Population structure of blackberry chlorotic ringspot virus in the United States

2012 ◽  
Vol 158 (3) ◽  
pp. 667-672 ◽  
Author(s):  
Bindu Poudel ◽  
Ioannis E. Tzanetakis
Keyword(s):  
United States ◽  
Population Structure ◽  
The United States ◽  
Ringspot Virus

scholarly journals First Report of Potato spindle tuber viroid Naturally Infecting Field Tomatoes in the Dominican Republic

Plant Disease ◽  
2014 ◽  
Vol 98 (5) ◽  
pp. 701-701
Author(s):  
K.-S. Ling ◽  
R. Li ◽  
D. Groth-Helms ◽  
F. M. Assis-Filho
Keyword(s):  
United States ◽  
Dominican Republic ◽  
Mosaic Virus ◽  
Potato Spindle Tuber Viroid ◽  
The United States ◽  
Disease Outbreak ◽  
Ringspot Virus ◽  
Rt Pcr ◽  
Spot Virus ◽  
Three Samples

In recent years, viroid disease outbreaks have resulted in serious economic losses to a number of tomato growers in North America (1,2,3). At least three pospiviroids have been identified as the causal agents of tomato disease, including Potato spindle tuber viroid (PSTVd), Tomato chlorotic dwarf viroid (TCDVd), and Mexican papita viroid (MPVd). In the spring of 2013, a severe disease outbreak with virus-like symptoms (chlorosis and plant stunting) was observed in a tomato field located in the Dominican Republic, whose tomato production is generally exported to the United States in the winter months. The transplants were produced in house. The disease has reached an epidemic level with many diseased plants pulled and disposed of accordingly. Three samples collected in May of 2013 were screened by ELISA against 16 common tomato viruses (Alfalfa mosaic virus, Cucumber mosaic virus, Impatiens necrotic spot virus, Pepino mosaic virus, Potato virus X, Potato virus Y, Tobacco etch virus, Tobacco mosaic virus, Tobacco ringspot virus, Tomato aspermy virus, Tomato bushy stunt virus, Tomato mosaic virus, Tomato ringspot virus, Tomato spotted wilt virus, Groundnut ringspot virus, and Tomato chlorotic spot virus), a virus group (Potyvirus group), three bacteria (Clavibacter michiganensis subsp. michiganensis, Pectobacterium atrosepticum, and Xanthomonas spp.), and Phytophthora spp. No positive result was observed, despite the presence of symptoms typical of a viral-like disease. Further analysis by RT-PCR using Agdia's proprietary pospiviroid group-specific primer resulted in positive reactions in all three samples. To determine which species of pospiviroid was present in these tomato samples, full-genomic products of the expected size (~360 bp) were amplified by RT-PCR using specific primers for PSTVd (4) and cloned using TOPO-TA cloning kit (Invitrogen, CA). A total of 8 to 10 clones from each isolate were selected for sequencing. Sequences from each clone were nearly identical and the predominant sequence DR13-01 was deposited in GenBank (Accession No. KF683200). BLASTn searches into the NCBI database demonstrated that isolate DR13-01 shared 97% sequence identity to PSTVd isolates identified in wild Solanum (U51895), cape gooseberry (EU862231), or pepper (AY532803), and 96% identity to the tomato-infecting PSTVd isolate from the United States (JX280944). The relatively lower genome sequence identity (96%) to the tomato-infecting PSTVd isolate in the United States (JX280944) suggests that PSTVd from the Dominican Republic was likely introduced from a different source, although the exact source that resulted in the current disease outbreak remains unknown. It may be the result of an inadvertent introduction of contaminated tomato seed lots or simply from local wild plants. Further investigation is necessary to determine the likely source and route of introduction of PSTVd identified in the current epidemic. Thus, proper control measures could be recommended for disease management. The detection of this viroid disease outbreak in the Dominican Republic represents further geographic expansion of the viroid disease in tomatoes beyond North America. References: (1). K.-S. Ling and M. Bledsoe. Plant Dis. 93:839, 2009. (2) K.-S. Ling and W. Zhang. Plant Dis. 93:1216, 2009. (3) K.-S. Ling et al. Plant Dis. 93:1075, 2009. (4) A. M. Shamloul et al. Can. J. Plant Pathol. 19:89, 1997.

scholarly journals Population structure of Drosophila suzukii and signals of multiple invasions into the continental United States

2021 ◽  
Author(s):  
Kyle M Lewald ◽  
Antoine Abrieux ◽  
Derek A Wilson ◽  
Yoosook Lee ◽  
William R Conner ◽  
...  
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Population Structure ◽  
Weather Conditions ◽  
The United States ◽  
Future Research ◽  
Drosophila Suzukii ◽  
Significant Damage ◽  
Wide Range ◽  
Multiple Invasions

Drosophila suzukii, or spotted-wing drosophila, is now an established pest in many parts of the world, causing significant damage to numerous fruit crop industries. Native to East Asia, D. suzukii infestations started in the United States a decade ago, occupying a wide range of climates. To better understand invasion ecology of this pest, knowledge of past migration events, population structure, and genetic diversity is needed. To improve on previous studies examining genetic structure of D. suzukii, we sequenced whole genomes of 237 individual flies collected across the continental U.S., as well as several representative sites in Europe, Brazil, and Asia, to identify hundreds of thousands of genetic markers for analysis. We analyzed these markers to detect population structure, to reconstruct migration events, and to estimate genetic diversity and differentiation within and among the continents. We observed strong population structure between West and East Coast populations in the U.S., but no evidence of any population structure North to South, suggesting there is no broad-scale adaptations occurring in response to the large differences in regional weather conditions. We also find evidence of repeated migration events from Asia into North America have provided increased levels of genetic diversity, which does not appear to be the case for Brazil or Europe. This large genomic dataset will spur future research into genomic adaptations underlying D. suzukii pest activity and development of novel control methods for this agricultural pest.

scholarly journals Contrasting Patterns of Genetic Diversity and Population Structure of Armillaria mellea sensu stricto in the Eastern and Western United States

2010 ◽  
Vol 100 (7) ◽  
pp. 708-718 ◽  
Author(s):  
Kendra Baumgartner ◽  
Renaud Travadon ◽  
Johann Bruhn ◽  
Sarah E. Bergemann
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Population Structure ◽  
Los Angeles ◽  
The United States ◽  
Sensu Stricto ◽  
Western United States ◽  
Eastern United States ◽  
Armillaria Mellea ◽  
Genetic Pools

Armillaria mellea infects hundreds of plant species in natural and managed ecosystems throughout the Northern hemisphere. Previously reported nuclear genetic divergence between eastern and western U.S. isolates is consistent with the disjunct range of A. mellea in North America, which is restricted mainly to both coasts of the United States. We investigated patterns of population structure and genetic diversity of the eastern (northern and southern Appalachians, Ozarks, and western Great Lakes) and western (Berkeley, Los Angeles, St. Helena, and San Jose, CA) regions of the United States. In total, 156 diploid isolates were genotyped using 12 microsatellite loci. Absence of genetic differentiation within either eastern subpopulations (θST = –0.002, P = 0.5 ) or western subpopulations (θST = 0.004, P = 0.3 ) suggests that spore dispersal within each region is sufficient to prevent geographic differentiation. In contrast to the western United States, our finding of more than one genetic cluster of isolates within the eastern United States (K = 3), revealed by Bayesian assignment of multilocus genotypes in STRUCTURE and confirmed by genetic multivariate analyses, suggests that eastern subpopulations are derived from multiple founder sources. The existence of amplifiable and nonamplifiable loci and contrasting patterns of genetic diversity between the two regions demonstrate that there are two geographically isolated, divergent genetic pools of A. mellea in the United States.

A novel assessment of population structure and gene flow in grey wolf populations of the Northern Rocky Mountains of the United States

2010 ◽  
Vol 19 (20) ◽  
pp. 4412-4427 ◽  
Author(s):  
BRIDGETT M. VONHOLDT ◽  
DANIEL R. STAHLER ◽  
EDWARD E. BANGS ◽  
DOUGLAS W. SMITH ◽  
MIKE D. JIMENEZ ◽  
...  
Keyword(s):  
United States ◽  
Population Structure ◽  
Gene Flow ◽  
Rocky Mountains ◽  
The United States ◽  
Grey Wolf ◽  
Northern Rocky Mountains

scholarly journals Pyricularia grisea Causing Gray Leaf Spot of Perennial Ryegrass Turf: Population Structure and Host Specificity

Plant Disease ◽  
2001 ◽  
Vol 85 (8) ◽  
pp. 817-826 ◽  
Author(s):  
G. Viji ◽  
B. Wu ◽  
S. Kang ◽  
W. Uddin ◽  
D. R. Huff
Keyword(s):  
United States ◽  
Population Structure ◽  
Winter Wheat ◽  
Perennial Ryegrass ◽  
Leaf Spot ◽  
Genetic Relationships ◽  
The United States ◽  
Gray Leaf Spot ◽  
Pyricularia Grisea ◽  
Highly Virulent

Gray leaf spot is a serious disease of perennial ryegrass (Lolium perenne) turf in the United States. Isolates of Pyricularia grisea causing the disease in perennial ryegrass were characterized using molecular markers and pathogenicity assays on various gramineous hosts. Genetic relationships among perennial ryegrass isolates were determined using different types of trans-posons as probes. Phylogenetic analysis using Pot2 and MGR586 probes, analyzed with AMOVA (analysis of molecular variance), showed that these isolates from perennial ryegrass consist of three closely related lineages. All the isolates belonged to a single mating type, MAT1-2. Among 20 isolates from 16 host species other than perennial ryegrass, only the isolates from wheat (Triticum aestivum) and triticale (× Triticosecale), showed notable similarity to the perennial ryegrass isolates based on their Pot2 fingerprints. The copy number and fingerprints of Pot2 and MGR586 in isolates of P. grisea from perennial ryegrass indicate that they are genetically distinct from the isolates derived from rice (Oryza sativa) in the United States. The perennial ryegrass isolates also had the same sequence in the internal transcribed spacer (ITS) region of the genes encoding ribosomal RNA as that of the wheat and triticale isolates, and exhibited rice isolate sequence polymorphisms. In pathogenicity assays, all the isolates of P. grisea from Legacy II perennial ryegrass caused characteristic blast symptoms on Marilee soft white winter wheat, Bennett hard red winter wheat, Era soft white spring wheat, and Presto triticale, and they were highly virulent on these hosts. An isolate from wheat and one from triticale (from Brazil) were also highly virulent on perennial ryegrass and Rebel III tall fescue (Festuca arundinacea). None of the isolates from perennial ryegrass caused the disease on Lagrue rice, and vice versa. Understanding the population structure of P. grisea isolates infecting perennial ryegrass and their relatedness to isolates from other gramineous hosts may aid in identifying alternate hosts for this pathogen.

scholarly journals First Report of Tobacco ringspot virus in Blackberry (Rubus sp.) in Alabama

Plant Disease ◽  
2008 ◽  
Vol 92 (12) ◽  
pp. 1708-1708 ◽  
Author(s):  
E. Coneva ◽  
J. F. Murphy ◽  
R. Boozer ◽  
N. Velásquez
Keyword(s):  
United States ◽  
North Carolina ◽  
South Carolina ◽  
Virus Infection ◽  
The United States ◽  
Negative Control ◽  
Ringspot Virus ◽  
First Report ◽  
Tobacco Ringspot Virus ◽  
Control Samples

In 2006, primocane stunted growth and crumbly berry development were observed on 4-year-old Kiowa and Apache blackberry cultivars grown at the Chilton Research and Extension Center, Clanton, AL. Samples from affected plants were tested for virus infection by ELISA kits (Agdia, Inc., Elkhart, IN) specific to each of 14 different viruses. Most samples tested positive for Tobacco ringspot virus (TRSV). TRSV was detected in blackberry samples from North Carolina and South Carolina (2). Bray et al. (1) studied the incidence of viruses in blackberry nursery stock in the United States and reported that 9% of the tested samples contained TRSV. Thus, a survey was conducted for TRSV incidence among commercial blackberry stands in eight counties in Alabama during July 2007. Blackberry plants were observed to express virus-like symptoms including chlorotic spots on leaves, leaf veinal chlorosis, stunting, and combinations thereof. Fruit-bearing plants sometimes had crumbly fruit symptoms characteristic of virus infection. Leaf samples that were collected from symptomatic and nonsymptomatic plants representing 14 cultivars were tested by TRSV ELISA (Agdia, Inc.). Of 180 blackberry samples, 68 tested positive for TRSV. Positive ELISA reactions for TRSV were on average 28 times greater than the reactions of known negative control samples considered negative for TRSV. Blackberry plants shown to be infected with TRSV during the 2007 survey were tested in July 2008 in an effort to confirm the presence of TRSV. Fifty-four percent of the samples tested positive by ELISA with the average positive ELISA value being 21 times higher than the average negative ELISA value for known negative control samples. To further confirm the occurrence of TRSV in Alabama-grown blackberry plants, leaf samples were tested by reverse transcription (RT)-PCR to amplify a 329-bp fragment of the viral coat protein gene (TRSV RNA 2 sequence accession no. NC_005096; primers TRSCP-F (5′-TCTGGCACTATAAGCGGAAG-3′) and TRSCP-R (5′-GAAAACATGGGAGGATGCAC-3′). A single band of the anticipated size was amplified (analyzed by agarose gel electorphoresis and visualized by ethidium bromide staining) from RNA samples extracted with a RNeasy Mini kit (Qiagen, Valencia, CA) from blackberry samples that tested positive for TRSV by ELISA and a known positive control. No amplified product resulted from a blackberry sample that tested negative for TRSV by ELISA. These results illustrate and confirm the presence of TRSV in blackberry leaf tissues grown in Alabama. To our knowledge, this is the first report of TRSV infection of blackberry plants in Alabama. References: (1) M. M. Bray et al. HortScience 40:874, 2005. (2) T. L. Guzmán-Baeny. Incidence, distribution, and symptom description of viruses in cultivated blackberry (Rubus subgenus Eubatus) in the southeastern United States. M.S. thesis, North Carolina State University, Raleigh, 2003.

scholarly journals First Report of Blackberry chlorotic ringspot virus in Rubus sp. in the United States

Plant Disease ◽  
2007 ◽  
Vol 91 (4) ◽  
pp. 463-463 ◽  
Author(s):  
I. E. Tzanetakis ◽  
J. D. Postman ◽  
R. R. Martin
Keyword(s):  
United States ◽  
The United States ◽  
Ringspot Virus ◽  
Tobacco Streak Virus ◽  
Rapid Decline ◽  
Streak Virus ◽  
Black Raspberry ◽  
Rt Pcr ◽  
Indicator Plants ◽  
First Report

Blackberry chlorotic ringspot virus (BCRV), genus Ilarvirus, has been found in Rubus sp. in Scotland (2) and rose in the United States (4). The possibility that BCRV infects other hosts in the United States was explored. We tested 18 accessions of Fragaria sp. and 30 of Rubus sp. maintained at the National Clonal Germplasm Repository in Corvallis, OR. Ilarviruses had been detected in these plants by reverse transcription (RT)-PCR, ELISA, or had caused symptoms typical of ilarviruses on indicator plants. The accessions were tested by RT-PCR with primers F (5′-GTTTCCTGTGCTCCTCA-3′) and R (5′-GTCACACCGAGGTACT-3′) (4) that amplify a 519 to 522 nt (depending on the isolate) region of the RNA 3 of BCRV. The virus was detected in two accessions of black raspberry (Rubus occidentalis L.): RUB433, cv. Lowden and RUB 9012, cv. New Logan. The sequences of the fragments amplified from these accessions (GenBank Accession Nos. EF041817 and EF041818, respectively) had 97% nt sequence identity to each other and 95 and 88% nt identity to the rose and Scottish isolates (GenBank Accession Nos. DQ329378 and DQ091195, respectively). Chenopodium quinoa indicator plants inoculated with isolate RUB 433 developed mild chlorotic spots on the inoculated leaves 4 days after inoculation. RT-PCR and sequencing of the amplicons verified BCRV infection of C. quinoa. RUB 9012 was used for the characterization of Black raspberry latent virus (BRLV), later thought to be an isolate of Tobacco streak virus (TSV). This accession was recently found to be infected with Strawberry necrotic shock virus (SNSV) but not TSV (3). It is possible that BRLV may be a mixture of SNSV and BCRV. SNSV is one of the most abundant viruses of Rubus sp. in the Pacific Northwest (1), and the finding of another ilarvirus, BCRV, may account in part for the rapid decline of Rubus sp. observed in several fields in Oregon and Washington. To our knowledge, this is the first report of BCRV infecting Rubus sp. outside the United Kingdom. References: (1) A. B. Halgren. Ph.D. Diss. Oregon State University, Corvallis, OR, 2006. (2) A. T. Jones et al. Ann. Appl. Biol. 149:125, 2006. (3) I. E. Tzanetakis et al. Arch. Virol. 149:2001, 2004. (4) I. E. Tzanetakis et al. Plant Pathol. 55:568, 2006.

scholarly journals Population genomics of Drosophila suzukii reveal longitudinal population structure and signals of migrations in and out of the continental United States

2021 ◽  
Author(s):  
Kyle M Lewald ◽  
Antoine Abrieux ◽  
Derek A Wilson ◽  
Yoosook Lee ◽  
William R Conner ◽  
...  
Keyword(s):  
United States ◽  
Population Structure ◽  
Population Genomics ◽  
The United States ◽  
Future Research ◽  
Drosophila Suzukii ◽  
Genomic Dataset ◽  
Significant Damage ◽  
Wide Range ◽  
Whole Genomes

Abstract Drosophila suzukii, or spotted-wing drosophila, is now an established pest in many parts of the world, causing significant damage to numerous fruit crop industries. Native to East Asia, D. suzukii infestations started in the United States (U.S.) a decade ago, occupying a wide range of climates. To better understand invasion ecology of this pest, knowledge of past migration events, population structure, and genetic diversity is needed. In this study, we sequenced whole genomes of 237 individual flies collected across the continental U.S., as well as several sites in Europe, Brazil, and Asia, to identify and analyze hundreds of thousands of genetic markers. We observed strong population structure between Western and Eastern U.S. populations, but no evidence of any population structure between different latitudes within the continental U.S., suggesting there is no broad-scale adaptations occurring in response to differences in winter climates. We detect admixture from Hawaii to the Western U.S. and from the Eastern U.S. to Europe, in agreement with previously identified introduction routes inferred from microsatellite analysis. We also detect potential signals of admixture from the Western U.S. back to Asia, which could have important implications for shipping and quarantine policies for exported agriculture. We anticipate this large genomic dataset will spur future research into the genomic adaptations underlying D. suzukii pest activity and development of novel control methods for this agricultural pest.

scholarly journals First Complete Genome Sequence of Papaya ringspotvirus-W Isolated from a Gourd in the United States

2017 ◽  
Vol 5 (2) ◽  
Author(s):  
Akhtar Ali
Keyword(s):  
United States ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
The United States ◽  
Ringspot Virus ◽  
Papaya Ringspot Virus ◽  
Commercial Field

ABSTRACT In the United States, the Papaya ringspot virus was first reported from papaya in Florida in 1949. Here, we determined the first complete genome sequence (10,302 nucleotides) of a Papaya ringspot virus-W isolate, which was collected from a commercial field of gourd in Tulsa, OK.

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