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United States Department of Agriculture

Agricultural Research Service

Jonathan Shao
Molecular Plant Pathology
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.)
Differential gene expression by Moniliophthora roreri while overcoming cacao tolerance in the field - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Book / Chapter) - (16-Aug-13)
Genome assembly of citurs leprosis virus nuclear type reveals a close association with orchid fleck virus - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Abstract Only)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (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.
Comparison of the 'Ca Liberibacter asiaticus' genome adapted for an intracellular lifestyle with other members of the rhizobiales - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (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.
Stress Induced Expression of a Beta vulgaris L. Gene for a Chloroplast-Targeted Signal Calmodulin-Binding Protein - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Abstract Only)
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 - (Abstract Only)
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 - (Abstract Only)
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 - (Peer Reviewed Journal)
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 - (Abstract Only)
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 - (Abstract Only)
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 - (Abstract Only)
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 - (Abstract Only)
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: 12/20/2014
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