@article{kaye_moyer_parks_carbone_cubeta_2011, title={Population Genetic Analysis of Tomato spotted wilt virus on Peanut in North Carolina and Virginia}, volume={101}, ISSN={["1943-7684"]}, DOI={10.1094/phyto-01-10-0035}, abstractNote={Exploring the genetic diversity and evolutionary history of plant viruses is critical to understanding their ecology and epidemiology. In this study, maximum-likelihood and population genetics-based methods were used to investigate the population structure, genetic diversity, and sources of genetic variation in field isolates of Tomato spotted wilt virus (TSWV) from peanut in North Carolina and Virginia. Selected regions of the nucleocapsid, movement, and RNA-dependent RNA polymerase genes were amplified and sequenced to identify haplotypes and infer genetic relationships between isolates of TSWV with heuristic methods. The haplotype structure of each locus consisted of 1 or 2 predominant haplotypes and >100 haplotypes represented by a single isolate. No specific haplotypes were associated with geographic area, peanut cultivar, or year of isolation. The population was panmictic at the regional level and high levels of genetic diversity were observed among isolates. There was evidence for positive selection on single amino acids in each gene on a background of predominant purifying selection acting upon each locus. The results of compatibility analyses and the persistence of specific gene sequences in isolates collected over three field seasons suggest that recombination was occurring in the population. Estimates of the population mutation rate suggest that mutation has had a significant effect on the shaping of this population and, together with purifying selection, these forces have been the predominant evolutionary forces influencing the TSWV population in peanut in North Carolina and Virginia.}, number={1}, journal={PHYTOPATHOLOGY}, author={Kaye, A. C. and Moyer, J. W. and Parks, E. J. and Carbone, I. and Cubeta, M. A.}, year={2011}, month={Jan}, pages={147–153} }
 @article{sullivan_parks_cubeta_gallup_melton_moyer_shew_2010, title={An Assessment of the Genetic Diversity in a Field Population of Phytophthora nicotianae with a Changing Race Structure}, volume={94}, ISSN={["1943-7692"]}, DOI={10.1094/pdis-94-4-0455}, abstractNote={One hundred fifty-three isolates of Phytophthora nicotianae that were collected over a 4-year period from a single field were subjected to amplified fragment length polymorphism (AFLP) analysis to investigate the effect of different types of resistance in tobacco (Nicotiana tabacum) on genetic diversity in the pathogen population. No race 1 isolates were detected in the field prior to initiating the study, but the race was present in multiple plots by the end of the 4-year period. There were 102 race 0 isolates and 51 race 1 isolates characterized. Seventy-six of the 153 isolates had a unique AFLP profile, whereas the remaining 77 isolates were represented by 27 AFLP profiles shared by at least two isolates. Isolates of both races were found in both the unique and shared AFLP profile groups. Twenty-three of the AFLP profiles were detected in multiple years, indicating a clonal component to the pathogen population. Race 1 isolates that were detected over multiple years were always obtained from the same plot. No race 1 profile was found in more than one plot, confirming the hypothesis that the multiple occurrences of the race throughout the field were the result of independent events and not pathogen spread. Three identical race 0 AFLP profiles occurred in noncontiguous plots, and in each case, the plots contained the same partially resistant variety. Cluster analysis provided a high level of bootstrap support for 41 isolates in 19 clusters that grouped primarily by race and rotation treatment. Estimates of genetic diversity ranged from 0.365 to 0.831 and varied depending on tobacco cultivar planted and race. When averaged over all treatments, diversity in race 1 isolates was lower than in race 0 isolates at the end of each season. Deployment of single-gene resistance initially decreased genetic diversity of the population, but the diversity increased each year, indicating the pathogen was adapting to the host genotypes deployed in the field.}, number={4}, journal={PLANT DISEASE}, author={Sullivan, M. J. and Parks, E. J. and Cubeta, M. A. and Gallup, C. A. and Melton, T. A. and Moyer, J. W. and Shew, H. D.}, year={2010}, month={Apr}, pages={455–460} }
 @article{abad_parks_new_fuentes_jester_moyer_2007, title={First report of Sweet potato chlorotic stunt virus, a component of sweetpotato virus disease, in North Carolina.}, volume={91}, ISSN={["0191-2917"]}, DOI={10.1094/PDIS-91-3-0327B}, abstractNote={Sweet potato chlorotic stunt virus (SPCSV) is the whitefly-transmitted component of the sweet potato virus disease (SPVD), a devastating disease originally described in Africa (4). Two isolates designated as G-01 and T-03 were obtained in North Carolina in July 2001 and October 2003, respectively, from plants of cv. Beauregard exhibiting symptoms typical of SPVD, including stunting, leaf narrowing and distortion, vein clearing, and chlorotic mosaic. Sap extract from symptomatic plants tested positive for SPCSV by nitrocellulose immuno-dot blot, using monoclonal antibodies specific for SPCSV obtained from the International Potato Center. Total RNA was extracted from 100 mg of symptomatic leaf tissue by using the PureLink Total RNA Purification System Kit from Invitrogen (Carlsbad, CA) with a minor modification (adding 2% PVP-40 and 1% 2-mercaptoethanol to the extraction buffer) (1). Results were confirmed by reverse transcription (RT)-PCR using primers CP1 and CP3 and HSP70-A/HSP70-B (2), corresponding to the capsid protein and 'heat shock' protein genes, respectively. HSP70 amplicons were cloned using the TOPO TA Cloning Kit (Invitrogen) and sequenced. At the nucleotide level, viral sequences from clones from both isolates were an average 99.4% similar to West Africa and 77.9% to East Africa sequences of SPCSV from Genbank (1). Although the isolates were collected from different fields, viral sequences generated from clones for T-03 and G-01 differed by only six nucleotides and were identical at the amino acid level. The neighbor-joining phylogenetic tree constructed using the HSP70 gene fragment (39 nt) delineated two major clusters with two subpopulations each: Cluster 1, "East Africa", consisted of East Africa and Peru subpopulations; Cluster 2, "West Africa", consisted of Argentina-Brazil and USA-West Africa subpopulations (1). In addition, SPCSV isolates from East Africa and West Africa clusters were sufficiently distant phylogenetically to suggest that they may correspond to two different criniviruses, with an average similarity between the populations of 78.14% and an average within the populations above 89%. Hudson's tests confirmed the presence of genetically distinct SPCSV groups with high statistical significance (1). Two groups (Peru and East Africa) were differentiated in the East Africa cluster, and three groups (Argentina-Brazil, USA, and West Africa) were differentiated in the West Africa cluster, suggesting that the USA population is not a recent introduction. Although SPCSV was previously reported in the United States, the source was a single accession of cv. White Bunch from the USDA Sweetpotato Germplasm Repository (3). Sweet potato feathery mottle virus (SPFMV) (family Potyviridae, genus Potyvirus), the other component of SPVD, was also detected in both cultivars. To our knowledge, this is the first report of SPCSV in sweetpotato fields in the United States. References: (1) J. A. Abad et al. Phytopathology (Abstr.) 96(suppl.):S1, 2006. (2) T. Alicai et al. Plant Pathol. 48:718, 1999. (3) G. Pio-Ribeiro et al. Plant Dis. 80:551, 1996. (4) G. A. Schaefer and E. R. Terry. Phytopathology 66:642, 1977.}, number={3}, journal={PLANT DISEASE}, author={Abad, J. A. and Parks, E. J. and New, S. L. and Fuentes, S. and Jester, W. and Moyer, J. W.}, year={2007}, month={Mar}, pages={327–327} }