57 research outputs found
Basic Amino Acid Mutations in the Nuclear Localization Signal of Hibiscus Chlorotic Ringspot Virus p23 Inhibit Virus Long Distance Movement
10.1371/journal.pone.0074000PLoS ONE89-POLN
Deep Sequencing of Small RNAs in Tomato for Virus and Viroid Identification and Strain Differentiation
Small RNAs (sRNA), including microRNAs (miRNA) and small interfering RNAs (siRNA), are produced abundantly in plants and animals and function in regulating gene expression or in defense against virus or viroid infection. Analysis of siRNA profiles upon virus infection in plant may allow for virus identification, strain differentiation, and de novo assembly of virus genomes. In the present study, four suspected virus-infected tomato samples collected in the U.S. and Mexico were used for sRNA library construction and deep sequencing. Each library generated between 5–7 million sRNA reads, of which more than 90% were from the tomato genome. Upon in-silico subtraction of the tomato sRNAs, the remaining highly enriched, virus-like siRNA pools were assembled with or without reference virus or viroid genomes. A complete genome was assembled for Potato spindle tuber viroid (PSTVd) using siRNA alone. In addition, a near complete virus genome (98%) also was assembled for Pepino mosaic virus (PepMV). A common mixed infection of two strains of PepMV (EU and US1), which shared 82% of genome nucleotide sequence identity, also could be differentially assembled into their respective genomes. Using de novo assembly, a novel potyvirus with less than 60% overall genome nucleotide sequence identity to other known viruses was discovered and its full genome sequence obtained. Taken together, these data suggest that the sRNA deep sequencing technology will likely become an efficient and powerful generic tool for virus identification in plants and animals
Multilocus variable number of tandem repeat analysis reveals multiple introductions in Spain of Xanthomonas arboricola pv. Pruni, the causal agent of bacterial spot disease of stone fruits and almond
Xanthomonas arboricola pv. pruni is the causal agent of the bacterial spot disease of stone fruits, almond and some ornamental Prunus species. In Spain it was first detected in 2002 and since then, several outbreaks have occurred in different regions affecting mainly Japanese plum, peach and almond, both in commercial orchards and nurseries. As the origin of the introduction(s) was unknown, we have assessed the genetic diversity of 239 X. arboricola pv. pruni strains collected from 11 Spanish provinces from 2002 to 2013 and 25 reference strains from international collections. We have developed an optimized multilocus variable number of tandem repeat analysis (MLVA) scheme targeting 18 microsatellites and five minisatellites. A high discriminatory power was achieved since almost 50% of the Spanish strains were distinguishable, confirming the usefulness of this genotyping technique at small spatio-temporal scales. Spanish strains grouped in 18 genetic clusters (conservatively delineated so that each cluster contained haplotype networks linked by up to quadruple-locus variations). Furthermore, pairwise comparisons among populations from different provinces showed a strong genetic differentiation. Our results suggest multiple introductions of this pathogen in Spain and redistribution through contaminated nursery propagative plant material
Population Structure of the Bacterial Pathogen Xylella fastidiosa among Street Trees in Washington D.C.
Funding for Open Access provided by the UMD Libraries Open Access Publishing Fund.Bacterial leaf scorch, associated with the bacterial pathogen Xylella fastidiosa, is a widely
established and problematic disease of landscape ornamentals in Washington D.C. A multilocus
sequence typing analysis was performed using 10 housekeeping loci for X. fastidiosa
strains in order to better understand the epidemiology of leaf scorch disease in this municipal
environment. Samples were collected from 7 different tree species located throughout
the District of Columbia, consisting of 101 samples of symptomatic and asymptomatic foliage
from 84 different trees. Five strains of the bacteria were identified. Consistent with
prior data, these strains were host specific, with only one strain associated with members of
the red oak family, one strain associated with American elm, one strain associated with
American sycamore, and two strains associated with mulberry. Strains found for asymptomatic
foliage were the same as strains from the symptomatic foliage on individual trees.
Cross transmission of the strains was not observed at sites with multiple species of infected
trees within an approx. 25 m radius of one another. X. fastidiosa strain specificity observed
for each genus of tree suggests a highly specialized host-pathogen relationship
Caratterizzazione molecolare della regione genomica del gene Vf di resistenza a ticchiolatura del melo
Dottorato di ricerca in biotecnologie molecolari e cellulari. 11. ciclo. Coordinatore Lanfranco Masotti. Tutore Andrea Masia. Cotutore Silviero SansaviniConsiglio Nazionale delle Ricerche - Biblioteca Centrale - P.le Aldo Moro, 7, Rome; Biblioteca Nazionale Centrale - Piazza Cavalleggeri, 1, Florence / CNR - Consiglio Nazionale delle RichercheSIGLEITItal
The Ability of PVX p25 to Form RL Structures in Plant Cells Is Necessary for Its Function in Movement, but Not for Its Suppression of RNA Silencing
Theoretical Prediction and Experimental Verification of Protein-Coding Genes in Plant Pathogen Genome Agrobacterium tumefaciens Strain C58
Validation of Reference Genes for Gene Expression Studies in Virus-Infected Nicotiana benthamiana Using Quantitative Real-Time PCR
Genetic and Physical Mapping of Candidate Genes for Resistance to Fusarium oxysporum f.sp. tracheiphilum Race 3 in Cowpea [Vigna unguiculata (L.) Walp]
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