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ARS Home Pacific West Area Davis, California Crops Pathology and Genetics Research Research





- Kluepfel, Daniel
- Poret-Peterson, Amisha
- Browne, Greg
- Kasuga, Takao
- Sudarshana, Mysore
- 2022
- 2021
- 2020
- 2019
- 2018
- 2017
- Publications
- Plant Diseases (303)

Research Project: **Location:
                            Crops Pathology and Genetics Research** Publications
                            (Clicking on the reprint icon
                                Reprint Icon
                                will take you to the publication reprint.) Comparative genomic analysis of 31 Phytophthora genomes reveals genome plasticity and horizontal gene transfer
                                
                            - (Peer Reviewed Journal)
                                
                                Kronmiller, B.A., Feau, N., Shen, D., Tabima, J.F., Ali, S.S., Armitage, A.D., Arredondo, F., Bailey, B.A., Bollmann, S.R., Dale, A., Harrison, R., Hrywkiw, K., Kasuga, T., Mcdougal, R., Nellist, C.F., Panda, P., Tripathy, S., Williams, N.M., Ye, W., Wang, Y., Hamelin, R.C., Grunwald, N.J. 2023. Comparative genomic analysis of 31 Phytophthora genomes reveals genome plasticity and horizontal gene transfer. Molecular Plant-Microbe Interactions. 36:26-46. https://doi.org/10.1094/MPMI-06-22-0133-R. Random forest analysis reveals taxa predictive of Prunus replant disease in peach root microbiomes
                                
                            - (Peer Reviewed Journal)
                                
                                Khan, A.R., Wicaksono, W., Ott, N.J., Poret-Peterson, A.T., Browne, G.T. 2022. Random forest analysis reveals taxa predictive of Prunus replant disease in peach root microbiomes. PLOS ONE. 17(10). Article e0275587. https://doi.org/10.1371/journal.pone.0275587. Effects of whole-orchard recycling on nitrate leaching potential in
almond production systems
                                
                            - (Peer Reviewed Journal)
                                
                                Jahanzad, E., Brewer, K., Poret-Peterson, A.T., Culumber, M., Holtz, B.A., Gaudin, A. 2022. Effects of whole-orchard recycling on nitrate leaching potential in almond production systems. Journal of Environmental Quality. 51(5):941-951. https://doi.org/10.1002/jeq2.20385. Energetically informed niche models of hydrogenotrophs detected in serpentinized fluids of the Samail Ophiolite of Oman
                            - (Peer Reviewed Journal) An in vitro bioassay for evaluating the virulence of Pseudomonas savastonoi pv savastanoi isolates on olive
                                
                            - (Peer Reviewed Journal)
                                
                                Salman, M., McClean, A.E., Kluepfel, D.A. 2022. An in vitro bioassay for evaluating the virulence of Pseudomonas savastonoi pv savastanoi isolates on olive. Australasian Plant Disease Notes. 17:1. https://doi.org/10.1007/s13314-022-00448-0. Grapevine red blotch disease etiology and its impact on grapevine physiology and berry and wine composition
                                
                            - (Review Article)
                                
                                Rumbaugh, A.C., Sudarshana, M.R., Oberholster, A. 2021. Grapevine red blotch disease etiology and its impact on grapevine physiology and berry and wine composition. Horticulturae. 7(12). Article 552. https://doi.org/10.3390/horticulturae7120552. Characterization of soils conducive and non-conducive to Prunus replant disease
                                
                            - (Peer Reviewed Journal)
                                
                                Khan, A.R., Wicaksono, W., Ott, N.J., Poret-Peterson, A.T., Browne, G.T. 2021. Characterization of soils conducive and non-conducive to Prunus replant disease. PLoS ONE. 16(12). Article e0260394. https://doi.org/10.1371/journal.pone.0260394. A rapid in vitro phenotypic assay of walnut shoots for prescreening resistance of Phytophthora pini
                                
                            - (Peer Reviewed Journal)
                                
                                Zaini, P.A., Lee, S.H., Leslie, C.A., Walawage, S.L., Jiang, C., Browne, G.T., Dandekar, A.M., Kasuga, T. 2021. A rapid in vitro phenotypic assay of walnut shoots for prescreening resistance of Phytophthora pini. Plant Health Progress. 22(3):235-239. https://doi.org/10.1094/PHP-05-21-0078-FI. Co-located quantitative trait loci for resistance to Agrobacterium tumefaciens, Phytophthora cinnamomi, and P. pini in Juglans microcarpa × J. regia hybrid rootstock
                                
                            - (Peer Reviewed Journal)
                                
                                Ramasamy, R.K., Luo, M., Leslie, C.A., Velasco, D.M., Ott, N.J., McClean, A.E., Dandekar, A.M., Aradhya, M.K., Brown, P.J., Browne, G.T., Kluepfel, D.A., Westphal, A., Dvorak, J. 2021. Co-located quantitative trait loci for resistance to Agrobacterium tumefaciens, Phytophthora cinnamomi, and P. pini in Juglans microcarpa × J. regia hybrid rootstock. Horticulture Research. 8. Article 111. https://doi.org/10.1038/s41438-021-00546-7. Innate resistance and phosphite treatment affect both the pathogen’s and host’s transcriptomes in the Tanoak-Phytophthora ramorum pathosystem
                                
                            - (Peer Reviewed Journal)
                                
                                Kasuga, T., Hayden, K., Eyre, C., Croucher, P., Schechter, S., Wright, J., Garbelotto, M. 2021. Innate resistance and phosphite treatment affect both the pathogen’s and host’s transcriptomes in the Tanoak-Phytophthora ramorum pathosystem. The Journal of Fungi. 7(3). Article 198. https://doi.org/10.3390/jof7030198. Analysis of volatile profiles for tracking asymptomatic infections of Phytophthora ramorum and other pathogens in rhododendron
                                
                            - (Peer Reviewed Journal)
                                
                                Thompson, C., McCartney, M., Roubtsova, T., Kasuga, T., Ebeler, S., Davis, C., Bostock, R. 2021. Analysis of volatile profiles for tracking asymptomatic infections of Phytophthora ramorum and other pathogens in rhododendron. Phytopathology. https://doi.org/10.1094/PHYTO-10-20-0472-R. Flooding by California rivers results in walnut scion infections by species of Phytophthora
                                
                            - (Peer Reviewed Journal)
                                
                                Browne, G.T., Hasey, J.K., Ott, N.J., Forbes, H., Arnold, K., Milliron, L.K. 2021. Flooding by California rivers results in walnut scion infections by species of Phytophthora. Plant Health Progress. https://doi.org/10.1094/PHP-02-20-0011-RS. First report of grapevine leafroll-associated virus 3 in Vitis vinifera in North Carolina
                                
                            - (Peer Reviewed Journal)
                                
                                Hoffmann, M., Talton, W., Nita, M., Jones, T., Al Rwahnih, M., Sudarshana, M.R., Almeyda, C. 2020. First report of grapevine leafroll-associated virus 3 in Vitis vinifera in North Carolina. Journal of Plant Pathology. 103:385-386. https://doi.org/10.1007/S42161-020-00710-3. Impact of grapevine Red Blotch Disease on primary and secondary metabolites in ‘Cabernet Sauvignon’ grape tissues
                                
                            - (Peer Reviewed Journal)
                                
                                Pereira, G.E., Padhi, E.M., Sudarshana, M.R., Fialho, F.B., Plaza, C.M., Girardello, R.C., Tseng, D., Bruce, R.C., Erdmann, J.N., Slupsky, C.M., Oberholster, A. 2020. Impact of grapevine Red Blotch Disease on primary and secondary metabolites in ‘Cabernet Sauvignon’ grape tissues. Journal of Food Chemistry. 342. Article 128312. https://doi.org/10.1016/j.foodchem.2020.128312. Predicting stomatal closure and turgor loss in woody plants using predawn and midday water potential
                                
                            - (Peer Reviewed Journal)
                                
                                Knipfer, T., Bambach, N., Hernandez, M.I., Bartlett, M.K., Sinclair, G., Duong, F., Kluepfel, D.A., McElrone, A.J. 2020. Predicting stomatal closure and turgor loss in woody plants using predawn and midday water potential. Plant Physiology. 184(2):881-894. https://doi.org/10.1104/pp.20.00500. Asexual evolution and forest conditions drive genetic parallelism in Phytophthora ramorum
                                
                            - (Peer Reviewed Journal)
                                
                                Yuzon, J., Travadon, R., Malar C, M., Tripathy, S., Rank, N., Mehl, H., Rizzo, D., Cobb, R., Small, C., Tang, T., McCown, H., Garbelotto, M., Kasuga, T. 2020. Asexual evolution and forest conditions drive genetic parallelism in Phytophthora ramorum. Microorganisms. 8(6). https://doi.org/10.3390/microorganisms8060940. Has agricultural intensification impacted maize root traits and rhizosphere interactions related to organic N acquisition?
                                
                            - (Peer Reviewed Journal)
                                
                                Schmidt, J.E., Poret-Peterson, A.T., Lowry, C.J., Gaudin, A.C. 2020. Has agricultural intensification impacted maize root traits and rhizosphere interactions related to organic N acquisition?. AoB Plants. 12(4). https://doi.org/doi:10.1093/aobpla/plaa026. Independent whole-genome duplications define the architecture of the genomes of the devastating West African cacao black pod pathogen Phytophthora megakarya and its close relative Phytophthora palmivora
                                
                            - (Peer Reviewed Journal)
                                
                                Morales-Cruz, A., Ali, S.S., Minio, A., Figueroa-Balderas, R., Garcia, J.F., Kasuga, T., Puig, A.S., Marelli, J., Bailey, B.A., Cantu, D. 2020. Independent whole-genome duplications define the architecture of the genomes of the devastating West African cacao black pod pathogen Phytophthora megakarya and its close relative Phytophthora palmivora. G3, Genes/Genomes/Genetics. 10(6). https://doi.org/10.1534/g3.120.401014. Field evaluation of olive (Olea europaea) genotypes for resistance to Pseudomonas savastanoi pv savastanoi
                                
                            - (Peer Reviewed Journal)
                                
                                Salman, M., Kluepfel, D.A., Greenhut, R., Preece, J.E., Ferguson, L. 2020. Field evaluation of olive (Olea europaea) genotypes for resistance to Pseudomonas savastanoi pv savastanoi. Journal of Plant Pathology. 102:663-670. https://doi.org/10.1007/s42161-020-00549-8. First report of Phytophthora chlamydospora causing crown and root rot on almond in California
                                
                            - (Peer Reviewed Journal)
                                
                                Browne, G.T., Ott, N.J., Forbes, H., Yaghmour, M.A., Milliron, L.K. 2020. First report of Phytophthora chlamydospora causing crown and root rot on almond in California. Plant Disease. 104(7):2033. https://doi.org/10.1094/PDIS-10-19-2072-PDN. A comparative study on physiological responses to drought in walnut genotypes (RX1, Vlach, VX211) commercially available as rootstocks
                                
                            - (Peer Reviewed Journal)
                                
                                Knipfer, T., Grom, J., Reyes, C., Momayyezi, M., McElrone, A.J., Kluepfel, D.A. 2020. A comparative study on physiological responses to drought in walnut genotypes (RX1, Vlach, VX211) commercially available as rootstocks. Trees. 34(3):665-678. https://doi.org/10.1007/s00468-019-01947-x. Temporal responses of microbial communities to anaerobic soil disinfestation
                                
                            - (Peer Reviewed Journal)
                                
                                Poret-Peterson, A.T., Sayed	, N., Glyzewski, N., Forbes, H., Gonzalez-Orta, E., Kluepfel, D.A. 2019. Temporal responses of microbial communities to anaerobic soil disinfestation. Microbial Ecology. 80:191-201. https://doi.org/10.1007/s00248-019-01477-6. First report of grapevine red blotch virus, the causal agent of grapevine red blotch disease in vitis vinifera in North Carolina
                                
                            - (Peer Reviewed Journal)
                                
                                Hoffmann, M., Talton, W., Nita, M., Taylor, J., Al Rwahnih, M., Sudarshana, M.R., Almeyda, C. 2020. First report of grapevine red blotch virus, the causal agent of grapevine red blotch disease in vitis vinifera in North Carolina. Plant Disease. 104(4):1266-1266. https://doi.org/10.1094/PDIS-07-19-1539-PDN. Homoethanol production from cellobionate and glycerol using recombinant Klebsiella oxytoca strains
                            - (Peer Reviewed Journal) First report of Phytopythium helicoides causing root rot on peach rootstock in California
                                
                            - (Peer Reviewed Journal)
                                
                                Browne, G.T., Ott, N.J., Fichtner, E. 2019. First report of Phytopythium helicoides causing root rot on peach rootstock in California. Plant Disease. 103(11):2968. https://doi.org/10.1094/PDIS-09-18-1697-PDN. Haplotype-phased genome assembly of virulent Phytophthora ramorum isolate ND886 facilitated by long-read sequencing reveals effector polymorphisms and copy number variation
                                
                            - (Peer Reviewed Journal)
                                
                                Malar, M.C., Yuzon, J.D., Das, S., Das, A., Panda, A., Ghosh, S., Tyler, B.M., Kasuga, T., Tripathy, S. 2019. Haplotype-phased genome assembly of virulent Phytophthora ramorum isolate ND886 facilitated by long-read sequencing reveals effector polymorphisms and copy number variation. Molecular Plant-Microbe Interactions. 32(8):1047-1060. https://doi.org/10.1094/MPMI-08-18-0222-R. Updated assembly of Phytophthora ramorum pr102 isolate incorporating long reads from PacBio sequencing
                                
                            - (Peer Reviewed Journal)
                                
                                Malar C, M., Yuzon, J.D., Panda, A., Kasuga, T., Tripathy, S. 2019. Updated assembly of Phytophthora ramorum pr102 isolate incorporating long reads from PacBio sequencing. Molecular Plant-Microbe Interactions. 32(11):1472-1474. https://doi.org/10.1094/MPMI-05-19-0147-A. Molecular analyses identify hybridization-mediated nuclear evolution in newly discovered fungal hybrids
                                
                            - (Peer Reviewed Journal)
                                
                                Sillo, F., Gonthier, P., Lockman, B., Kasuga, T., Garbelotto, M. 2019. Molecular analyses identify hybridization-mediated nuclear evolution in newly discovered fungal hybrids. Ecology and Evolution. 00:1–18. https://doi.org/10.1002/ece3.5238. Sequencing a Juglans regia × J. microcarpa hybrid yields high-quality genome assemblies of parental species
                                
                            - (Peer Reviewed Journal)
                                
                                Zhu, T., Wang, L., You, F.M., Rodriguez, J., Deal, K., Chen, L., Li, J., Chakraborty, S., Balan, B., Jiang, C., Browne, P.J., Leslie, C., Aradhya, M.K., Dandekar, A., McGuire, P.E., Kluepfel, D.A., Dvorak, J., Ming-Chen, L. 2019. Sequencing a Juglans regia × J. microcarpa hybrid yields high-quality genome assemblies of parental species. Horticulture Research. 6:55. https://doi.org/10.1038/s41438-019-0139-1. A Grapevine red blotch virus vector: the three-cornered alfalfa hopper (3CAH), Spissistilus festinus, in Napa vineyards
                            - (Trade Journal)
                                
                                Preto, C.R., Sudarshana, M.R., Zalom, F.G. 2019. A Grapevine red blotch virus vector: the three-cornered alfalfa hopper (3CAH), Spissistilus festinus, in Napa vineyards. American Vineyard Magazine. 28:14-18. Seasonal dynamics of Spissistilus festinus (Hemiptera: Membracidae) in a Californian vineyard
                                
                            - (Peer Reviewed Journal)
                                
                                Preto, C.R., Bahder, B.W., Bick, E.N., Sudarshana, M.R., Zalom, F.G. 2019. Seasonal dynamics of Spissistilus festinus (Hemiptera: Membracidae) in a Californian vineyard. Journal of Economic Entomology. 112(3):1138-1144. https://doi.org/10.1093/jee/toz022. Spatial associations of vines infected with grapevine red blotch virus in Oregon vineyards
                                
                            - (Peer Reviewed Journal)
                                
                                Dalton, D.T., Hilton, R.J., Kaiser, C., Daane, K.M., Sudarshana, M.R., Vo, J., Zalom, F., Buser, J.Z., Walton, V.M. 2019. Spatial associations of vines infected with grapevine red blotch virus in Oregon vineyards. Plant Disease. 103(7):1507-1514. https://doi.org/10.1094/PDIS-08-18-1306-RE. Shifts in soil bacterial communities as a function of carbon source used during anaerobic soil disinfestation
                                
                            - (Peer Reviewed Journal)
                                
                                Poret-Peterson, A.T., Albu, S., McClean, A.E., Kluepfel, D.A. 2019. Shifts in soil bacterial communities as a function of carbon source used during anaerobic soil disinfestation. Frontiers in Environmental Science. 6:160. https://doi.org/10.3389/FENVS.2018.00160. Homoethanol production from Glycerol and Gluconate using recombinant Klebsiella Oxytoca strains
                                
                            - (Peer Reviewed Journal)
                                
                                Tao, W., Wang, Y., Walters, E., Lin, H., Li, S., He, H., Kasuga, T., Zhiliang, F. 2019. Homoethanol production from glycerol and gluconate using recombinant Klebsiella oxytoca strains. Applied and Environmental Microbiology. 85:e02122-18. https://doi.org/10.1128/AEM.02122-18. Characterization of grapevine leafroll-associated virus 3 genetic variants and application towards RT-qPCR assay design
                                
                            - (Peer Reviewed Journal)
                                
                                Diaz-Lara, A., Klaassen, V., Stevens, K., Sudarshana, M.R., Rowhani, A., Maree, H.J., Chooi, K.M., Blouin, A.G., Habili, N., Song, Y., Aram, K., Arnold, K., Cooper, M.L., Wunderlich, L., Battany, M.C., Bettiga, L.J., Smith, R.J., Bester, R., Xiao, H., Meng, B., Preece, J.E., Golino, D., Alrwahnih, M. 2018. Characterization of grapevine leafroll-associated virus 3 genetic variants and application towards RT-qPCR assay design. PLoS One. 13(12):e0208862. https://doi.org/10.1371/journal.pone.0208862. Vitis vinifera (Vitales: Vitaceae) as a reproductive host of Spissistilus festinus (Hemiptera: Membracidae)
                                
                            - (Peer Reviewed Journal)
                                
                                Preto, C.R., Sudarshana, M.R., Bollinger, M.L., Zalom, F.G. 2018. Vitis vinifera (Vitales: Vitaceae) as a reproductive host of Spissistilus festinus (Hemiptera: Membracidae). Journal of Insect Science. 18(6):1-7. https://doi.org/10.1093/jisesa/iey129. Anaerobic soil disinfestation as an alternative to soil fumigation for management of Prunus replant disease: effects on tree growth and yield
                                
                            - (Peer Reviewed Journal)
                                
                                Browne, G.T., Ott, N.J., Poret-Peterson, A.T., Lampinen, B.D., Metcalf, S.G., Yaghmour, M.A., Holtz, B.A., Culumber, M., Brar, G., Doll, D.A. 2018. Anaerobic soil disinfestation as an alternative to soil fumigation for management of Prunus replant disease: effects on tree growth and yield. Acta Horticulturae. 1219:287-294. https://doi.org/10.17660/ActaHortic.2018.1219.44. Feeding and reproductive hosts of Spissistilus festinus (Say) (Hemiptera: Membracidae) found in Californian vineyards
                                
                            - (Peer Reviewed Journal)
                                
                                Preto, C.R., Sudarshana, M.R., Zalom, F.G. 2018. Feeding and reproductive hosts of Spissistilus festinus (Say) (Hemiptera: Membracidae) found in Californian vineyards. Journal of Economic Entomology. 111(6), 2531-2535. https://doi.org/10.1093/jee/toy236. Genomic variation among and within six Juglans species
                                
                            - (Peer Reviewed Journal)
                                
                                Stevens, K.A., Woeste, K., Chakraborty, S., Crepeau, M.W., Leslie, C.A., Martinez-Garcia, P.J., Puiu, D., Romero-Severson, J., Coggeshall, M., Dandekar, A.M., Kluepfel, D.A., Neale, D.B., Salzberg, S.L., Langley, C.H. 2018. Genomic variation among and within six Juglans species. G3, Genes/Genomes/Genetics. 8(7):2153-2165. https://doi.org/10.1534/g3.118.200030. Characterization of phenotypic variation and genome aberrations observed among Phytophthora ramorum isolates from diverse hosts
                                
                            - (Peer Reviewed Journal)
                                
                                Elliot, M., Yuzon, J., Malar, M.C., Tripathy, S., Bui, M., Chastagner, G.A., Coats, K., Rizzo, D.M., Garbelotto, M., Kasuga, T. 2018. Characterization of phenotypic variation and genome aberrations observed among Phytophthora ramorum isolates from diverse hosts. BMC Genomics. 19:320. https://doi.org/10.1186/s12864-018-4709-7. Draft genome sequence of agrobacterium tumefaciens biovar 1 strain 186, isolated from walnut
                                
                            - (Peer Reviewed Journal)
                                
                                Poret-Peterson, A.T., Bhatnagar, S., McClean, A.E., Kluepfel, D.A. 2017. Draft genome sequence of agrobacterium tumefaciens biovar 1 strain 186, isolated from walnut. Genome Announcements. 5(46):e01232-17. https://doi.org/10.1128/genomeA.01232-17. Investigating the spread and effect of Grapevine red blotch virus in California-grown Zinfandel
                            - (Proceedings)
                                
                                Wunderlich, L.R., Bollinger, M.L., Castillo, M.N., Preto, C.R., Bahder, B.W., Zalom, F.G., Sudarshana, M.R. 2017. Investigating the spread and effect of Grapevine red blotch virus in California-grown Zinfandel. In: Proceedings of XXth Group of International Experts of Vitivinicultural Systems for CoOperation(GiESCO) International Meeting, November 5-10, Mendoza, Argentina. Implicated vectors and spread of grapevine red blotch-associated virus in Oregon vineyards
                            - (Abstract Only)
                                
                                Dalton, D.T., Walton, V.M., Hilton, R.J., Sudarshana, M.R. 2017. Implicated vectors and spread of grapevine red blotch-associated virus in Oregon vineyards. Oregon Wine Research Institute Grape Day, April 6, 2017, Corvallis, Oregon. Red blotch in Oregon
                            - (Abstract Only)
                                
                                Walton, V.M., Dalton, D.T., Hilton, R.J., Sudarshana, M.R. 2017. Red blotch in Oregon. Oregon Wine Research Institute Grape Day, April 6, 2017, Corvallis, Oregon.


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