiviral vector based in PHYVV component A, displaying that silencing of CchGLP in accession BG-3821, increased susceptibility to geminivirus single and mixed infections. These results suggested that CchGLP is an important factor for geminivirus resistance in C. chinense BG-3821 accession.


Subject(s)
Capsicum/immunology , Capsicum/virology , Disease Resistance , Geminiviridae/growth & development , Geminiviridae/immunology , Plant Proteins/metabolism , Capsicum/genetics , Coinfection/immunology , Coinfection/virology , Gene Silencing , Plant Diseases/genetics , Plant Diseases/immunology , Plant Diseases/virology , Plant Proteins/genetics
SELECTION OF CITATIONS
SEARCH DETAIL