Emerging Pests and Pathogens Research
CALS - SIPS - Plant Path & Plant-Microbe Bio Section

321 Plant Science Building
236 Tower Road
Ithaca, NY 14853

Phone: 607-280-0232

Robert W Holley Center, USDA-ARS
538 Tower Road
Ithaca, NY 14850-2901

• Projects

  Genomic and Molecular Characterization of Bacterial Strategies Used in Plant Pathogen Interactions Cooperative Agreement (A)   Accession Number:441078

  Advancing Knowledge of the Biology and Etiology of Bacterial Plant Pathogens Towards Management Strategies In-House Appropriated (D)   Accession Number:441736

• Publications

  • (Clicking on the reprint icon will take you to the publication reprint.)
  • Analysis of soft rot Pectobacteriaceae population diversity in US potato growing regions between 2015 and 2022-(Peer Reviewed Journal)
    
    
  • Identifying genes impacting Dickeya fitness in potato stems using an advanced high throughput sequencing technology-(Abstract Only)
    Gonzalez-Tobon, J., Helmann, T.C., Stodghill, P., Filiatrault, M.J. 2024. Identifying genes impacting Dickeya fitness in potato stems using an advanced high throughput sequencing technology. American Phytopathological Society Annual Meeting. https://www.apsnet.org/meetings/annual/meetingarchives/PH2024/Pages/default.aspx.
    
  • Understanding how Dickeya senses its environment: the importance of untranslated regions-(Abstract Only)
    Gonzalez-Tobon, J., Stodghill, P., Filiatrault, M.J. 2024. Understanding how Dickeya senses its environment: the importance of untranslated regions. Plant Pathogenic Bacteria International Conference Proceedings. https://iobc-wprs.org/meeting/icppb-biocontrol-2024/.
    
  • Surviving the potato stems: differences in genes required for fitness by Dickeya dadantii and Dickeya dianthicola -(Peer Reviewed Journal)
    Gonzalez-Tobon, J., Helmann, T., Stodghill, P., Filiatrault, M.J. 2024. Surviving the potato stems: differences in genes required for fitness by Dickeya dadantii and Dickeya dianthicola. Phytopathology. 114:1106-1117. https://doi.org/10.1094/PHYTO-09-23-0351-KC.
    
  • Complete genome sequence resource for xanthomonas hortorum isolated from Greek oregano -(Rapid Release Publication)
    Gonzalez-Tobon, J., Helmann, T., Daughtry, M., Stodghill, P., Filiatrault, M.J. 2024. Complete genome sequence resource for xanthomonas hortorum isolated from Greek oregano. Phytopathology. 107:3259-3263. https://doi.org/10.1094/PDIS-10-22-2399-A.
    
  • Identification of a Pseudomonas amygdali isolate from Hibiscus rosa-sinensis -(Peer Reviewed Journal)
    Gonzalez-Tobon, J., Diaz, A., Helmann, T.C., Daughtrey, M., Stodghill, P., Filiatrault, M.J. 2023. Identification of a Pseudomonas amygdali isolate from Hibiscus rosa-sinensis. International Journal of Systematic and Evolutionary Microbiology. 115:110600. https://doi.org/10.1016/j.ygeno.2023.110600.
    
  • Characterization of novel factors modulating pseudomonas syringae pv. tomato DC3000 pathogenicity-(Abstract Only)
    
    
  • Genome-wide identification of genes important for growth of dickeya dadantii and dickeya dianthicola in potato (solanum tuberosum) tubers -(Peer Reviewed Journal)
    Helmann, T.C., Filiatrault, M.J., Stodghill, P. 2022. Genome-wide identification of genes important for growth of dickeya dadantii and dickeya dianthicola in potato (solanum tuberosum) tubers. Frontiers in Microbiology. 13:778927. https://doi.org/10.3389/fmicb.2022.778927.
    
  • Functional genomics characterization of the interactions between Dickeya and Pectobacterium spp. during potato soft rot infection-(Abstract Only)
    Helmann, T.C., Filiatrault, M.J., Stodghill, P. 2021. Functional genomics characterization of the interactions between Dickeya and Pectobacterium spp. during potato soft rot infection. Meeting Abstract. https://www.ismpmi.org/Pages/default.aspx.
    
  • Identification of IAA-regulated genes in Pseudomonas syringae pv. tomato strain DC3000 -(Peer Reviewed Journal)
    Djami-Tchatchou, A., Li, Z., Stodghill, P., Filiatrault, M.J., Kunkel, B. 2021. Identification of IAA-regulated genes in Pseudomonas syringae pv. tomato strain DC3000. Journal of Bacteriology. https://doi.org/10.1128/JB.00380-21.
    
  • Genome-wide identification of genes important for growth of Dickeya dadantii and D. dianthicola in potato (Solanum tuberosum) tubers-(Pre-print Publication)
    Helmann, T.C., Filiatrault, M.J., Stodghill, P. 2021. Genome-wide identification of genes important for growth of Dickeya dadantii and D. dianthicola in potato (Solanum tuberosum) tubers. bioRxiv. doi: https://doi.org/10.1101/2021.09.16.460530;.
    
  • Unraveling the molecular interactions between Dickeya sp. and potato during blackleg infection-(Abstract Only)
    Tobon-Gonzalez, J., Helmann, T.C., Stodghill, P., Filiatrault, M.J. 2021. Unraveling the molecular interactions between Dickeya sp. and potato during blackleg infection. 2021 International Society for Molecular Plant-Microbe Interactions Congress, eSymposium Series, December 1-2, 2020, Plant-Microbe Interactions in the Environment. Virtual meeting.
    
  • Distinct transcriptional regulators contribute to growth of Dickeya dadantii and D. dianthicola in potato tubers-(Abstract Only)
    Helmann, T.C., Filiatrault, M.J., Stodghill, P. 2021. Distinct transcriptional regulators contribute to growth of Dickeya dadantii and D. dianthicola in potato tubers. American Phytopathological Society. https://www.aps.org/publications/apsnews/202102/march.cfm.
    
  • Identification of Pectobacterium versatile causing blackleg of potato from New York State-(Peer Reviewed Journal)
    
    
  • Complete genome sequence resource for the necrotrophic plant-pathogenic bacterium Dickeya dianthicola 67-19 isolated from New Guinea Impatiens -(Peer Reviewed Journal)
    Liu, Y., Helmann, T.C., Stodghill, P., Filiatrault, M.J. 2020. Complete genome sequence resource for the necrotrophic plant-pathogenic bacterium Dickeya dianthicola 67-19 isolated from New Guinea Impatiens. Plant Disease. Published Online. https://doi.org/10.1094/PDIS-09-20-1968-A.
    
  • Complete genome sequence resource for the necrotrophic plant-pathogenic bacterium Pectobacterium carotovorum WPP14 -(Peer Reviewed Journal)
    Liu, Y., Helmann, T.C., Stodghill, P., Filiatrault, M.J. 2020. Complete genome sequence resource for the necrotrophic plant-pathogenic bacterium Pectobacterium carotovorum WPP14. Plant Disease. https://doi.org/10.1094/PDIS-05-20-1059-A.
    
  • Complete genome sequence of a gram positive bacterium Leifsonia sp. strain PS1209, a potato endophyte -(Peer Reviewed Journal)
    Liu, Y., Ma, X., Helmann, T.C., Mclane, H., Stodghill, P., Swingle, B.M., Filiatrault, M.J., Perry, K.L. 2020. Complete genome sequence of a gram positive bacterium Leifsonia sp. strain PS1209, a potato endophyte. Microbiology Resource Announcements. 9(26). https://doi.org/10.1128/MRA.00447-20.
    
  • A high-density transposon insertion screen in Dickeya dadantii 3937 to identify genes required for host colonization-(Abstract Only)
    
    
  • Proteome profile and genome refinement of the tomato-pathogenic bacterium Clavibacter michiganensis subsp. michiganensis -(Peer Reviewed Journal)
    Peritore-Galve, F., Schneider, D.J., Yang, Y., Thannhauser, T.W., Smart, C.D., Stodghill, P. 2019. Proteome profile and genome refinement of the tomato-pathogenic bacterium Clavibacter michiganensis subsp. michiganensis. Proteomics. https://doi.org/10.1002/pmic.201800224.
    
  • Complete genome sequence of Dickeya dianthicola ME23, a pathogen causing Blackleg and Soft Rot Diseases of potato -(Peer Reviewed Journal)
    Swingle, B.M., Perna, N.T., Glasner, J.D., Hao, J., Johnson, S., Charkowski, A., Perry, K.L., Stodghill, P. 2019. Complete genome sequence of the potato blackleg pathogen Dickeya dianthicola ME23. Microbiology Resource Announcements. 8(7). https://doi.org/10.1128/MRA.01526-18.
    
  • Transcriptomic profiling suggests that promysalin alters metabolic flux, motility, and iron regulation in Pseudomonas putida KT2440 -(Peer Reviewed Journal)
    Giglio, K., Keohane, C.E., Stodghill, P., Steele, A.D., Fetzer, C., Sieber, S., Filiatrault, M.J., Wuest, W.M. 2018. Transcriptomic profiling suggests that promysalin alters metabolic flux, motility, and iron regulation in Pseudomonas putida KT2440. ACS Infectious Diseases. https://doi.org/10.1021/acsinfecdis.8b00041.
    
  • The Ca2+ induced two-component system, CvsSR regulates the Type III secretion system and the extracytoplasmic function sigma-factor AlgU in Pseudomonas syringae pv. tomato DC3000-(Peer Reviewed Journal)
    Fishman, M., Zhang, J., Bronstein, P., Stodghill, P., Filiatrault, M.J. 2017. The Ca2+ induced two-component system, CvsSR regulates the Type III secretion system and the extracytoplasmic function sigma-factor AlgU in Pseudomonas syringae pv. tomato DC3000. Journal of Bacteriology. doi:10.1128/JB.00538-17.
    
  • Identification of the CvsSR regulon in Pseudomonas syringae reveals overlap with the Type-III secretion and AlgU regulons-(Abstract Only)
    Fishman, M., Stodghill, P., Filiatrault, M.J. 2017. Identification of the CvsSR regulon in Pseudomonas syringae reveals overlap with the Type-III secretion and AlgU regulons. International Conference on Pseudomonas. P5.
    
  • The ECF sigma factor, PSPTO_1043, in Pseudomonas syringae pv. tomato DC3000 is induced by oxidative stress and regulates genes involved in oxidative stress response -(Peer Reviewed Journal)
    Butcher, B., Bao, Z., Wilson, J., Stodghill, P., Swingle, B.M., Filiatrault, M.J., Schneider, D.J., Cartinhour, S.W. 2017. The ECF sigma factor, PSPTO_1043, in Pseudomonas syringae pv. tomato DC3000 is induced by oxidative stress and regulates genes involved in oxidative stress response. PLoS One. DOI: 10.1371/journal.pone.0180340.
    
  • AlgU controls expression of virulence genes in Pseudomonas syringae pv. tomato DC3000-(Peer Reviewed Journal)
    Markel, E.J., Stodghill, P., Bao, Z., Myers, C., Swingle, B.M. 2016. AlgU controls expression of virulence genes in Pseudomonas syringae pv. tomato DC3000. Journal of Bacteriology. 198(17):2330-2344.
    
  • Dissecting the regulon of the two-component system CvsSR: Identifying new virulence genes in Pseudomonas syringae pv. tomato DC3000-(Abstract Only)
    Fishman, M., Stodghill, P., Filiatrault, M.J. 2016. Dissecting the regulon of the two-component system CvsSR: Identifying new virulence genes in Pseudomonas syringae pv. tomato DC3000. International Congress on Molecular Plant-Microbe Interactions. P6-141. p. 43.
    
  • Probing Pseudomonas syringae host interactions using metatranscriptomics-(Abstract Only)
    Filiatrault, M.J., Fishman, M., Stodghill, P. 2016. Probing Pseudomonas syringae host interactions using metatranscriptomics. American Phytopathological Society Annual Meeting. p. 44.
    
  • The involvement of catabolite repression in the virulence of Pseudomonas syringae-(Abstract Only)
    Filiatrault, M.J., Butcher, B., D'Amico, K.M., Chakravarthy, S., Fishman, M., Stodghill, P. 2015. The involvement of catabolite repression in the virulence of Pseudomonas syringae. ASM Conference. p. 44.
    
  • Identification of a previously uncharacterized global regulator in Pseudomonas syringae pv. tomato DC3000-(Abstract Only)
    Fishman, M.R., Zhang, J., Bronstein, P.A., Stodghill, P., Filiatrault, M.J. 2015. Identification of a previously uncharacterized global regulator in Pseudomonas syringae pv. tomato DC3000. American Phytopathology Society. 705-P.
    
  • Characterizing the regulon of the two-component system, PSPTO_3380 and PSPTO_3381-(Abstract Only)
    Fishman, M.R., D'Amico, K.M., Stodghill, P., Filiatrault, M.J. 2015. Characterizing the regulon of the two-component system, PSPTO_3380 and PSPTO_3381. International Conference on Pseudomonas syringae Pathovars. p. 99.
    
  • Pseudomonas syringae pv. Tomato DC3000 Type III secretion effector polymutants reveal an interplay between hopAD1 and AvrPtoB-(Peer Reviewed Journal)
    Wei, H., Chakravarthy, S., Mathieu, J., Helmann, T.C., Stodghill, P., Swingle, B.M., Martin, G.B., Collmer, A. 2015. Pseudomonas syringae pv. Tomato DC3000 Type III secretion effector polymutants reveal an interplay between hopAD1 AvrPtoB. Cell Host and Microbe. 17(6):752-62.
    
  • Global analysis of the HrpL regulon in the plant pathogen Pseudomonas syringae pv. tomato DC3000 reveals new regulon members with diverse functions-(Peer Reviewed Journal)
    Lam, H.N., Chakravarthy, S., Wei, H., Buinguyen, H., Stodghill, P., Swingle, B.M., Collmer, A., Cartinhour, S.W. 2014. Global analysis of the HrpL regulon in the plant pathogen Pseudomonas syringae pv. tomato DC3000 reveals new regulon members with diverse functions. PLoS Pathogens. 9(8):e106115. DOI: 10.1371/journal.pone.0106115.
    
  • Analysis of the small RNA spf in the plant pathogen Pseudomonas syringae pv. tomato strain DC3000-(Peer Reviewed Journal)
    Park, S., Bao, Z., Butcher, B., D'Amico, K.M., Xu, Y., Stodghill, P., Schneider, D.J., Cartinhour, S.W., Filiatrault, M.J. 2014. Analysis of the small RNA spf in the plant pathogen Pseudomonas syringae pv. tomato strain DC3000. Microbiology. 160(Pt 5):941-953.
    
  • Genomic plasticity enables phenotypic variation of Pseudomonas syringae pv. tomato DC3000-(Peer Reviewed Journal)
    Swingle, B.M., Bao, Z., Stodghill, P., Myers, C.R., Lam, H., Markel, E.J., Collmer, A., Cartinhour, S.W., Schweitzer, P. 2014. Genomic plasticity enables phenotypic variation of Pseudomonas syringae pv. tomato DC3000. PLoS One. 9(2):e86628. DOI: 10.1371/Journal.pone.0086628.
    
  • CrcZ and CrcX regulate carbon utilization in Pseudomonas syringae pathovar tomato strain DC3000-(Peer Reviewed Journal)
    Filiatrault, M.J., Stodghill, P., Wilson, J.M., Butcher, B.G., Chen, H., Meyers, C.R., Cartinhour, S.W. 2013. CrcZ and CrcX regulate carbon utilization in Pseudomonas syringae pathovar tomato strain DC3000. RNA Biology. 10(2):243-253.
    
  • Regulons of the Pseudomonas syringae pv. tomato DC3000 iron starvation sigma factors PSPTO_0444, PSPTO_1209 and PSPTO_1286-(Peer Reviewed Journal)
    Swingle, B.M., Markel, E.J., Butcher, B.G., Myers, C.R., Stodghill, P., Cartinhour, S.W. 2013. Regulons of the Pseudomonas syringae pv. tomato DC3000 iron starvation sigma factors PSPTO_0444, PSPTO_1209 and PSPTO_1286. Applied and Environmental Microbiology. 79(2):725-727.
    
  • Genome-wide identification of transcriptional start sites in the plant pathogen Pseudomonas syringae pv. tomato str. DC3000-(Peer Reviewed Journal)
    Filiatrault, M.J., Stodghill, P., Myers, C.R., Bronstein, P.A., Butcher, B.G., Lam, H., Grills, G., Schweitzer, P., Wang, W., Schneider, D.J., Cartinhour, S.W. 2011. Genome-wide identification of transcriptional start sites in the plant pathogen Pseudomonas syringae pv. tomato str. DC3000. PLoS One. 6(12). Available: http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029335.
    
  • An ECF sigma factor mediated cell surface signaling system in Pseudomonas syringae pv. tomato DC3000 regulates gene expression in response to heterologous siderophores-(Peer Reviewed Journal)
    Swingle, B.M., Markel, E.J., Maciak, C.L., Butcher, B., Myers, C., Stodghill, P., Cartinhour, S.W., Bao, Z. 2011. An ECF sigma factor mediated cell surface signaling system in Pseudomonas syringae pv. tomato DC3000 regulates gene expression in response to heterologous siderophores. Journal of Bacteriology. 193:5775-5783.
    
  • The small RNA transcriptome of Pseudomonas syringae pathovar tomato DC3000-(Abstract Only)
    Filiatrault, M.J., Moll, S., Bao, Z., Maciak, C.L., Chen, H., Myers, C.R., Stodghill, P., Cartinhour, S.W. 2011. The small RNA transcriptome of Pseudomonas syringae pathovar tomato DC3000. International Conference on Pseudomonas syringae Pathovars. 13:20.
    
  • Characterization of the Fur regulon in Pseudomonas syringae pv. tomato DC3000-(Peer Reviewed Journal)
    Butcher, B.G., Bronstein, P., Myers, C., Stodghill, P., Bolton, J.J., Markel, E.J., Filiatrault, M.J., Swingle, B.M., Gaballa, A., Helmann, J.D., Schneider, D.J., Cartinhour, S.W. 2011. Characterization of the Fur regulon in Pseudomonas syringae pv. tomato DC3000. Journal of Bacteriology. 193(18):4598-4611. Available: http://www.ncbi.nlm.nih.gov/pubmed/21784947.
    
  • Global survey of Fur binding refines the iron responsive regulon of Pseudomonas syringae-(Abstract Only)
    Bronstein, P., Butcher, B.G., Myers, C.R., Stodghill, P., Swingle, B.M., Cartinhour, S.W. 2010. Global survey of Fur binding refines the iron responsive regulon of Pseudomonas syringae [abstract]. p. 31.
    
  • Construction of an rsmX co-variance model and identification of five rsmX-like ncRNAs in Pseudomonas syringae pv. tomato DC3000-(Peer Reviewed Journal)
    Moll, S., Schneider, D.J., Stodghill, P., Myers, C.R., Cartinhour, S.W., Filiatrault, M.J. 2010. Construction of an rsmX co-variance model and identification of five rsmX-like ncRNAs in Pseudomonas syringae pv. tomato DC3000. RNA Biology. 7(5):1-10.
    
  • Analyzing the transcriptome of Pseudomonas syringae using high-throughput sequencing methodologies-(Abstract Only)
    Filiatrault, M.J., Bronstein, P., Stodghill, P., Moll, S., Schneider, D.J., Cartinhour, S.W. 2010. Analyzing the transcriptome of Pseudomonas syringae using high-throughput sequencing methodologies. Meeting Abstract. p. 31.
    
  • Transcriptome analysis of Pseudomonas syringae identifies new genes, ncRNAs, and antisense activity-(Peer Reviewed Journal)
    Filiatrault, M.J., Stodghill, P., Bronstein, P., Moll, S., Lindeberg, M., Grills, G., Schweitzer, P., Wang, W., Schroth, G., Luo, S., Khrebtukova, I., Thannhauser, T.W., Yang, Y., Butcher, B.G., Cartinhour, S.W., Schneider, D.J. 2010. Transcriptome analysis of Pseudomonas syringae identifies new genes, ncRNAs, and antisense activity. Journal of Bacteriology. 192(9):2359-2372.
    
  • Integrating molecular and computational methods to evaluate the Pseudomonas syringae transcriptome I & II-(Proceedings)
    Filiatrault, M.J., Stodghill, P. 2009. Integrating molecular and computational methods to evaluate the Pseudomonas syringae transcriptome I & II. American Phytopathological Society Abstracts.
    
  • High-throughput identification of transcriptional start sites in Pseudomonas syringae-(Abstract Only)
    Filiatrault, M.J., Stodghill, P., Wang, W., Schweitzer, P., Grills, G., Cartinhour, S.W., Schneider, D.J. 2009. High-throughput identification of transcriptional start sites in Pseudomonas syringae. American Society for Microbiology. p. 251.
    
  • Investigating the role of two iron-regulated small RNAs of Pseudomonas syringae-(Abstract Only)
    Bronstein, P., Filiatrault, M.J., Stodghill, P., Schneider, D.J., Cartinhour, S.W. 2009. Investigating the role of two iron-regulated small RNAs of Pseudomonas syringae. American Society for Microbiology. p. 20.
    
  • Characterization of two small RNAs of Pseudomonas syringae DC3000-(Abstract Only)
    Filiatrault, M.J., Bronstein, P., Stodghill, P., Cartinhour, S.W. 2008. Characterization of two small RNAs of Pseudomonas syringae DC3000. American Society for Microbiology Meeting.
    
  • Shotgun Sequencing of the Pseudomonas syringae DC3000 Transcriptome-(Abstract Only)
    Filiatrault, M.J., Bronstein, P., Stodghill, P., Declerck, G.A., Schneider, D.J., Cartinhour, S.W. 2007. Shotgun Sequencing of the Pseudomonas syringae DC3000 Transcriptome. American Society for Microbiology Conference. p. 20.
    

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