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United States Department of Agriculture

Agricultural Research Service

Related Topics

Jonathan Shao
Molecular Plant Pathology Laboratory
Bioinformaticist

Phone: (301) 504-6290
Fax: (301) 504-5449
Room 118

10300 BALTIMORE AVENUE
BLDG 004 BARC-WEST
BELTSVILLE , MD 20705


Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
Transcriptome analysis of sweet orange trees infected with ‘Candidatus Liberibacter asiaticus’ and two strains of citrus tristeza virus -
Fu, S., Shao, J.Y., Zhou, C., Hartung, J.S. 2016. Transcriptome analysis of sweet orange trees infected with ‘Candidatus Liberibacter asiaticus’ and two strains of citrus tristeza virus. BMC Genomics. 17:349.
Gene expression profiling in viable but not culturable (VBNC) cells of Pseudomonas syringae pv syringae -
Postnikova, O., Shao, J.Y., Mock, N.M., Baker, C.J., Nemchinov, L.G. 2015. Gene expression profiling in viable but not culturable (VBNC) cells of Pseudomonas syringae pv syringae. Frontiers in Microbiology. 6:1419.
Citrus blight research -
Schneider, W.L., Roy, A., Hartung, J.S., Shao, J.Y., Brlansky, R. 2015. Citrus blight research. Citrus Industry. page 12-14.
Complete genome sequence of Spiroplasma turonicum, a parasite of horse fly, Haematopota sp. (Diptera: Tabanidae) -
Davis, R.E., Shao, J.Y., Zhao, Y., Gasparich, G., Gaynor, B., Donofrio, N. 2015. Complete genome sequence of Spiroplasma turonicum, a parasite of horse fly, Haematopota sp. (Diptera: Tabanidae). Genome Announcements. 3(6):e01367-15.
Complete genome sequence of Spiroplasma kunkelii strain CR2-3x, causal agent of corn stunt disease in Zea mays L. -
Davis, R.E., Shao, J.Y., Dally, E.L., Zhao, Y., Gasparich, G.E., Gaynor, B.J., Athey, J.C., Harrison, N.A., Donofrio, N. 2015. Complete genome sequence of Spiroplasma kunkelii strain CR2-3x, causal agent of corn stunt disease in Zea mays L. Genome Announcements. 3(5):e01216-15.
Draft genome sequence of ‘Candidatus Phytoplasma pruni’ strain CX, a plant pathogenic bacterium -
Lee, I., Shao, J.Y., Bottner-Parker, K.D., Gundersen, D.E., Zhao, Y., Davis, R.E. 2015. Draft genome sequence of ‘Candidatus Phytoplasma pruni’ strain CX, a plant pathogenic bacterium. Genome Announcements. 3(5):e01117-15.
Combination of RNAseq and SNP nanofluidic array reveals the center of genetic diversity of cacao pathogen Moniliophthora roreri in the upper Magdalena Valley of Colombia and its clonality -
Ali, S., Shao, J.Y., Strem, M.D., Phillips-Mora, W., Zhang, D., Meinhardt, L.W., Bailey, B.A. 2015. Combination of RNAseq and SNP nanofluidic array reveals the center of genetic diversity of cacao pathogen Moniliophthora roreri in the upper Magdalena Valley of Colombia and its clonality. Frontiers in Microbiology. doi: 10.3389/fmicb.2015.00850.
Specific detection and identification of mulberry-infecting strains of Xylella fastidiosa by polymerase chain reaction -
Guan, W., Shao, J.Y., Davis, R.E., Zhao, T., Huang, Q. 2015. Specific detection and identification of mulberry-infecting strains of Xylella fastidiosa by polymerase chain reaction. PLoS One. DOI: 10.1371/journal.pone.0129330.
History and diversity of Citrus leprosis virus recorded in herbarium specimens Reprint Icon -
Hartung, J.S., Roy, A., Fu, S., Shao, J.Y., Schneider, W.L., Brlansky, R.H. 2015. History and diversity of Citrus leprosis virus recorded in herbarium specimens. Phytopathology. 105:1277-1284.
Role bending: complex relationships between viruses, hosts and vectors related to citrus leprosis, an emerging disease Reprint Icon -
Roy, A., Hartung, J.S., Schneider, W.L., Shao, J.Y., Leon, G.M., Melzer, M.J., Beard, J.J., Otero-Colina, G., Bauchan, G.R., Ochoa, R., Brlansky, R.H. 2015. Role bending: complex relationships between viruses, hosts and vectors related to citrus leprosis, an emerging disease. Phytopathology. DOI: 10.1094/PHYTO-12-14-0375-FI.
Complete genome sequence of the alfalfa latent virus -
Nemchinov, L.G., Shao, J.Y., Postnikova, O.A. 2015. Complete genome sequence of the alfalfa latent virus. Genome Announcements. 3(2):e00250-15.
Transcriptome analysis of resistant and susceptible alfalfa cultivars infected with root-knot nematode Meloidogyne incognita -
Postnikova, O., Hult, M.N., Shao, J.Y., Skantar, A.M., Nemchinov, L.G. 2015. Transcriptome analysis of resistant and susceptible alfalfa cultivars infected with root-knot nematode Meloidogyne incognita. PLoS One. 10(3):e0123157.
Identification and molecular characterization of nuclear Citrus leprosis virus, an unassigned Dichorhavirus genus member associated with citrus leprosis disease in Mexico -
Roy, A., Stone, A.L., Shao, J.Y., Colina, G., Wei, G., Choudary, N., Achor, D., Nakhla, M., Levy, L., Hartung, J.S., Schneider, W.L., Brlansky, R. 2015. Identification and molecular characterization of nuclear Citrus leprosis virus, an unassigned Dichorhavirus genus member associated with citrus leprosis disease in Mexico. Virus Research. 105:564-575.
A multiplex PCR assay to detect and differentiate select agent strains of Ralstonia solanacearum -
Stulberg, M.J., Shao, J.Y., Huang, Q. 2014. A multiplex PCR assay to detect and differentiate select agent strains of Ralstonia solanacearum. Applied and Environmental Microbiology. 99:333-341.
Genome sequence of a Xylella fastidiosa strain causing sycamore leaf scorch disease in Virginia -
Guan, W., Shao, J.Y., Davis, R.E., Zhao, T., Huang, Q. 2014. Genome sequence of a Xylella fastidiosa strain causing sycamore leaf scorch disease in Virginia. Genome Announcements. 2(4):e00773-14.
Differential gene expression by Moniliophthora roreri while overcoming cacao tolerance in the field -
Bailey, B.A., Melnick, R.L., Strem, M.D., Crozier, J., Shao, J.Y., Sicher, Jr., R.C., Ali, S.S., Zhang, D., Philips-Mora, W., Meinhardt, L.W. 2014. Differential gene expression by Moniliophthora roreri while overcoming cacao tolerance in the field. Molecular Plant Pathology. DOI:10.1111/mpp.12134.
Successful pod infections by Moniliophthora roreri result in differential Theobroma cacao gene expression depending on the clone’s level of tolerance -
Ali, S., Melnick, R., Strem, M.D., Crozier, J., Shao, J.Y., Sicher Jr, R.C., Zhang, D., Philips-Mora, W., Meinhardt, L.W., Bailey, B.A. 2014. Successful pod infections by Moniliophthora roreri result in differential Theobroma cacao gene expression depending on the clone’s level of tolerance. Molecular Plant Pathology. DOI:10.1111/mpp.12126.
Genome and secretome analysis of the hemibiotrophic fungal pathogen, Moniliophthora roreri, which causes frosty pod rot disease of cacao: mechanisms of the biotrophic and necrotrophic phases -
Meinhardt, L.W., Thomazella, D.P., Teixeira, P.J., Costa, G.G., Carazzolle, M., Schuster, S., Carlson, J.E., Guiltinan, M.J., Mieczkowski, P., Crow, J., Farmer, A., Ramaraj, T., Crosier, J., Davis, R.E., Shao, J.Y., Pereira, G.A., Bailey, B.A. 2014. Genome and secretome analysis of the hemibiotrophic fungal pathogen, Moniliophthora roreri, which causes frosty pod rot disease of cacao: mechanisms of the biotrophic and necrotrophic phases. Biomed Central (BMC) Genomics. 15:164.
In silico identification of transcription factors in medicago sativa using available transcriptomic resources -
Postnikova, O., Shao, J.Y., Nemchinov, L.G. 2014. In silico identification of transcription factors in medicago sativa using available transcriptomic resources. Molecular Genetics and Genomics. 289:457-468.
A population of endogenous pararetrovirus genomes in carrizo citrange Reprint Icon -
Roy, A., Shao, J.Y., Schneider, W.L., Hartung, J.S., Brlansky, R.H. 2013. A population of endogenous pararetrovirus genomes in carrizo citrange. Genome Announcements. 2(1):e01063-13.
Phytoplasma genomes: Evolution through mutually complimentary mechanisms, gene loss and horizontal acquisition -
Genome assembly of citurs leprosis virus nuclear type reveals a close association with orchid fleck virus Reprint Icon -
Roy, A., Choudary, N., Colina, G., Stone, A.L., Shao, J.Y., Levy, L., Nakhla, M., Hollingsworth, C., Hartung, J.S., Schneider, W.L., Brlansky, R. 2013. Genome assembly of citurs leprosis virus nuclear type reveals a close association with orchid fleck virus. Genome Announcements. doi:10.1128/genomeA.00519-13.
A case study on discovery of novel Citrus leprosis virus cytoplasmic type 2 utilizing small RNA libraries by next generation sequencing and bioinformatic analyses Reprint Icon -
Roy, A., Shao, J.Y., Hartung, J.S., Schneider, W.L., Brlansky, R. 2013. A case study on discovery of novel Citrus leprosis virus cytoplasmic type 2 utilizing small RNA libraries by next generation sequencing and bioinformatic analyses. Journal of Data Mining in Genomics & Proteomics. 4:129. doi: 10.4172/2153-0602.1000129.
Analysis of alfalfa root transcriptome in response to salinity stress -
Postnikova, O.A., Shao, J.Y., Nemchinov, L.G. 2013. Analysis of alfalfa root transcriptome in response to salinity stress. Plant And Cell Physiology. 54(7):1041-1055.
A novel emerging virus with indistinguishable symptoms and genome structure similar to citrus leprosis virus C identified by small RNA deep sequencing Reprint Icon -
Roy, A., Choudhary, N., Govindarajulu, A., Shao, J.Y., Hartung, J.S., Brlansky, R. 2012. A novel emerging virus with indistinguishable symptoms and genome structure similar to citrus leprosis virus C identified by small RNA deep sequencing. Phytopathology. 103:488-500.
A TaqMan-based real time PCR assay for specific detection and quantification of Xylella fastidiosa strains causing bacterial leaf scorch in oleander -
Guan, W., Shao, J.Y., Singh, R., Davis, R.E., Huang, Q. 2012. A TaqMan-based real time PCR assay for specific detection and quantification of Xylella fastidiosa strains causing bacterial leaf scorch in oleander. Current Microbiology. 92:108-112.
'Ca. Liberibacter asiaticus' proteins orthologous with pSymA-encoded proteins of Sinorhizobium meliloti: hypothetical roles in plant host interation -
Kuykendall, L.D., Shao, J.Y., Hartung, J.S. 2012. 'Ca. Liberibacter asiaticus' proteins orthologous with pSymA-encoded proteins of Sinorhizobium meliloti: hypothetical roles in plant host interation. PLoS One. 7:e38725.
Ca. Liberibacter asiaticus genes orthologous with pSymA-borne genes of Sinorhizobium meliloti: suggested roles in eukaryotic host interactions Reprint Icon -
Hartung, J.S., Shao, J.Y., Kuykendall, L.D. 2012. Ca. Liberibacter asiaticus genes orthologous with pSymA-borne genes of Sinorhizobium meliloti: suggested roles in eukaryotic host interactions. American Phytopathological Society Potomac Division Meeting. 102(6):S3-3.
Global analysis of tomato gene expression during potato spindle tuber viroid infection reveals a complex array of changes affecting hormone signaling -
Owens, R.A., Tech, K.B., Shao, J.Y., Sano, T., Baker, C.J. 2012. Global analysis of tomato gene expression during potato spindle tuber viroid infection reveals a complex array of changes affecting hormone signaling. Molecular Plant-Microbe Interactions. 25:582-598.
Conservation of gene order and content in the circular chromosomes of 'Candidatus Liberibacter' asiaticus and other rhizbiales Reprint Icon -
Kuykendall, L.D., Shao, J.Y., Hartung, J.S. 2012. Conservation of gene order and content in the circular chromosomes of 'Candidatus Liberibacter' asiaticus and other rhizbiales. PLoS One. 7(4):e34673.
The iPhyClassifier, an interactive online tool for phytoplasma classification and taxonomic assignment -
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.
Comparison of the 'Ca Liberibacter asiaticus' genome adapted for an intracellular lifestyle with other members of the rhizobiales -
Hartung, J.S., Shao, J.Y., Kuykendall, L.D. 2011. Comparison of the 'Ca Liberibacter asiaticus' genome adapted for an intracellular lifestyle with other members of the rhizobiales. PLoS One. 6(8):e23289.
Genes encoding a callose synthase and phytochrome A are adjacent to a MAP3Ka-like gene in Beta vulgaris USH20 -
Kuykendall, L.D., Shao, J.Y. 2011. Genes encoding a callose synthase and phytochrome A are adjacent to a MAP3Ka-like gene in Beta vulgaris USH20. International Journal of Plant Genomics. DOI: 10.1155/2011/370548.
A plant gene encodes a 'HSFA9-like' heat shock factor and is part of a cluster of orthologous genes including NPR1, CaMP and CK1 in Beta vulgaris, Populus trichocarpa, Solanum lycopersicum and Vitis vinifera -
Kuykendall, L.D., Burdekin, K.A., Shao, J.Y., Conway, L.B. 2011. A plant gene encodes a 'HSFA9-like' heat shock factor and is part of a cluster of orthologous genes including NPR1, CaMP and CK1 in Beta vulgaris, Populus trichocarpa, Solanum lycopersicum and Vitis vinifera. Advanced Studies in Biology. 3(1):13-24.
A nest of LTR retrotransposons adjacent the disease resistance-priming gene NPR1 in Beta vulgaris L. U.S. Hybrid H20 -
Kuykendall, L.D., Shao, J.Y., Trimmer, K.A. 2009. A nest of LTR retrotransposons adjacent the disease resistance-priming gene NPR1 in Beta vulgaris L. U.S. Hybrid H20. International Journal of Plant Genomics. 2009: Article ID 576742, 8 pages.
Construction of an interactive online phytoplasma classification tool, iPhyClassifier, and its application in analysis of the peach X-disease phytoplasma group (16SrIII) Reprint Icon -
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.
Stress Induced Expression of a Beta vulgaris L. Gene for a Chloroplast-Targeted Signal Calmodulin-Binding Protein -
Kuykendall, L.D., Shao, J.Y., Kurushko, T., Burdekin, K.A. 2009. Stress Induced Expression of a Beta vulgaris L. Gene for a Chloroplast-Targeted Signal Calmodulin-Binding Protein. Advanced Studies in Biology. 1(7):323-332.
Conserved Microsynteny of NPR1 with Genes Encoding. A Signal Calmodulin-Binding Protein and a CK1-class Protein Kinase in Beta vulgaris and Two Other Eudicots -
Kuykendall, L.D., Shao, J.Y., Mcgrath, J.M., Murphy, T.S. 2008. Conserved Microsynteny of NPR1 with Genes Encoding. A Signal Calmodulin-Binding Protein and a CK1-class Protein Kinase in Beta vulgaris and Two Other Eudicots. International Journal of Plant Genomics. Available at http://dx.doi.org/10.1155/2008/391259.
Coel is a LTR retrotransopson-like element, in Beta vulgaris L., and contains a Tnp2-domain transposase gene -
Kuykendall, L.D., Shao, J.Y., Trimmer, K.A. 2008. Coel is a LTR retrotransopson-like element, in Beta vulgaris L., and contains a Tnp2-domain transposase gene. International Journal of Plant Genomics. Available: http://dx.doi.org/10.1155/2008/360874.
Nucleotide Sequence Analyses of a Sugar Beet Genomic NPR1-class Disease Resistance Gene -
Kuykendall, L.D., Murphy, T.S., Shao, J.Y., Mcgrath, J.M. 2007. Nucleotide Sequence Analyses of a Sugar Beet Genomic NPR1-class Disease Resistance Gene. Journal of Sugarbeet Research. 44:35-49.
PHYLOGENY AND CHARACTERIZATION OF PHYTOPLASMAL NUSA and USE OF THE NUSA GENE IN DETECTION OF GROUP 16Srl STRAINS -
Shao, J.Y., Jomantiene, R., Dally, E.L., Zhao, Y., Lee, I., Nuss, D.L., Davis, R.E. 2006. Phyogeny and characterization of phytoplasma NusA and use of the nusA gene in detection of group 16SrI strains. Journal of Plant Pathology. 88:193-201.
THE RNA POLYMERASE II GENE ENCODING THE SECOND LARGEST PEPTIDE SUBUNIT (RPB2) IN PHAEOSPHAERIA NODORUM -
Malkus, A., Chang, P., Zuzga, S.M., Chung, K., Shao, J.Y., Arseniuk, E., Ueng, P.P. 2006. The rna polymerase ii gene encoding the second largest peptide subunit (rpb2) in phaeosphaeria nodorum. Federation of European Microbiological Societies Microbiology Letters. 110:1152-1154.
COMPARATIVE GENOMICS OF 'CANDIDATUS PHYTOPLASMA ASTERIS' AND ACHOLEPLASMA PALMAE: COMMON ANCESTRAL GENES LOST DURING PHYTOPLASMA EVOLUTION -
Davis, R.E., Jomantiene, R., Lee, I., Zhao, Y., Hammond, R., Shao, J.Y., Dally, E.L., Dawe, A., Davis, K., Nuss, D. 2006. Comparative genomics of 'candidatus phytoplasma asteris' and acholeplasma palmae: common ancestral genes lost during phytoplasma evolution. International Organization for Mycoplasmology.
DEVELOPMENT OF AN INTERACTIVE WEB-BASED RESOURCE CENTER FOR PHYTOPLASMA RESEARCH -
Shao, J.Y., Lee, I., Zhao, Y., Wei, W., Jomantiene, R., Davis, R.E. 2006.Development of an interactive web-based resource center for phytoplasma research. American Phytopathological Society Potomac Division Meeting.
AN ACHOLEPLASMA GENOME ENCODES ENZYMES WITH THE POTENTIAL TO DEGRADE AND UTILIZE PLANT CELL WALL COMPONENTS -
Davis, R.E., Jomantiene, R., Lee, I., Zhao, Y., Hammond, R., Shao, J.Y., Dally, E.L., Dawe, A., Davis, K., Nuss, D. 2006. An acholeplasma genome encodes enzymes with the potential to degrade and utilize plant cell wall components. Phytopathology.
MOLECULAR ANALYSIS OF A CRYPTIC PLASMID ENCODING A PUTATIVE ADHESIN AND TYPE IV SECRETION SYSTEM COMPONENTS IN THE WALL-LESS PLANT PATHOGEN SPIROPLASMA KUNKELII -
Davis, R.E., Dally, E.L., Jomantiene, R., Zhao, Y., Roe, B., Lin, S., Shao, J.Y. 2005. Molecular analysis of a cryptic plasmid encoding a putative adhesin and type IV secretion system components in the wall-less plant pathogen Spiroplasma kunkelii. Plasmid. 53:179-190.
EVOLUTION OF THE PROKARYOTIC PROTEIN NUSA: COMPARISON OF NUSA IN CLOVER PHYLLODY (CPH) PHYTOPLASMA AND OTHER FIRMICUTES -
Shao, J.Y., Davis, R.E., Jomantiene, R., Dally, E.L. 2004. Evolution of the prokaryotic protein nusa: comparison of nusa in clover phyllody (cph) phytoplasma and other firmicutes. Phytopathology. p. 129.
SEQUENCING THE GENOME OF SPIROPLASMA KUNKELII GENOME: INSIGHTS TO A LIFESTYLE OF PARASITISM AND PATHOGENICITY IN INSECTS AND PLANTS -
Davis, R.E., Zhao, Y., Dally, E.L., Jomantiene, R., Shao, J.Y. 2004. Sequencing the genome of spiroplasma kunkelii genome: insights to a lifestyle of parasitism and pathogenicity in insects and plants. International Organization for Mycoplasmology. p. 63.
AN ADHESIN AND TYPE IV SECRETION ELEMENTS ENCODED BY CRYPTIC PLASMID PSKU146 FROM THE WALL-LESS PLANT PATHOGEN SPIROPLASMA KUNKELII -
Davis, R.E., Dally, E.L., Zhao, Y., Jomantiene, R., Shao, J.Y. 2004. An adhesin and type iv secretion elements encoded by cryptic plasmid psku146 from the wall-less plant pathogen spiroplasma kunkelii. International Organization for Mycoplasmology. p. 134-135.
THE SPIROPLASMA KUNKELII GENOME: CLUES TO A PARASITIC LIFESTYLE IN INSECTS AND PLANTS -
Davis, R.E., Zhao, Y., Dally, E.L., Jomantiene, R., Lin, S., Roe, B., Shao, J.Y. 2004. The spiroplasma kunkelii genome: clues to a parasitic lifestyle in insects and plants. Phytopathology. 94(3):123.
Last Modified: 5/2/2016
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