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ARS Home » People & Locations » Jonathan Shao

Jonathan Shao
Office of The Area Director
Computational Biologist

Phone: (301) 504-6292
Fax:
Room 220

10300 BALTIMORE AVENUE
BLDG 003 BARC-WEST
BELTSVILLE, MD 20705

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
Identification of complete genome sequencing of alfalfa virus S diagnosed in alfalfa plants (Medicago sativa L.) from Washington State, USA Reprint Icon - (Peer Reviewed Journal)
Nemchinov, L.G., Grinstead, S.C., Irish, B.M., Shao, J.Y. 2020. Identification of complete genome sequencing of alfalfa virus S diagnosed in alfalfa plants (Medicago sativa L.) from Washington State, USA. Plant Disease. https://doi.org/10.1094/PDIS-06-20-1374-PDN.
Effect of butyric acid glycerol esters on ileal and cecal mucosal and luminal microbiota in chickens challenged with Eimeria maxima Reprint Icon - (Peer Reviewed Journal)
Proszkowiec-Wegla, M.K., Miska, K.B., Schreier, L.L., Grim, C.J., Jarvis, K.G., Shao, J.Y., Vaessen, S., Sygall, R., Jenkins, M.C., Kahl, S., Russell, B.A. 2020. Effect of butyric acid glycerol esters on ileal and cecal mucosal and luminal microbiota in chickens challenged with Eimeria maxima. Poultry Science. https://doi.org/10.1016/j.psj.2020.06.022.
Cabbage looper (Trichoplusia ni) salivary glands contain unique bacterial flora in contrast with their alimentary canal, mandibular gland and Malpighian tubules - (Peer Reviewed Journal)
Lawrence, S.D., Novak, N.G., Shao, J.Y., Ghosh, S.B., Blackburn, M.B. 2020. Cabbage looper (Trichoplusia ni) salivary glands contain unique bacterial flora in contrast with their alimentary canal, mandibular gland and Malpighian tubules . MicrobiologyOpen. 9(4):e994.
Draft genome sequence of `Candidatus Phytoplasma pini'-related strain MDPP: a resource for comparative genomics of gymnosperm-infecting phytoplasmas Reprint Icon - (Peer Reviewed Journal)
Cai, W., Shao, J.Y., Zhao, Y., Davis, R.E., Costanzo, S. 2020. Draft genome sequence of `Candidatus Phytoplasma pini'-related strain MDPP: a resource for comparative genomics of gymnosperm-infecting phytoplasmas. Plant Disease. 104/1009-1010. https://doi.org/10.1094/PDIS-10-19-2127-A.
Transcriptomic analyses reveal physiological changes in sweet orange roots affected by citrus blight Reprint Icon - (Peer Reviewed Journal)
Fu, S., Shao, J.Y., Roy, A., Brlansky, R., Zhou, C., Hartung, J.S. 2019. Transcriptomic analyses reveal physiological changes in sweet orange roots affected by citrus blight. BMC Genomics. 20:969. https://doi.org/10.1186/s12864-019-6339-0.
Identification of emerging viral genomes in transcriptomic datasets of alfalfa (Medicago sativa L.) Reprint Icon - (Peer Reviewed Journal)
Jiang, P., Shao, J.Y., Nemchinov, L.G. 2019. Identification of emerging viral genomes in transcriptomic datasets of alfalfa (Medicago sativa L.). Virology Journal. 16:153. https://doi.org/10.1186/s12985-019-1257-y.
Genome and transcriptome analysis of the latent pathogen lasiodiplodia Theobromae, an emerging threat to cacao industry - (Peer Reviewed Journal)
Ali, S., Shao, J.Y., Adi, A., Balidion, J., Strem, M., Puig, A.S., Meinhardt, L.W., Bailey, B.A. 2019. Genome and transcriptome analysis of the latent pathogen lasiodiplodia Theobromae, an emerging threat to cacao industry. Genes, Genomes, and Genomics. 63:37–52.
Draft genome sequence of fastidious pathogen Ceratobasidium theobromae, which causes vascular-streak dieback (VSD) in Theobroma cacao - (Peer Reviewed Journal)
Ali, S., Asman, A., Shao, J.Y., Firmansyah, A., Susilo, A., Rosamana, A., Mcmahon, P., Junaid, M., Guest, D., Kheng, T., Meinhardt, L.W., Bailey, B.A. 2019. Draft genome sequence of fastidious pathogen Ceratobasidium theobromae, which causes vascular-streak dieback (VSD) in Theobroma cacao. Fungal Biology and Biotechnology. 6:14.
Identification of the coding-complete genome of Cycas necrotic stunt virus in transcriptomic data sets of alfalfa (Medicago sativa) Reprint Icon - (Peer Reviewed Journal)
Jiang, P., Shao, J.Y., Nemchinov, L.G. 2019. Identification of the coding-complete genome of Cycas necrotic stunt virus in transcriptomic data sets of alfalfa (Medicago sativa). Microbiology Resource Announcements. 8:e00981-19. https://doi.org/10.1128/MRA.00981-19.
Rapid detection and identification of ‘Candidatus Phytoplasma pini’-related strains in Lithuania based on genomic markers present in 16S rRNA and tuf genes Reprint Icon - (Peer Reviewed Journal)
Valiunas, D., Jomantiene, R., Ivanauskas, A., Sneideris, D., Zizyte-Eidetiene, M., Shao, J.Y., Zhao, Y., Costanzo, S., Davis, R.E. 2019. Rapid detection and identification of ‘Candidatus Phytoplasma pini’-related strains in Lithuania based on genomic markers present in 16S rRNA and tuf genes. Forest Pathology. 49:e12553. https://doi.org/10.1111/efp.12553.
Cellular and trancriptional responses of resistant and susceptible cultivars of alfalfa to the root lesion nematode, Pratylenhus penetrans Reprint Icon - (Peer Reviewed Journal)
Vieira, P., Mowery, J.D., Eisenback, J.D., Shao, J.Y., Nemchinov, L.G. 2019. Cellular and trancriptional responses of resistant and susceptible cultivars of alfalfa to the root lesion nematode, Pratylenhus penetrans. Frontiers in Plant Science. 10:971. https://doi.org/10.3389/fpls.2019.00971.
Transcriptome analysis reveals a complex array of differentially expressed genes accompanying a source-to-sink changes in phytoplasma-infected sweet cherry leaves - (Peer Reviewed Journal)
Complete genome sequence of Spiroplasma phoeniceum strain P40T, a plant pathogen isolated from diseased plants of Madagascar periwinkle (Catharanthus roseus (L.) G. Don) Reprint Icon - (Peer Reviewed Journal)
Davis, R.E., Shao, J.Y., Zhao, Y., Wei, W., Bottner-Parker, K.D., Silver, A.B., Stump, Z.A., Gasparich, G.E., Donofrio, N. 2019. Complete genome sequence of Spiroplasma phoeniceum strain P40T, a plant pathogen isolated from diseased plants of Madagascar periwinkle (Catharanthus roseus (L.) G. Don). Microbiology Resource Announcements. https://doi.org/10.1128/MRA.01612-18.
Automated detection of ‘Ca. Liberibacter asiaticus’ infection in citrus using immune tissue prints and machine learning - (Abstract Only)
The transcriptome of roots of sweet orange tree with symptoms of citrus blight - (Abstract Only)
First report of alphapartitiviruses infecting alfalfa (Medicago sativa) in the United States - (Peer Reviewed Journal)
Nemchinov, L.G., Lee, M., Shao, J.Y. 2018. First report of alphapartitiviruses infecting alfalfa (Medicago sativa) in the United States. Genome Announcements. https://doi.org/mra.asm.org/content/7/21/e01266-18.
Genotype-specific suppression of multiple defense pathways in apple root during infection by Pythium ultimum Reprint Icon - (Peer Reviewed Journal)
Zhu, Y., Shao, J.Y., Zhou, Z., Davis, R.E. 2019. Genotype-specific suppression of multiple defense pathways in apple root during infection by Pythium ultimum. Horticulture Research. 6:10. https://doi.org/10.1038/s41438-018-0087-1.
Complete nucleotide sequence of a novel Hibiscus-infecting Cilevirus from Florida and its relationship with closely associated Cileviruses - (Peer Reviewed Journal)
Roy, A., Stone, A.L., Melzer, M.J., Hartung, J.S., Shao, J.Y., Mavrodieva, V., Nakhla, M.K., Brlansky, R.H., Schneider, W.L. 2018. Complete nucleotide sequence of a novel Hibiscus-infecting Cilevirus from Florida and its relationship with closely associated Cileviruses. Genome Announcements. 6(4):e01521-17.
Resistant and susceptible responses in alfalfa (Medicago sativa) to bacterial stem blight caused by Pseudomonas syringae pv. syringae - (Peer Reviewed Journal)
Nemchinov, L.G., Shao, J.Y., Lee, M., Postnikova, O.A., Samac, D.A. 2017. Resistant and susceptible responses in alfalfa (Medicago sativa) to bacterial stem blight caused by Pseudomonas syringae pv. syringae. PLoS One. 12(12):e0189781.
The porcine translational research database: A manually curated, genomics and proteomics-based research resource - (Peer Reviewed Journal)
Dawson, H.D., Chen, C.T., Gaynor, B., Shao, J.Y., Urban Jr, J.F. 2017. The porcine translational research database: A manually curated, genomics and proteomics-based research resource. Biomed Central (BMC) Genomics. doi: 10.1186/s12864-017-4009-7.
Co-infection of sweet orange with severe and mild strains of citrus tristeza virus is overwhelmingly dominated by the severe strain on both the transcriptional and biological levels Reprint Icon - (Peer Reviewed Journal)
Shimin, F., Shao, J.Y., Zhao, C., Hartung, J.S. 2017. Co-infection of sweet orange with severe and mild strains of citrus tristeza virus is overwhelmingly dominated by the severe strain on both the transcriptional and biological levels. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2017.01419.
Comparative transcriptome analysis reveals a preformed defense system in apple root of a resistant genotype of G.935 in the absence of pathogen - (Peer Reviewed Journal)
Zhu, Y., Shao, J.Y., Zhou, Z., Davis, R.E. 2017. Comparative transcriptome analysis reveals a preformed defense system in apple root of a resistant genotype of G.935 in the absence of pathogen. International Journal of Plant Genomics. doi: 10.1155/2017/8950746.
Complete genome sequence of Spiroplasma citri strain R8-A2T, causal agent of stubborn disease in Citrus spp - (Peer Reviewed Journal)
Davis, R.E., Shao, J.Y., Zhao, Y., Gasparich, G.E., Gaynor, B.J., Donofrio, N. 2017. Complete genome sequence of Spiroplasma citri strain R8-A2T, causal agent of stubborn disease in Citrus spp. Genome Announcements. 5:e00206-17.
Phytophthora megakarya and P. palmivora, closely related causal agents of cacao black pod rot, underwent increases in genome sizes and gene numbers by different mechanisms - (Peer Reviewed Journal)
Ali, S., Shao, J.Y., Strem, M.D., Amoako-Attah, I., Melnick, R., Yaw Akrofi, A., Coulibaly, K., Ismael Kebe, K., Guiltinan, Begoude, B., Ten Hoopen, G., Shen, D., Lary, D.J., Kronmiller, B., Tyler, B., Meinhardt, L.W., Bailey, B.A. 2017. Phytophthora megakarya and P. palmivora, closely related causal agents of cacao black pod rot, underwent increases in genome sizes and gene numbers by different mechanisms. Genome Biology and Evolution. 9:536-557.
Phytophthora megakarya and P. palmivora, closely related causal agents of cacao black pod induce similar reactions when infecting pods of a susceptible cacao genotype - (Peer Reviewed Journal)
Ali, S., Shao, J.Y., Strem, M.D., Lary, D.J., Meinhardt, L.W., Bailey, B.A. 2017. Phytophthora megakarya and P. palmivora, closely related causal agents of cacao black pod induce similar reactions when infecting pods of a susceptible cacao genotype. Frontiers in Plant Science. 8:169.
Independent origins of diploidy in the entomopathogen Metarhizium - (Peer Reviewed Journal)
Kepler, R.M., Chen, Y., Kilcrease, J., Shao, J.Y., Rehner, S.A. 2017. Independent origins of diploidy in the entomopathogen Metarhizium. Mycologia. 108(6):1091-1103.
Serological detection of ‘Candidatus Liberibacter asiaticus’ in citrus, and the identification of a promising secreted chaperone protein responding to cellular pathogens - (Peer Reviewed Journal)
Ding, F., Duan, Y., Yuan, Q., Shao, J.Y., Hartung, J.S. 2016. Serological detection of ‘Candidatus Liberibacter asiaticus’ in citrus, and the identification of a promising secreted chaperone protein responding to cellular pathogens. Scientific Reports. 6:29272. doi: 10.1038/srep29272.
Transcriptome analysis of sweet orange trees infected with ‘Candidatus Liberibacter asiaticus’ and two strains of citrus tristeza virus - (Peer Reviewed Journal)
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. doi.10.1186/s12864-016-2663-9.
Gene expression profiling in viable but not culturable (VBNC) cells of Pseudomonas syringae pv syringae - (Peer Reviewed Journal)
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) - (Peer Reviewed Journal)
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. doi:10.1128/genomeA.01367-15.
Complete genome sequence of Spiroplasma kunkelii strain CR2-3x, causal agent of corn stunt disease in Zea mays L. - (Peer Reviewed Journal)
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. doi:10.1128/genomeA.01216-15.
Draft genome sequence of ‘Candidatus Phytoplasma pruni’ strain CX, a plant pathogenic bacterium - (Peer Reviewed Journal)
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. doi: 10.1128/genomeA.01117-15.
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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. http://dx.doi.org/10.1094/PHYTO-03-15-0064-R.
Transcriptome analysis of citrus sinensis in response to dual infection by Citrius tristeza virus and ’Candidatus liberibacter asiaticus' - (Abstract Only)
Fu, S., Shao, J.Y., Paul, C., Hartung, J.S. 2015. Transcriptome analysis of citrus sinensis in response to dual infection by Citrius tristeza virus and ’Candidatus liberibacter asiaticus'. Phytopathology. 105:1013-1025. http://dx.doi.org/10.1094/PHYTO-03-15-0064-R.
Role bending: complex relationships between viruses, hosts and vectors related to citrus leprosis, an emerging disease Reprint Icon - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (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 Reprint Icon - (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 ()
Zhao, Y., Davis, R.E., Wei, W., Shao, J.Y., Jomantiene, R. 2014. Phytoplasma genomes: Evolution through mutually complimentary mechanisms, gene loss and horizontal acquisition. Genomics of Plant-associated Bacteria. 235-271.
Genome assembly of citurs leprosis virus nuclear type reveals a close association with orchid fleck virus Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 ()
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) - (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.