Insect-to-insect horizontal transmission of a phytoreovirus in the absence of an infected plant host.

Vertical transmission of Homalodisca vitripennis reovirus (HoVRV) from glassy-winged sharpshooter (GWSS, Homalodisca vitripennis (Germar)) females to progeny occurred in laboratory assays at frequencies too low (2.6%-15.4%) to account for HoVRV incidence (90-100%) in field populations resident in citrus. Because citrus is immune to HoVRV and no plant host is known, horizontal transmission of HoVRV from insect-to-insect was evaluated. Exposure of colony-reared, virus-free test nymphs to HoVRV-infected source adults held in the same cage for 10 days on virus-immune cowpea resulted in HoVRV transmission (13.3%-30.7%) to test nymphs. HoVRV was not transmitted when exposure was indirect and required passive movement of virions through the xylem of immune citrus seedlings. Collectively, these results demonstrate direct insect-to-insect horizontal transmission of HoVRV, providing a plausible explanation for high incidence of HoVRV in GWSS field populations in the absence of efficient vertical transmission or a plant host.

Xylella fastidiosa and Glassy-Winged Sharpshooter Population Dynamics in the Southern San Joaquin Valley of California.

Xylella fastidiosa is a vector-transmitted bacterial plant pathogen that affects a wide array of perennial crops, including grapevines (Pierce's disease). In the southern San Joaquin Valley of California, epidemics of Pierce's disease of grapevine were associated with the glassy-winged sharpshooter, Homalodisca vitripennis. During the growing season, rates of X. fastidiosa spread in vineyards are affected by changes in pathogen distribution within chronically infected grapevines and by vector population dynamics. Grapevines chronically infected with X. fastidiosa rarely tested positive for the pathogen prior to July, suggesting vector acquisition of X. fastidiosa from grapevines increases as the season progresses. This hypothesis was supported by an increase in number of X. fastidiosa-positive glassy-winged sharpshooters collected from vineyards during July through September. Analysis of insecticide records indicated that vineyards in the study area were typically treated with a systemic neonicotinoid in spring of each year. As a result, abundance of glassy-winged sharpshooters was typically low in late spring and early summer, with abundance of glassy-winged sharpshooter adults increasing in late June and early July of each year. Collectively, the results suggest that late summer is a crucial time for X. fastidiosa secondary spread in vineyards in the southern San Joaquin Valley, because glassy-winged sharpshooter abundance, number of glassy-winged sharpshooters testing positive for X. fastidiosa, and grapevines with detectable pathogen populations were all greatest during this period.

Complete Genome Sequence Data of Three Xylella fastidiosa subsp. multiplex Strains Isolated from Olive Trees in California, U.S.A.

Xylella fastidiosa is a xylem-limited bacterial plant pathogen that causes disease on numerous hosts. Additionally, X. fastidiosa asymptomatically colonizes a wide range of plant species. X. fastidiosa subsp. multiplex has been detected in olive (Olea europaea) trees grown in California, U.S.A., as well as in Europe. Strains of X. fastidiosa subsp. multiplex isolated from California olive trees are not known to cause disease on olive, although some can induce leaf-scorch symptoms on almond (Prunus dulcis). No genome assemblies currently exist for olive-associated X. fastidiosa subsp. multiplex strains; therefore, a hybrid assembly method was used to generate complete genome sequences for three X. fastidiosa subsp. multiplex strains (Fillmore, LM10, and RH1) isolated from olive trees grown in Ventura and Los Angeles counties of California.

Lost and found: Rediscovery and genomic characterization of sowthistle yellow vein virus after a 30+ year hiatus.

Beginning in the 1960's, sowthistle yellow vein virus (SYVV) was the subject of pioneering research that demonstrated propagation of a plant virus in its insect vector. Since the 1980's there has been a paucity of research on SYVV, with historic isolates no longer maintained and no genomic sequence available. Once commonly observed infecting sowthistle (Sonchus oleraceous L.) in California, SYVV incidence declined ca. 1990, likely due to displacement of the black currant aphid (Hyperomyzus lactucae L.) by an invasive non-vector aphid. In 2018, SYVV was fortuitously rediscovered infecting sowthistle in an organic citrus grove in Kern County, CA. The SYVV genome sequence (13,719 nts) obtained from the 2018 sample (designated HWY65) encoded all six expected genes: N, P, MP, M, G, and L. Nucleotide sequence (representing ∼86 % of the genome) of the SYVV Berkeley lab isolate, used by E. S. Sylvester and colleagues for the paradigm-shifting research mentioned above, was determined from an archived library of cDNA clones constructed in 1986. The two nucleotide sequences share 98.5 % identity, confirming both represent the same virus, thereby linking biology of the historic isolate with extant SYVV rediscovered in 2018. Phylogenetic analysis of the L protein indicated SYVV is positioned within a clade containing a subset of viruses currently assigned to the genus Nucleorhabdovirus. As Nucleorhabdovirus is paraphyletic, the International Committee on the Taxonomy of Viruses has proposed abolishment of the genus and establishment of three new genera. In this revised taxonomy, the clade containing SYVV constitutes a new genus designated Betanucleorhabdovirus.

Patterns of inter- and intrasubspecific homologous recombination inform eco-evolutionary dynamics of Xylella fastidiosa.

High rates of homologous recombination (HR) in the bacterial plant pathogen Xylella fastidiosa have been previously detected. This study aimed to determine the extent and explore the ecological significance of HR in the genomes of recombinants experimentally generated by natural transformation and wild-type isolates. Both sets of strains displayed widespread HR and similar average size of recombined fragments consisting of random events (2-10 kb) of inter- and intrasubspecific recombination. A significantly higher proportion and greater lengths (>10 kb, maximum 31.5 kb) of recombined fragments were observed in subsp. morus and in strains isolated in Europe from intercepted coffee plants shipped from the Americas. Such highly recombinant strains pose a serious risk of emergence of novel variants, as genetically distinct and formerly geographically isolated genotypes are brought in close proximity by global trade. Recently recombined regions in wild-type strains included genes involved in regulation and signaling, host colonization, nutrient acquisition, and host evasion, all fundamental traits for X. fastidiosa ecology. Identification of four recombinant loci shared between wild-type and experimentally generated recombinants suggests potential hotspots of recombination in this naturally competent pathogen. These findings provide insights into evolutionary forces possibly affecting the adaptive potential to colonize the host environments of X. fastidiosa.

Genomic Diversity and Recombination among Xylella fastidiosa Subspecies.

Xylella fastidiosa is an economically important bacterial plant pathogen. With insights gained from 72 genomes, this study investigated differences among the three main subspecies, which have allopatric origins: X. fastidiosa subsp. fastidiosa, multiplex, and pauca The origin of recombinogenic X. fastidiosa subsp. morus and sandyi was also assessed. The evolutionary rate of the 622 genes of the species core genome was estimated at the scale of an X. fastidiosa subsp. pauca subclade (7.62 × 10-7 substitutions per site per year), which was subsequently used to estimate divergence time for the subspecies and introduction events. The study characterized genes present in the accessory genome of each of the three subspecies and investigated the core genome to detect genes potentially under positive selection. Recombination is recognized to be the major driver of diversity in X. fastidiosa, potentially facilitating shifts to novel plant hosts. The relative effect of recombination in comparison to point mutation was calculated (r/m = 2.259). Evidence of recombination was uncovered in the core genome alignment; X. fastidiosa subsp. fastidiosa in the United States was less prone to recombination, with an average of 3.22 of the 622 core genes identified as recombining regions, whereas a specific clade of X. fastidiosa subsp. multiplex was found to have on average 9.60 recombining genes, 93.2% of which originated from X. fastidiosa subsp. fastidiosa Interestingly, for X. fastidiosa subsp. morus, which was initially thought to be the outcome of genome-wide recombination between X. fastidiosa subsp. fastidiosa and X. fastidiosa subsp. multiplex, intersubspecies homologous recombination levels reached 15.30% in the core genome. Finally, there is evidence of X. fastidiosa subsp. pauca strains from citrus containing genetic elements acquired from strains infecting coffee plants as well as genetic elements from both X. fastidiosa subsp. fastidiosa and X. fastidiosa subsp. multiplex In summary, our data provide new insights into the evolution and epidemiology of this plant pathogen.IMPORTANCEXylella fastidiosa is an important vector-borne plant pathogen. We used a set of 72 genomes that constitutes the largest assembled data set for this bacterial species so far to investigate genetic relationships and the impact of recombination on phylogenetic clades and to compare genome content at the subspecies level, and we used a molecular dating approach to infer the evolutionary rate of X. fastidiosa The results demonstrate that recombination is important in shaping the genomes of X. fastidiosa and that each of the main subspecies is under different selective pressures. We hope insights from this study will improve our understanding of X. fastidiosa evolution and biology.

Effects of Nymphal Diet and Adult Feeding on Allocation of Resources to Glassy-Winged Sharpshooter Egg Production.

The glassy-winged sharpshooter is an invasive insect capable of transmitting the bacterial pathogen Xylella fastidiosa. Pre-oviposition periods of laboratory-reared glassy-winged sharpshooters are variable. Here, two questions were addressed: does nymphal diet affect pre-oviposition period and how do allocation patterns of resources differ for females that produce eggs versus females that do not? Nymphs were reared on one of three host plant species: cowpea, sunflower, or sorghum. Half of the females were sacrificed at emergence. The remaining adult females were held on cowpea, a host plant species known to support egg maturation via adult feeding. Females were sacrificed on the day of first oviposition or after 9 wk if no eggs were deposited. Females reared as nymphs on sorghum had longer development times and were smaller (head capsule width and hind tibia length) than females reared as nymphs on cowpea and sunflower. However, nymphal diet did not affect percentage of dry weight that was lipid at emergence. Further, nymphal diet did not affect time to deposition of the first egg mass or total number of eggs matured at the time of first oviposition. Egg production reduced the allocation of resources to insect bodies, with body lipid content decreasing with increasing egg production. In general, females increased wet weight 1.4-fold during the first week after adult emergence, with wet weights plateauing over the remaining 9 wk that adults were monitored. Thus, it seems reasonable to hypothesize that resources required for egg production were acquired via adult feeding during the first week after adult emergence.

Effects of Energy Reserves and Diet on Glassy-Winged Sharpshooter Egg Maturation.

The glassy-winged sharpshooter is an invasive insect capable of transmitting the plant pathogen Xylella fastidiosa. As rates of pathogen spread are a function of vector abundance, identification of factors contributing to glassy-winged sharpshooter egg production will aid in predicting population growth. Here, effects of stored energy reserves and adult diet on glassy-winged sharpshooter egg maturation were evaluated. To estimate energy reserves available to adult females at the beginning of feeding assays, residuals from a regression of wet weight on size were used. Analysis of a subset of females sacrificed at the beginning of feeding assays, demonstrated that females with a positive residual wet weight had higher lipid content and carried more eggs than females with a negative residual wet weight. To evaluate effects of diet and energy reserves on egg maturation, energy reserves available to females entering feeding assays on cowpea and grapevine were estimated. For females held on cowpea, residual wet weight and quantity of excreta produced over a 6-d feeding period affected egg production. In contrast, for females held on grapevine, only residual wet weight affected egg production. Comparison of cowpea and grapevine xylem sap determined that eight amino acids were more concentrated in xylem sap from cowpea than from grapevine. Collectively, the results suggest that glassy-winged sharpshooter population growth within crop monocultures will not depend solely on the nutritional quality of the specific crop for producing mature eggs but also on the quantity of energy reserves accumulated by females prior to entering that crop habitat.

Effects of Xylem-Sap Composition on Glassy-Winged Sharpshooter (Hemiptera: Cicadellidae) Egg Maturation on High- and Low-Quality Host Plants.

Glassy-winged sharpshooters must feed as adults to produce mature eggs. Cowpea and sunflower are both readily accepted by the glassy-winged sharpshooter for feeding, but egg production on sunflower was reported to be lower than egg production on cowpea. To better understand the role of adult diet in egg production, effects of xylem-sap chemistry on glassy-winged sharpshooter egg maturation was compared for females confined to cowpea and sunflower. Females confined to cowpea consumed more xylem-sap than females held on sunflower. In response, females held on cowpea produced more eggs, had heavier bodies, and greater lipid content than females held on sunflower. Analysis of cowpea and sunflower xylem-sap found that 17 of 19 amino acids were more concentrated in cowpea xylem-sap than in sunflower xylem-sap. Thus, decreased consumption of sunflower xylem-sap was likely owing to perceived lower quality, with decreased egg production owing to a combination of decreased feeding and lower return per unit volume of xylem-sap consumed. Examination of pairwise correlation coefficients among amino acids indicated that concentrations of several amino acids within a plant species were correlated. Principal component analyses identified latent variables describing amino acid composition of xylem-sap. For females held on cowpea, egg maturation was affected by test date, volume of excreta produced, and principal components describing amino acid composition of xylem-sap. Principal component analyses aided in identifying amino acids that were positively or negatively associated with egg production, although determining causality with respect to key nutritional requirements for glassy-winged sharpshooter egg production will require additional testing.

The DinJ/RelE Toxin-Antitoxin System Suppresses Bacterial Proliferation and Virulence of Xylella fastidiosa in Grapevine.

Xylella fastidiosa, the causal agent of Pierce's disease of grapes, is a slow-growing, xylem-limited, bacterial pathogen. Disease progression is characterized by systemic spread of the bacterium through xylem vessel networks, causing leaf-scorching symptoms, senescence, and vine decline. It appears to be advantageous to this pathogen to avoid excessive blockage of xylem vessels, because living bacterial cells are generally found in plant tissue with low bacterial cell density and minimal scorching symptoms. The DinJ/RelE toxin-antitoxin system is characterized here for a role in controlling bacterial proliferation and population size during plant colonization. The DinJ/RelE locus is transcribed from two separate promoters, allowing for coexpression of antitoxin DinJ with endoribonuclease toxin RelE, in addition to independent expression of RelE. The ratio of antitoxin/toxin expressed is dependent on bacterial growth conditions, with lower amounts of antitoxin present under conditions designed to mimic grapevine xylem sap. A knockout mutant of DinJ/RelE exhibits a hypervirulent phenotype, with higher bacterial populations and increased symptom development and plant decline. It is likely that DinJ/RelE acts to prevent excessive population growth, contributing to the ability of the pathogen to spread systemically without completely blocking the xylem vessels and increasing probability of acquisition by the insect vector.

Sequence polymorphism in an insect RNA virus field population: A snapshot from a single point in space and time reveals stochastic differences among and within individual hosts.

Population structure of Homalodisca coagulata Virus-1 (HoCV-1) among and within field-collected insects sampled from a single point in space and time was examined. Polymorphism in complete consensus sequences among single-insect isolates was dominated by synonymous substitutions. The mutant spectrum of the C2 helicase region within each single-insect isolate was unique and dominated by nonsynonymous singletons. Bootstrapping was used to correct the within-isolate nonsynonymous:synonymous arithmetic ratio (N:S) for RT-PCR error, yielding an N:S value ~one log-unit greater than that of consensus sequences. Probability of all possible single-base substitutions for the C2 region predicted N:S values within 95% confidence limits of the corrected within-isolate N:S when the only constraint imposed was viral polymerase error bias for transitions over transversions. These results indicate that bottlenecks coupled with strong negative/purifying selection drive consensus sequences toward neutral sequence space, and that most polymorphism within single-insect isolates is composed of newly-minted mutations sampled prior to selection.

Plasmid Vectors for Xylella fastidiosa Utilizing a Toxin-Antitoxin System for Stability in the Absence of Antibiotic Selection.

The phytopathogen Xylella fastidiosa causes disease in a variety of important crop and landscape plants. Functional genetic studies have led to a broader understanding of virulence mechanisms used by this pathogen in the grapevine host. Plasmid shuttle vectors are important tools in studies of bacterial genetics but there are only a limited number of plasmid vectors available that replicate in X. fastidiosa, and even fewer that are retained without antibiotic selection. Two plasmids are described here that show stable replication in X. fastidiosa and are effective for gene complementation both in vitro and in planta. Plasmid maintenance is facilitated by incorporation of the PemI/PemK plasmid addiction system, consisting of PemK, an endoribonuclease toxin, and its cognate antitoxin, PemI. Vector pXf20pemIK utilizes a native X. fastidiosa replication origin as well as a high-copy-number pUC origin for propagation in Escherichia coli cloning strains. Broad-host-range vector pBBR5pemIK is a medium- to low-copy-number plasmid based on the pBBR1 backbone. Both plasmids are maintained for extended periods of time in the absence of antibiotic selection, as well as up to 14 weeks in grapevine, without affecting bacterial fitness. These plasmids present an alternative to traditional complementation and expression vectors which rely on antibiotic selection for plasmid retention.

A Temperature-Independent Cold-Shock Protein Homolog Acts as a Virulence Factor in Xylella fastidiosa.

Xylella fastidiosa, causal agent of Pierce's disease (PD) of grapevine, is a fastidious organism that requires very specific conditions for replication and plant colonization. Cold temperatures reduce growth and survival of X. fastidiosa both in vitro and in planta. However, little is known regarding physiological responses of X. fastidiosa to temperature changes. Cold-shock proteins (CSP), a family of nucleic acid-binding proteins, act as chaperones facilitating translation at low temperatures. Bacterial genomes often encode multiple CSP, some of which are strongly induced following exposure to cold. Additionally, CSP contribute to the general stress response through mRNA stabilization and posttranscriptional regulation. A putative CSP homolog (Csp1) with RNA-binding activity was identified in X. fastidiosa Stag's Leap. The csp1 gene lacked the long 5' untranslated region characteristic of cold-inducible genes and was expressed in a temperature-independent manner. As compared with the wild type, a deletion mutant of csp1 (∆csp1) had decreased survival rates following cold exposure and salt stress in vitro. The deletion mutant also was significantly less virulent in grapevine, as compared with the wild type, in the absence of cold stress. These results suggest an important function of X. fastidiosa Csp1 in response to cellular stress and during plant colonization.

Disentangling Effects of Vector Birth Rate, Mortality Rate, and Abundance on Spread of Plant Pathogens.

Models on the spread of insect-transmitted plant pathogens often fix vector population size by assuming that deaths are offset by births. Although such mathematical simplifications are often justified, deemphasizing parameters that govern vector population size is problematic, as reproductive biology and mortality schedules of vectors of plant pathogens receive little empirical attention. Here, the importance of explicitly including parameters for vector birth and death rates was evaluated by comparing results from models with fixed vector population size with models with logistic vector population growth. In fixed vector population size models, increasing vector mortality decreased percentage of inoculative vectors, but had no effect on vector population size, as deaths were offset by births. In models with logistic vector population growth, increasing vector mortality decreased percentage of inoculative vectors and decreased vector population size. Consequently, vector mortality had a greater effect on pathogen spread in models with logistic vector population growth than in models with fixed vector population size. Further, in models with logistic vector population growth, magnitude of vector birth rate determined time required for vector populations to reach large size, thereby determining when pathogen spread occurred quickly. Assumptions regarding timing of vector mortality within a time step also affected model outcome. A greater emphasis of vector entomologists on studying reproductive biology and mortality schedules of insect species that transmit plant pathogens will facilitate identification of conditions associated with rapid growth of vector populations and could lead to development of novel control strategies.

Effects of Glassy-Winged Sharpshooter (Hemiptera: Cicadellidae) Feeding, Size, and Lipid Content on Egg Maturation.

The glassy-winged sharpshooter (Homalodisca vitripennis) is synovigenic and must feed as an adult to produce eggs. Egg maturation rates depend on the host plant species provided to the adult female for feeding and are variable for females provided with the same host plant species. Here, the contribution of female size and lipid content to variation in egg maturation rates among females held on the same host plant species was assessed. To assess effects of female size and lipid content on egg maturation, feeding assays followed by measurements of egg load, female size, and lipid content were conducted. To accomplish this, females were field collected and held on cowpea until producing approximately 0, 12, 25, or 50 ml of excreta. After reaching prescribed excreta thresholds, females were dissected to determine egg load, hind tibia length, and head capsule width. Mature eggs were removed from the abdomen and dry weight of eggs and bodies (head, thorax, and abdomen) were obtained. Lipid content of eggs and bodies were determined using a quantitative colorimetric assay. Rates of body weight gain and body lipid gain were rapid with low levels of feeding (12 ml of excreta) but decelerated with additional feeding (>12 ml of excreta). In contrast, low levels of feeding (12 ml of excreta) resulted in little egg production, with rates of egg production accelerating with additional feeding (>12 ml of excreta). Accordingly, egg production was preceded by an increase in body dry weight and body lipid content. In agreement, probability that a female carried eggs increased with body lipid content in the 0-, 12-, and 25-ml feeding treatments. Across treatments, larger females carried more eggs than smaller females. Collectively, results suggest that variation in glassy-winged sharpshooter egg maturation rates partially may be explained by availability of lipid reserves at the start of a feeding bout and female size.

Evaluation of Olive as a Host of Xylella fastidiosa and Associated Sharpshooter Vectors.

Olive (Olea europaea) trees exhibiting leaf scorch or branch dieback symptoms in California were surveyed for the xylem-limited, fastidious bacterium Xylella fastidiosa. Only approximately 17% of diseased trees tested positive for X. fastidiosa by polymerase chain reaction, and disease symptoms could not be attributed to X. fastidiosa infection of olive in greenhouse pathogenicity assays. Six strains of X. fastidiosa were isolated from olive in Southern California. Molecular assays identified strains recovered from olive as belonging to X. fastidiosa subsp. multiplex. Pathogenicity testing of olive strains on grapevine and almond confirmed that X. fastidiosa strains isolated from olive yield disease phenotypes on almond and grapevine typical of those expected for subsp. multiplex. Mechanical inoculation of X. fastidiosa olive strains to olive resulted in infection at low efficiency but infections remained asymptomatic and tended to be self-limiting. Vector transmission assays demonstrated that glassy-winged sharpshooter (Homalodisca vitripennis) could transmit strains of both subspp. multiplex and fastidiosa to olive at low efficiency. Insect trapping data indicated that two vectors of X. fastidiosa, glassy-winged sharpshooter and green sharpshooter (Draeculacephala minerva), were active in olive orchards. Collectively, the data indicate that X. fastidiosa did not cause olive leaf scorch or branch dieback but olive may contribute to the epidemiology of X. fastidiosa-elicited diseases in California. Olive may serve as an alternative, albeit suboptimal, host of X. fastidiosa. Olive also may be a refuge where sharpshooter vectors evade intensive areawide insecticide treatment of citrus, the primary control method used in California to limit glassy-winged sharpshooter populations and, indirectly, epidemics of Pierce's disease of grapevine.

Draft Genome Sequence of Xylella fastidiosa subsp. multiplex Strain Griffin-1 from Quercus rubra in Georgia.

The draft genome sequence of Xylella fastidiosa subsp. multiplex strain Griffin-1, isolated from a red oak tree (Quercus rubra) in Georgia, is reported here. The bacterium has a genome size of 2,387,314 bp, with a G+C content of 51.7%. The Griffin-1 strain genome contains 2,903 predicted open reading frames and 50 RNA genes.

Occurrence, sequence polymorphism and population structure of Circulifer tenellus virus 1 in a field population of the beet leafhopper.

Circulifer tenellus virus 1 (CiTV1) is the prototypical example of an unusual group of dsRNA viruses associated with insects and for which ecological data are lacking. A San Joaquin Valley (SJV), California population of the beet leafhopper (BLH; Circulifer tenellus [Baker]) was sampled for CiTV1 in 2010. Among 365 BLH sampled, 119 (32.6%) were positive for CiTV1, with at least one CiTV1-positive BLH collected from each of 35 locations. Chi-square tests indicated that observed CiTV1 incidence differed from expected values based on collection season but not geography within the SJV. Sequence comparisons identified three CiTV1 strains, designated A, B, and C. Strain A predominated (82.4%), strain B was less common (16.8%), and only one (0.8%) strain C isolate was encountered. Chi-square tests demonstrated that observed frequencies of strains A and B did not differ from expected values in space or time, indicating that the SJV population of CiTV1 was unstructured.

Small RNA populations for two unrelated viruses exhibit different biases in strand polarity and proximity to terminal sequences in the insect host Homalodisca vitripennis.

Next generation sequence analyses were used to assess virus-derived small RNA (vsRNA) profiles for Homalodisca coagulata virus-1 (HoCV-1), family Dicistroviridae, and Homalodisca vitripennis reovirus (HoVRV), family Reoviridae, from virus-infected H. vitripennis, the glassy-winged sharpshooter. The vsRNA reads were mapped against the monopartite genome of HoCV-1 and all 12 genome segments of HoVRV, and 21nt vsRNAs were most common. However, strikingly contrasting patterns for the HoCV-1 and HoVRV genomic RNAs were observed. The majority of HoCV-1 vsRNAs mapped to the genomic positive-strand RNA and, although minor hotspots were observed, vsRNAs mapped across the entire genomic RNA. In contrast, HoVRV vsRNAs mapped to both positive and negative-sense strands for all genome segments, but different genomic segments showed distinct hotspots. The HoVRV vsRNAs were more common for 5' and 3' regions of HoVRV regions of all segments. These data suggest that taxonomically different viruses in the same host offer different targets for RNA-antiviral defense.

Roguing with replacement in perennial crops: conditions for successful disease management.

Replacement of diseased plants with healthy plants is commonly used to manage spread of plant pathogens in perennial cropping systems. This strategy has two potential benefits. First, removing infected plants may slow pathogen spread by eliminating inoculum sources. Second, replacing infected plants with uninfected plants may offset yield losses due to disease. The extent to which these benefits are realized depends on multiple factors. In this study, sensitivity analyses of two spatially explicit simulation models were used to evaluate how assumptions concerning implementation of a plant replacement program and pathogen spread interact to affect disease suppression. In conjunction, effects of assumptions concerning yield loss associated with disease and rates of plant maturity on yields were simultaneously evaluated. The first model was used to evaluate effects of plant replacement on pathogen spread and yield on a single farm, consisting of a perennial crop monoculture. The second model evaluated effects of plant replacement on pathogen spread and yield in a 100 farm crop growing region, with all farms maintaining a monoculture of the same perennial crop. Results indicated that efficient replacement of infected plants combined with a high degree of compliance among farms effectively slowed pathogen spread, resulting in replacement of few plants and high yields. In contrast, inefficient replacement of infected plants or limited compliance among farms failed to slow pathogen spread, resulting in replacement of large numbers of plants (on farms practicing replacement) with little yield benefit. Replacement of infected plants always increased yields relative to simulations without plant replacement provided that infected plants produced no useable yield. However, if infected plants produced useable yields, inefficient removal of infected plants resulted in lower yields relative to simulations without plant replacement for perennial crops with long maturation periods in some cases.