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United States Department of Agriculture

Agricultural Research Service

Research Project: GENOME-BASED STRATEGIES FOR DETECTION AND IDENTIFICATION OF PLANT PATHOGENIC PHYTOPLASMAS AND SPIROPLASMAS Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)

'Candidatus Phytoplasmas pruni', a novel taxon associated with X-disease of stone fruits, Prunus spp.: multilocus characterization based on 16S rRNA, secY, and ribosomal protein genes - (Peer Reviewed Journal)
Davis, R.E., Zhao, Y., Dally, E.L., Lee, I., Jomantiene, R., Douglas, S.M. 2013. 'Candidatus Phytoplasmas pruni', a novel taxon associated with X-disease of stone fruits, Prunus spp.: multilocus characterization based on 16S rRNA, secY, and ribosomal protein genes. International Journal of Systematic and Evolutionary Microbiology. 63:766-776.
Candidatus Phytoplasma malaysianum, a novel taxon associated with virescence and phyllody of Madagascar periwinkle (Catharanthus roseus) - (Peer Reviewed Journal)
Nejat, N., Vadamalai, G., Davis, R.E., Harrison, N.A., Sijam, K., Dickinson, M., Abdullah, S., Zhao, Y. 2012. Candidatus Phytoplasma malaysianum, a novel taxon associated with virescence and phyllody of Madagascar periwinkle (Catharanthus roseus). International Journal of Systematic and Evolutionary Microbiology. 63:540-548.
Salicylic acid-mediated elicitation of tomato defense against infection by potato purple top phytoplasma - (Peer Reviewed Journal)
Wu, W., Ding, Y., Wei, W., Davis, R.E., Lee, I., Hammond, R., Zhao, Y. 2012. Salicylic acid-mediated elicitation of tomato defense against infection by potato purple top phytoplasma. Annals of Applied Biology. 161:36-45.
Differentiation and classification of phytoplasmas in the pigeon pea witches'-broom group (16SrIX): an update based on multiple gene sequence analysis - (Peer Reviewed Journal)
Lee, I., Bottner-Parker, K.D., Zhao, Y., Bertaccini, A., Davis, R.E. 2012. Differentiation and classification of phytoplasmas in the pigeon pea witches'-broom group (16SrIX): an update based on multiple gene sequence analysis. International Journal of Systematic and Evolutionary Microbiology. 62:2279-2285.
Identification of two new phylogenetically distant phytoplasmas from Senna surattensis plants exhibiting stem fasciation and shoot proliferation symptoms - (Peer Reviewed Journal)
Wu, W., Cai, H., Wei, W., Davis, R.E., Lee, I., Chen, H., Zhao, Y. 2012. Identification of two new phylogenetically distant phytoplasmas from Senna surattensis plants exhibiting stem fasciation and shoot proliferation symptoms. Annals of Applied Biology. 160:25-34.
The iPhyClassifier, an interactive online tool for phytoplasma classification and taxonomic assignment - (Book / Chapter)
Zhao, Y., Wei, W., Lee, I., Shao, J.Y., Suo, X., Davis, R.E. 2012. The iPhyClassifier, an interactive online tool for phytoplasma classification and taxonomic assignment. Methods in Molecular Biology. 938:329-338.
Nested PCR and RFLP analysis based on the 16S rRNA gene - (Book / Chapter)
Duduk, B., Paltrinieri, S., Lee, I., Bertaccini, A. 2012. Nested PCR and RFLP analysis based on the 16S rRNA gene. In: Dickinson, M., Hodgetts, J., editors. Springer Protocols: Methods in Molecular Biology. New York, NY: Humana Press. p. 159-172.
PCR and RFLP analyses based on the ribosomal protein operon - (Book / Chapter)
Martini, M., Lee, I. 2012. PCR and RFLP analyses based on the ribosomal protein operon. In: Dickinson, M., Hodgetts, J., editors. Springer Protocols: Methods in Molecular Biology. New York, NY: Humana Press. p. 173-188.
'Candidatus Phytoplasma sudamericanum' a novel taxon from diseased passion fruit (Passiflora edulis f. flavicarpa Deg.) - (Peer Reviewed Journal)
Davis, R.E., Zhao, Y., Dally, E.L., Jomantiene, R., Lee, I., Wei, W., Kitajima, E. 2012. 'Candidatus Phytoplasma sudamericanum' a novel taxon from diseased passion fruit (Passiflora edulis f. flavicarpa Deg.). International Journal of Systematic and Evolutionary Microbiology. 62:984-989.
A new phytoplasma associated with little leaf disease in azalea: multilocus sequence characterization reveals a distinct lineage within the aster yellows phytoplasma group - (Peer Reviewed Journal)
Wei, W., Cai, H., Jiang, Y., Lee, I., Davis, R.E., Ding, Y., Yuan, E., Chen, H., Zhao, Y. 2011. A new phytoplasma associated with little leaf disease in azalea: multilocus sequence characterization reveals a distinct lineage within the aster yellows phytoplasma group. Annals of Applied Biology. 158:318-330.
"Candidatus phytoplasma costaricanum" a new phytoplasma associated with a newly emerging disease in soybean in Costa Rica - (Peer Reviewed Journal)
Lee, I., Bottner-Parker, K.D., Zhao, Y., Villalobos, W., Loreira, L. 2011. "Candidatus phytoplasma costaricanum" a new phytoplasma associated with a newly emerging disease in soybean in Costa Rica. International Journal of Systematic and Evolutionary Microbiology. 61:2822-2826.
Phytoplasma infecting cherry and lilac represent two distinct lineages having close evolutionary affinities with clover phyllody phytoplasma - (Peer Reviewed Journal)
Jomantiene, R., Zhao, Y., Lee, I., Davis, R.E. 2011. Phytoplasma infecting cherry and lilac represent two distinct lineages having close evolutionary affinities with clover phyllody phytoplasma. European Journal of Plant Pathology. 130:97-107.
Onion is a host for two phytoplasma lineages, subgroups 16SrI-A and 16SrI-L, in Lithuania: a HinfI site revealed a SNP marking divergent branches of evolution - (Peer Reviewed Journal)
Jomantiene, R., Davis, R.E., Lee, I., Zhao, Y., Bottner-Parker, K.D., Valiunas, D., Petkauskaite, R. 2010. Onion is a host for two phytoplasma lineages, subgroups 16SrI-A and 16SrI-L, in Lithuania: a HinfI site revealed a SNP marking divergent branches of evolution. Journal of Plant Pathology. 92:461-470.
Phylogenetic analysis and delineation of phytoplasmas based on the secY gene     Reprint Icon - (Peer Reviewed Journal)
Lee, I., Bottner-Parker, K.D., Zhao, Y., Davis, R.E., Harrison, N. 2010. Phylogenetic analysis and delineation of phytoplasmas based on the secY gene. International Journal of Systematic and Evolutionary Microbiology. 60:2887-2897.
First report of a new subgroup 16SrIX-E, 'Candidatus Phytoplasma phoenicium'-related, phytoplasma associated with juniper witches' broom disease in Oregon     Reprint Icon - (Peer Reviewed Journal)
Davis, R.E., Dally, E.L., Zhao, Y., Lee, I., Jomantiene, R., Detweiler, A.J., Putnam, M.L. 2010. First report of a new subgroup 16SrIX-E, 'Candidatus Phytoplasma phoenicium'-related, phytoplasma associated with juniper witches' broom disease in Oregon. Plant Pathology. 20:35.
Recent advances in 16S rRNA gene-based phytoplasma differentiation, classification and taxonomy - (Book / Chapter)
Zhao, Y., Wei, W., Davis, R.E., Lee, I. 2010. Recent advances in 16S rRNA gene-based phytoplasma differentiation, classification and taxonomy. In: Weintraub, P., Jones, P., editors. Phytoplasmas: Genomes, Plant Hosts and Vector. Wallingford, UK: CABI Publishing. p. 64-92.
Prospect of multiple gene-based systems for differentiation and classification of phytoplasmas - (Book / Chapter)
Lee, I., Zhao, Y., Davis, R.E. 2010. Prospect of multiple gene-based systems for differentiation and classification of phytoplasmas. In: Weintraub, P., Jones, P., editors. Phytoplasmas: Genomes, Plant Hosts and Vectors. Wallingford, UK: CABI Publishing. p. 51-63.
Multiplex real-time PCR for detection, identification and quantification of "Candidatus Liberibacter solanacearum" in potato plants with zebra chip - (Peer Reviewed Journal)
Li, W.N., Abad, J.A., French-Monar, R.D., Rascoe, J., Wen, A., Gudmestad, G., Secor, G.A., Lee, I., Levy, L. 2009. Multiplex real-time PCR for detection, identification and quantification of "Candidatus Liberibacter solanacearum" in potato plants with zebra chip. Phytopathology. 78:59-65.
First Report of a New Phytoplasma Subgroup, 16SrIII-S, Associated with Decline Disease Affecting Sweet and Sour Cherry Trees     Reprint Icon - (Peer Reviewed Journal)
Valiunas, D., Jomantiene, R., Ivanauskas, A., Abraitis, R., Staniene, G., Zhao, Y., Davis, R.E. 2009. First Report of a New Phytoplasma Subgroup, 16SrIII-S, Associated with Decline Disease Affecting Sweet and Sour Cherry Trees. Plant Disease. 93:550.
An emerging potato purple top disease caused by a new 16SrIII group phytoplasma in Montana - (Peer Reviewed Journal)
Lee, I., Bottner, K.D., Sun, M. 2009. An emerging potato purple top disease caused by a new 16SrIII group phytoplasma in Montana. Plant Disease. 93:574-583.
Association of "Candidatus Liberibacter solanacearum" with zebra chip disease of potato established by graft and psyllid transmission, electron microscopy and PCR     Reprint Icon - (Peer Reviewed Journal)
Secor, G.A., Rivera, V.V., Abad, J.A., Lee, I., Clover, G.R., Liefting, L.W., Li, X., De Boer, S.H. 2009. Association of "Candidatus Liberibacter solanacearum" with zebra chip disease of potato established by graft and psyllid transmission, electron microscopy and PCR. Plant Disease. 93:574-583.
Construction of an interactive online phytoplasma classification tool, iPhyClassifier, and its application in analysis of the peach X-disease phytoplasma group (16SrIII)     Reprint Icon - (Peer Reviewed Journal)
Zhao, Y., Wei, W., Lee, I., Shao, J.Y., Suo, X., Davis, R.E. 2009. Construction of an interactive online phytoplasma classification tool, iPhyClassifier, and its application in analysis of the peach X-disease phytoplasma group (16SrIII). International Journal of Systematic and Evolutionary Microbiology. 59(10):2582-2593.
'Candidatus Phytoplasma tamaricis', a novel taxon discovered in witches'-broom diseased salt cedar (Tamarix chinensis Lour.)     Reprint Icon - (Peer Reviewed Journal)
Zhao, Y., Sun, Q., Wei, W., Davis, R.E., Wu, W., Liu, Q. 2009. 'Candidatus Phytoplasma tamaricis', a novel taxon discovered in witches'-broom diseased salt cedar (Tamarix chinensis Lour.). International Journal of Systematic and Evolutionary Microbiology. 59:2496-2504.
First report of new phytoplasma diseases associated with soybean, sweet pepper, and passion fruit in Costa Rica - (Peer Reviewed Journal)
Villalobos, W., Moreira, L., Rivera, C., Lee, I. 2009. First report of new phytoplasma diseases associated with soybean, sweet pepper, and passion fruit in Costa Rica. Plant Disease. 93:201.
New 16Sr subgroups and distinct SNP lineages among grapevine Bois noir phytoplasma populations - (Peer Reviewed Journal)
Quaglino, F., Zhao, Y., Bianco, P.A., Wei, W., Casati, P., Durante, G., Davis, R.E. 2009. New 16Sr subgroups and distinct SNP lineages among grapevine Bois noir phytoplasma populations. Annals of Applied Biology. 154:279-289.
Identification of Phytoplasma Species Associated With Potato Diseases in Russia - (Proceedings)
Girsova, N., Bottner, K.D., Mozhaeva, K.A., Kastalyeva, T.B., Owens, R.A., Lee, I. 2008. Identification of Phytoplasma Species Associated With Potato Diseases in Russia. International Symposium on Crop Protection. vol. 73(2). pp. 331-333.
Stable expression of a bacterial GUS gene in vegetatively propagated transgenic pear lines - (Peer Reviewed Journal)
Sun, Q., Sun, H., Zhao, Y., Hammond, R., Davis, R.E. 2008. Stable expression of a bacterial GUS gene in vegetatively propagated transgenic pear lines. PLANT PHYSIOLOGY COMMUNICATIONS. 44:465-468.
Ancient, recurrent phage attacks and recombination events shaped dynamic sequence-variable mosaic structures at the root of phytoplasma genome evolution - (Peer Reviewed Journal)
Wei, W., Davis, R.E., Jomantiene, R., Zhao, Y. 2008. Ancient, recurrent phage attacks and recombination events shaped dynamic sequence-variable mosaic structures at the root of phytoplasma genome evolution. Proceedings of the National Academy of Sciences. 105:11827-11832.
Automated RFLP pattern comparison and similarity coefficient calculation for rapid delineation of new and distinct phytoplasma 16S rDNA subgroup lineages - (Peer Reviewed Journal)
Wei, W., Lee, I., Davis, R.E., Suo, X., Zhao, Y. 2008. Automated RFLP pattern comparison and similarity coefficient calculation for rapid delineation of new and distinct phytoplasma 16S rDNA subgroup lineages. International Journal of Systematic and Evolutionary Microbiology. 58:2368-2377.
Transgene expression in pear (Pyrus communis L.) driven by a phloem-specific promoter - (Peer Reviewed Journal)
Sun, Q., Sun, H., Zhao, Y., Hammond, R., Davis, R.E. 2008. Transgene expression in pear (Pyrus communis L.) driven by a phloem-specific promoter. Acta Horticulturae Sinica. 35:487-492.
Molecular detection and identification of group 16SrI and 16SrXII phytoplasmas associated with diseased potatoes in Russia - (Research Notes)
Girsova, N., Bottner, K.D., Mozhaeva, K.A., Kastalyeva, T.B., Owens, R.A., Lee, I. 2008. Molecular detection and identification of group 16SrI and 16SrXII phytoplasmas associated with diseased potatoes in Russia. Plant Disease. 92:654.
First report of purple coneflower phyllody associated with a 16SrI-B phytoplasma in Maryland - (Research Notes)
Lee, I., Bottner, K.D., Dally, E.L., Davis, R.E. 2008. First report of purple coneflower phyllody associated with a 16SrI-B phytoplasma in Maryland. Plant Disease. 92:654.
Genetic diversity among phytoplasmas infecting Opuntia: virtual RFLP analysis identifies new subgroups in the peanut witches'-broom phytoplasma group - (Peer Reviewed Journal)
Cai, H., Wei, W., Davis, R.E., Chen, H., Zhao, Y. 2008. Genetic diversity among phytoplasmas infecting Opuntia: virtual RFLP analysis identifies new subgroups in the peanut witches'-broom phytoplasma group. International Journal of Systematic and Evolutionary Microbiology. 58:1448-1457.
Identification of viral and phytoplasmal agents responsible for diseases affecting plants of Gaillardia Foug. in Lithuania - (Peer Reviewed Journal)
Valiunas, D., Samuitiene, M., Navalinskiene, M., Davis, R.E. 2008. Identification of viral and phytoplasmal agents responsible for diseases affecting plants of Gaillardia Foug. in Lithuania. Agronomy Journal. 6:109-111.
Virtual RFLP analysis of 16S rDNA sequences identifies new subgroups in the clover proliferation phytoplasma group - (Abstract Only)
Wei, W., Lee, I., Davis, R.E., Suo, X., Zhao, Y. 2007. Virtual RFLP analysis of 16S rDNA sequences identifies new subgroups in the clover proliferation phytoplasma group. Bulletin of Insectology. 60:349:350.
Prospects of DNA-based Systems for Differentiation and Classification of Phytoplasmas - (Review Article)
Lee, I., Zhao, Y., Davis, R.E., Wei, W., Martini, M. 2007. Prospects of DNA-based Systems for Differentiation and Classification of Phytoplasmas. Bulletin of Insectology. 60:239-244.
Dynamic structures in phytoplasma genomes: sequence variable mosaics (SVMs) of clustered genes - (Abstract Only)
Davis, R.E., Jomantiene, R., Zhao, Y. 2007. Dynamic structures in phytoplasma genomes: sequence variable mosaics (SVMs) of clustered genes. Bulletin of Insectology. LX(2):119-120.
Molecular identification of a new phytoplasma strain associated with the first observation of jujube witches'-broom disease in northeastern China - (Peer Reviewed Journal)
Wei, W., Hua, J., Yang, Y., Youfu, W., Davis, R.E., Zhao, Y. 2007. Molecular identification of a new phytoplasma strain associated with the first observation of jujube witches'-broom disease in northeastern China. Plant Disease. 91:1364.
Last Modified: 8/1/2014
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