Publications and Manuscripts
2023
Sorkin, M.L., Markham, K.K., Zorich, S., Menon, A., Edgeworth, K. N., Ricono, A., Bryant, D., Bart, R.S., Nusinow, D. A., Greenham, K. Assembly and operation of an imaging system for long-term monitoring of bioluminescent and fluorescent reporters in plants. Plant Methods 19, 19 (2023) https://doi.org/10.1186/s13007-023-00997-0
Pettit, N., Gowda, S. A., Shrestha, N., Harris, T., Bart, R., Bourland, F., Brown-Guedira, G., Jones, D. C., & Kuraparthy, V. (2023). Development and validation of Kompetitive allele-specific PCR (KASP) markers for bacterial blight resistant locus BB-13 in Upland cotton (Gossypium hirsutum L.). Crop Science, 63, 2636–2649. https://doi.org/10.1002/csc2.21072
Veley, K.M., Elliott, K., Jensen, G., Zhong, Z., Feng, S., Yoder, M., Gilbert, K.B., Berry, J.C., Ghoshal, B., Gallego- Bartolomé, J., Norton, J., Motomura-Wages, S., Carrington, J.C., Jacobsen, S.E., Bart, R.S.* Improving cassava bacterial blight resistance by editing the epigenome. Nat Commun 14, 85 (2023). https://doi.org/10.1038/s41467-022-35675-7
2022
Zhong, Z., Feng, S., Mansfeld, B. N., Ke, Y., Qi, W., Lim, Y. W., Gruissem, W., Bart, R. S., & Jacobsen, S. E. (2022). Haplotype-resolved DNA methylome of African cassava genome. Plant biotechnology journal, 10.1111/pbi.13955. Advance online publication. https://doi.org/10.1111/pbi.13955
Gowda, S.A., Shrestha, N., Harris, T.M. Phillips A.Z., Fang, H., Sood S., Zhang, K., Bourland F., Bart, R.S. Kuraparthy V. Identification and genomic characterization of major effect bacterial blight resistance locus (BB-13) in Upland cotton (Gossypium hirsutum L.). Theor Appl Genet (2022). https://doi.org/10.1007/s00122-022-04229-2
Berry, J.C., Qi, M., Sonawane, B.V., Sheflin, A., Cousins, A.B., Prenni, J., Schachtman, D.P., Liu, P., Bart, R.S. (2022) Increased signal to noise ratios within experimental field trials by regressing spatially distributed soil properties as principal components. eLife Sciences, https://doi.org/10.7554/eLife.70056
Lim, Y.W., Mansfeld, B.N., Schläpfer, P., Gilbert, K.B., Narayanan, N.N., Qi, W., Wang, Q., Z. Zhong, Z., Boyher, A., Gehan, J., Beyene, G., Lin, Z.D., Esuma, W., Feng, S., Chanez, C., Eggenberger, N., Adiga, G., Alicai, T., Jacobsen, S.E., Taylor, N.J., Gruissem, W., Bart, R.S. (2022) Mutations in DNA polymerase subunit 1 mediate CMD2-type resistance to Cassava Mosaic Geminiviruses. Nat Commun 13, 3933 (2022). https://doi.org/10.1038/s41467-022-31414-0
Elliott, K., Berry, J.C., Kim, H., and Bart, R.S. A comparison of ImageJ and machine learning based image analysis methods to measure cassava bacterial blight disease severity. Plant Methods 18, 86 (2022). https://doi.org/10.1186/s13007-022-00906-x
Qi, M., Berry, J.C., Veley, K., O’Connor, L., Finkel, O.M., Salas-González, I., Kuhs, M., Jupe, J., Holcomb, E., del Rio, T.G., Creech, C., Liu, P., Tringe, S., Dangl, J.L., Schachtman, D., Bart, R.S. Identification of beneficial and detrimental bacteria impacting sorghum responses to drought using multi-scale and multi-system microbiome comparisons. ISME J 16, 1957–1969 (2022). https://doi.org/10.1038/s41396-022-01245-4
Wheeler, T., Harris, T., Bart, R.S, Isakeit, T., Woodward, J., Allen T.W., Kemerait, R.C. (2022) Response of Xanthomonas citri pv. malvacearum isolates to cotton differing in susceptibility to the bacterium and their predicted type III effectors. Plant Health Progress 23(1) https://doi.org/10.1094/PHP-06-21-0090-RS
2021
Mansfeld, B.N., Boyher, A., Berry, J.C., Wilson, M., Ou, S., Polydore, S., Michael, T.P., Fahlgren, N. and Bart, R.S. (2021), Large structural variations in the haplotype-resolved African cassava genome. Plant J, 108: 1830-1848. https://doi.org/10.1111/tpj.15543
Lyons, J.B., Bredeson, J.V., Mansfeld B.N., Bauchet, G.J., Berry, J., Boyher, A., Mueller, L.A., Rokhsar, D.S., Bart, R. (2021) Current status and impending progress for cassava structural genomics. Plant Mol Biol; https://doi.org/10.1007/s11103-020-01104
Wang, Q.; Shakoor, N., Boyher, A., Veley, K.M., Berry, J.C., Mockler, T.C., Bart, R.S. (2021) Escalation in the host-pathogen arms race: A host resistance response corresponds to a heightened bacterial virulence response. PLoS Pathogens. http://doi.org/10.1371/journal.ppat.1009175
Veley, K.M., Okwuonu, I., Jensen, G., Yoder, M., Taylor, N.J. Meyers, B.C. Bart, R.S. (2021) Gene-tagging via CRISPR-mediated homology-directed repair in cassava, G3, http://doi.org/10.1093/g3journal/jkab028
Casto, A.,Schul, H, Tovar, J.C., Wang, Q., Bart, R.S, Fahlgren, N, Gehan, M. (2021) Picturing the future of food. The Plant Phenome Journal, http://doi.org/10.1002/ppj2.20014
2020
Odipio, J., Beyene, G., Chauhan, R.D., Alicai, T., Bart, R.S., Nusinow, D. A., Taylor, N. J. (2020) Transgenic overexpression of endogenous FLOWERING LOCUS T-like gene MeFT1 produces early flowering in cassava, PLoS One, http://doi.org/10.1371/journal.pone.0227199
Gaffney, J., Tibebu, R., Bart, R.S., Beyene, G, Girma, D., Kane, N.A., Mace, E.S., Mockler, T, Nickson, T.E., Taylor, N.J., Zastrow-Hayes, G. (2020) Open access to genetic sequence data maximizes value to scientists, farmers and society. Global Food Security, http://doi.org/10.1016/j.gfs.2020.100411
2019
Lin, Z.J.D., Taylor, N.J., Bart, R.S., (2019) Engineering Disease-Resistant Cassava. Cold Spring Harb Perspect Biol, http://doi.org/10.1101/cshperspect.a034595
Bart, R.S., Shirasu, K. (2019) Editorial Overview: Biotic interactions-Hosts, microbes and a changing environment. Current Opinion in Plant Biology, http://doi.org/10.1016/j.pbi.2019.08.001
2018
Gomez, M.A., Lin, Z.D., Moll T., Luebbert, C., Chauhan, R.D., Vijayaraghavan, A., Renninger, K., Beyene, G., Taylor, N.J., Carrington, J.C., Staskawicz, B.J., Bart, R. (2018) Simultaneous CRISPR/Cas9-mediated editing of cassava eIF4E isoforms nCBP-I and nCBP-2 confers elevated resistance to cassava brown streak disease. Plant Biotechnology Journal. https://doi.org/10.1111/pbi.12987
Hummel, A. W., Chauhan, R. D., Cermak, T., Mutka, A. M., Vijayaraghavan, A., Boyher, A., Starker, C. G., Bart, R., Voytas, D. F., & Taylor, N. J. (2018). Allele exchange at the EPSPS locus confers glyphosate tolerance in cassava. Plant biotechnology journal, 16(7), 1275–1282. https://doi.org/10.1111/pbi.12868
Berry, J., Fahlgren, N., Bart, R., Veley, K. A statistical method for image set standardization including measurement of variation. PeerJ. 10.7717/peerj.5727
Phillips, A.Z., Wheeler, T., Woodward, J., Bart, R. (2018) “Pseudomonas syringae pathogen causes foliar disease of Upland Cotton in Texas” Plant Disease. https://doi.org/10.1094/PDIS-11-17-1700-PDN
2017
Odipio, J., Alicai, T., Ingelbrecht, I., Nusinow D.A., Bart, R., Taylor, N.J. (2017) Efficient CRISPR/Cas9 Genome Editing of Phytoene desaturase in Cassava. Frontiers in Plant Science 8:1780. doi: 10.3389/fpls.2017.01780
Veley, K.M., Berry, J.C., Fentress, S.J., Schachtman, D.P., Baxter, I., Bart, R. (2017) High-throughput profiling identifies resource use efficient and abiotic stress tolerant sorghum varieties. Plant Direct, 2017;00:1–13. https://doi.org/10.1002/pld3.23
Phillips, A.Z., Berry, J.C., Wilson, M.C., Vijayaraghavan, A., Burke, J., Bunn, I., Allen, T.W., Wheeler, T., Bart, R. (2017) Genomics-enabled analysis of the emergent disease cotton bacterial blight. PLoS Genetics 13(9): e1007003. https://doi.org/10.1371/journal.pgen.1007003
Michelmore, R., Coaker, G., Bart, R., et.al. (2017) Foundational and translational research opportunities to improve plant health. Molecular Plant-Microbe Interactions, 30, no.7: 515-516. https://doi.org/10.1094/MPMI-01-17-0010-CR
Bart, R.S., Taylor, N.J. (2017) New opportunities and challenges to engineer disease resistance in cassava, a staple food of African small-holder farmers. PLOS Pathogens. 13, no.5. https://doi.org/10.1371/journal.ppat.1006287
Wilson, M.C., Mutka, A.M., Hummel, A.W., Berry, J., Chauhan, R.D., Vijayaraghavan, A., Taylor, N.J., Voytas, D.F., Chitwood, D.H., Bart, R.S. (2017) Gene expression analysis provides insight into the physiology of the important staple food crop cassava. New Phytologist, 213, no.4:1632-1641. doi:10.11112/nph.14443
Ramu, P., Esuma W., Kawuki R., Rabbi I.Y., Egesi, C., Bredeson J.V., Bart, R.S., Verma J., Buckler, E.S., Lu F. (2017) Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation. Nature Genetics, 49: 959-963. doi:10.1038/ng.3845
2016
Pauli, D., Chapman, S.C., Bart, R., Topp, C.N., Lawrence-Dill, C.J., Poland, J., Gore, M.A. (2016) The quest for understanding phenotypic variation via integrated approaches in the field environment. Plant Physiology, 172, no.2: 622-634. https://doi.org/10.1104/pp.16.00592
Fahlgren N, Bart R, Herrera-Estrella L, Rellan-Alvarez R, Chitwood DH, Dinneny JR. Plant scientists: GM technology is safe. Science. 2016;351(6275):824-824. doi:10.1126/science.351.6275.824-a.
Mutka, A.M., Fentress, S.J., Sher, J.W., Berry, J.C., Pretz, C., Nusinow, D.A., Bart, R.S. (2016) Quantitative, image-based phenotyping methods provide insight into spatial and temporal dimensions of plant disease. Plant Physiology, 172, no. 2: 650-660. dx.doi.org/10.1104/pp.16.00984
Bredeson, J.V., Lyons, J.B., Prochnik, S.E., Wu, G.A., Ha, C.M., Edsinger-Gonzales, E., Grimwood, J., Schmutz, J., Rabbi, I.Y., Egesi, C., Nauluvula, P., Lebot, V., Ndunguru, J., Mkamilo, G., Bart, R. S., Setter, T.L., Gleadow, R.M., Kulakow, P., Ferguson, M.E., Rounsley, S., Rokhsar, D. S. (2016). Sequencing Wild and Cultivated Cassava and Related Species Reveals Extensive Interspecific Hybridization and Genetic Diversity. Nat. Biotechnol., 34, no. 5: 562–570. doi:10.1038/nbt.3535
Chern, M., Xu Q, Bart, R.S., Bai, W., Ruan, D., Sze-To, W.H., Canlas, P.E., Jain, R., Chen, X., Ronald, P.C. (2016) A Genetic Screen Identifies a Requirement for Cysteine-Rich–Receptor-Like Kinases in Rice NH1 (OsNPR1)-Mediated Immunity. PLoS Genet., 12(5): e1006049. doi: 10.1371/journal.pgen.1006049
2015
Wang, H., Beyene, G., Zhai, J., Feng, S., Fahlgren, N., Taylor, N., Bart, R., Carrington, J.C., Jacobsen, S.E., Ausin, I. (2015). CG gene body DNA methylation changes and evolution of duplicated genes in cassava. PNAS, 112 (44) 13729-13734; published ahead of print October 19, 2015,https://doi.org/10.1073/pnas.1519067112
Schwartz, A. R., Potnis, N., Timilsina, S., Wilson, M., Patané, J., Martins, J., Jr, Minsavage, G. V., Dahlbeck, D., Akhunova, A., Almeida, N., Vallad, G. E., Barak, J. D., White, F. F., Miller, S. A., Ritchie, D., Goss, E., Bart, R. S., Setubal, J. C., Jones, J. B., & Staskawicz, B. J. (2015). Phylogenomics of Xanthomonas field strains infecting pepper and tomato reveals diversity in effector repertoires and identifies determinants of host specificity. Frontiers in microbiology, 6, 535. https://doi.org/10.3389/fmicb.2015.00535
Mutka, A. M., & Bart, R. S. (2015). Image-based phenotyping of plant disease symptoms. Frontiers in plant science, 5, 734. https://doi.org/10.3389/fpls.2014.00734
Schwessinger, B., Bart, R., Krasileva, K. V., & Coaker, G. (2015). Focus issue on plant immunity: from model systems to crop species. Frontiers in plant science, 6, 195. https://doi.org/10.3389/fpls.2015.00195
2014-2006
Timilsina, S., Jibrin, M., Potnis, N., Minsavage, G., Kebede, M., Schwartz, A., Bart, R., Staskawicz, B., Boyer, C., Vallad, G., Pruvost, O., Jones, J.B., Goss, E.M. (2014). Multilocus sequence analysis of xanthomonads causing bacterial spot of tomato and pepper reveals strains generated by recombination among species and recent global spread of Xanthomonas gardneri. Appl. Environ. Microbiol., 81:1520-1529. doi: 10.1128/AEM.03000-14.
Cohn, M.*, Bart, R.*, Shybut, M., Dahlbeck, D., Gomez, M., Morbitzer, R., Hou, B. H., Frommer, W. B., Lahaye, T., Staskawicz, B. J. (2014). Xanthomonas axonopodis virulence is promoted by a transcription activator like (TAL) effector mediated induction of a SWEET sugar transporter in cassava. Mol. Plant Microbe Interact., 27: 1186-1198. http://dx.doi.org/10.1094/MPMI-06-14-0161-R. *Equal contribution.
Arrieta-Ortiz, M. L., Rodriguez-R, L. M., Perez-Quintero, A. L., Poulin, L., Díaz, A. C., Arias Rojas, N., Trujillo, C., Restrepo Benavides, M. Bart, R., et al. (2013). Genomic Survey of Pathogenicity Determinants and VNTR Markers in the Cassava Bacterial Pathogen Xanthomonas axonopodis pv. Manihotis Strain CIO151. PLoS One, 8(11), e79704. doi:10.1371/journal.pone.0079704
Bart, R., Cohn, M., Kassen, A., McCallum, E. J., Shybut, M., Petriello, A., Krasileva, K., Dahlbeck, D., Medina, C., Alicai, T., Kumar, L., Moreira, L.M., Rodrigues Neto, J., Verdier, V., Santana, M.A., Kositcharoenkul, N., Vanderschuren, H., Gruissem, W., Bernal, A. & Staskawicz, B. (2012). High-throughput genomic sequencing of cassava bacterial blight strains identifies conserved effectors to target for durable resistance. PNAS, 109(28), E1972–E1979. doi:10.1073/pnas.1208003109
Bart, R. S., Chern, M., Vega-Sánchez, M. E., Canlas, P., & Ronald, P. C. (2010). Rice Snl6, a cinnamoyl-CoA reductase-like gene family member, is required for NH1-mediated immunity to Xanthomonas oryzae pv. oryzae. PLoS Genetics, 6(9), e1001123. doi:10.1371/journal.pgen.1001123
Park, C.-J., Bart, R., Chern, M., Canlas, P. E., Bai, W., & Ronald, P. C. (2010). Overexpression of the endoplasmic reticulum chaperone BiP3 regulates XA21-mediated innate immunity in rice. PloS One, 5(2), e9262. doi:10.1371/journal.pone.0009262
Ding, X., Richter, T., Chen, M., Fujii, H., Seo, Y. S., Xie, M., et al. (2009). A rice kinase-protein interaction map. Plant Physiol., 149(3), 1478–1492. doi:10.1104/pp.108.128298
Park, C.-J., Peng, Y., Chen, X., Dardick, C., Ruan, D., Bart, R., et al. (2008). Rice XB15, a protein phosphatase 2C, negatively regulates cell death and XA21-mediated innate immunity. PLoS Biol., 6(9), e231. doi:10.1371/journal.pbio.0060231
Bart, R., Chern, M., Park, C.-J., Bartley, L., & Ronald, P. C. (2006a). A novel system for gene silencing using siRNAs in rice leaf and stem-derived protoplasts. Plant Methods, 2(1), 13. doi:10.1186/1746-4811-2-13
Bart, R., Ronald, P., & Hake, S. (2006b). Fertility versus disease resistance, a hard choice. Genes & Develop., 20(10), 1215–1217. doi:10.1101/gad.1437706