Daniel Peterson

Daniel Peterson

Professor

Plant Genomics and Molecular Biology



Mailing Address:
Box 9555
Mississippi State, MS 39762
Mailing Address:
424 Dorman Hall
Mississippi State, MS 39762
Education:
  • Ph.D., Colorado State University
  • M.S., Colorado State University
  • B.S., Colorado State University

Courses:
  • Genomes and Genomics
  • Topics in Genomics

Society Membership:
  • Genetics Society of America (GSA)
  • American Society of Plant Biologists (ASPB)

Recognitions and Awards:
  • 2012 Cotton Biotechnology Award, Cotton Incorporated
  • 2008 Distinguished Fellow, Life Sciences and Biotechnology Institute, Mississippi State University
  • 2007 Grantsmanship Award - Mississippi Agricultural and Forestry Experiment Station (MAFES), Mississippi State University
  • 2007 Sigma Xi Scientific Research Society, Mississippi State University
  • 2006 Fellow of the Institute for Digital Biology (IDB) at Mississippi State University
  • 2004 Grantsmanship Award - Mississippi Agricultural and Forestry Experiment Station (MAFES), Mississippi State University

Publications

  • Hsu, C.-Y., M. A. Arick, Q. Miao, S. Saha, J. N. Jenkins, M. S. Ayubov, I. Y. Abdurakhmonov, D. G. Peterson, D.-P. Ma, 2018. Transcriptome analysis of ten days post anthesis elongating fiber in the upland cotton (Gossypium hirsutum) chromosome substitution line CS-B25. American Journal of Plant Sciences 9(6):1334-1361. Download
  • Wright, A. A., M. Rodriguez-Carres, R. Sasidharan, L. Koski, D. G. Peterson, V. K. Nandula, J. D. Ray, J. A. Bond, D. R. Shaw. 2018. Multiple herbicide-resistant Junglerice (Echinochloa colona): Identification of genes potentially involved in resistance through differential gene expression analysis. Weed Science 66:347-354. Download
  • Wright, A. A., R. Sasidharan, L. Koski, M. Rodriguez-Carres, D. G. Peterson, V. K. Nandula, J. D. Ray, J. A. Bond, D. R. Shaw. 2018. Transcriptomic changes in Echinochloa colona in response to treatment with the herbicide imazamox. Planta 247(2):369-379. Download
  • Showmaker, K. C., M. A. Arick II, C.-Y. Hsu, B. E. Martin, X. Wang, J. Jia, M. J. Wubben, R. L. Nichols, T. W. Allen, D. G. Peterson, S. Lu. 2017. The genome of the cotton bacterial blight pathogen Xanthomonas citri pv. malvacearum strain MSCT1. Standards in Genomic Sciences 12:42. Download
  • Deng, P., X. Wang, S. M. Baird, K. C. Showmaker, L. J. Smith, D. G. Peterson, S. Lu. 2016. Comparative genome-wide analysis reveals that Burkholderia contaminans MS14 possesses multiple antimicrobial biosynthesis genes but not major genetic loci required for pathogenesis. MicrobiologyOpen 5(3):353-369. Download
  • Shanmugam, S. G., N. W. Buehring, M. W. Ebelhar, M. S. Cox, J. L. Oldham, D. G. Peterson, W. L. Kingery. 2016. Short-term effects of tillage treatments on soil microbial biodiversity under soybean-corn rotation. International Journal of Agriculture and Environmental Research 2(5):1277-1303. Download
  • Shanmugam, S.,G., Z. V. Magbanua, M. A. Williams, K. Jangid, W. B. Whitman, D. G. Peterson, W. L. Kingery. 2016. Bacterial diversity patterns differ in soils developing in sub-tropical and cool-temperate ecosystems. Microbial Ecology 73(3):556-569. Download
  • Wright, A. A., V. K. Nandula, L. Grier, K. C. Showmaker, J. A. Bond, D. G. Peterson, J. D. Ray, D. R. Shaw. 2016. Characterization of fenoxaprop-p-ethyl-resistant junglerice (echinochloa colona) from Mississippi. Weed Science 64(4):588-596. Download
  • Jaratlerdsiri, W., J. Deakin, R.M. Godinez, X. Shan, D.G. Peterson, S. Marthey, E. Lyons, F.M. McCarthy, S.R. Isberg, D.P. Higgins, A.Y. Chong, J.A. St. John, T.C. Glenn, D.A. Ray, and J. Gongora.. 2014. Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC . PLoS ONE, Vol. 9(12):e114631., Download
  • Magbanua, Z.V., M. Arick, T.J. Buza, C. Hsu, K.C. Showmaker, P. Chouvarine, P. Deng, D.G. Peterson, and S. Lu. 2014. Transcriptomic dissection of the rice - Burkholderia glumae interaction. BMC Genomics, Vol. 15:755., Download
  • Wang, X., K.C. Showmaker, X.Q. Yu, T. Bi, C. Hsu, S.M. Baird, D.G. Peterson, X.D. Li, and S. Lu. 2014. Draft genome sequence of Burkholderia pyrrocinia Lyc2, a biological control strain that can suppress multiple plant microbial pathogens. Genome Announcements, Vol. 2(5):e00991-14., Download
  • Chouvarine, P., A.M. Cooksey, F.M. McCarthy, D.A. Ray, B.S. Baldwin, S.C. Burgess, D.G. Peterson. 2012. Transcriptome-based differentiation of closely-related Miscanthus lines. PLoS ONE 7(1):e29850. Download
  • Paterson, A.H., J.F. Wendel, H. Gundlach, H. Guo, J. Jenkins, D. Jin, D. Llewellyn, K.C. Showmaker, S. Shu, J. Udall, M. Yoo, R. Byers, W. Chen, A. Doron-Faigenboim, M.V. Duke, L. Gong, J. Grimwood, C. Grover, K. Grupp, G. Hu, T. Lee, J. Li, L. Lin, T. Liu, B. S. Marler, J.T. Page, A.W. Roberts, E. Romanel, W.S. Sanders, E. Szadkowski, X. Tan, H. Tang, C. Xu, J. Wang, Z. Wang, D. Zhang, L. Zhang, H. Ashrafi, F. Bedon, J.E. Bowers, C.L. Brubaker, P.W. Chee, S. Das, A.R. Gingle, C.H. Haigler, D. Harker, L. V. Hoffmann, R. Hovav, D.C. Jones, C. Lemke, S. Mansoor, M. ur Rahman, L.N. Rainville, A. Rambani, U.K. Reddy, J. Rong, Y. Saranga, B.E. Scheffler, J.A. Scheffler, D.M. Stelly, B.A. Triplett, A. Van Deynze, M.F. S. Vaslin, V.N. Waghmare, S.A. Walford, R.J. Wright, E.A. Zaki, T. Zhang, E.S. Dennis, K.F.X. Mayer, D.G. Peterson, D.S. Rokhsar, X.Wang, J. Schmutz. 2012. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature 492:423-427
  • St. John, J.A., E.L. Braun, S.R. Isberg, L.G. Miles, A.Y. Chong, J. Gongora, P. Dalzell, C. Moran, B. Bed'Hom, A. Abzhanov, S.C. Burgess, A.M. Cooksey, T.A. Castoe, N.G. Crawford, L.D. Densmore, J.C. Drew, S.V. Edwards, C. Faircloth, M.K. Fujita, M.J. Greenwold, F.G. Hoffmann, T. Iguchi, D.E. Janes, S.I. Khan, S. Kohno, A.P. de Koning, S.L. Lance, F.M. McCarthy, J.E. McCormack, M.E. Merchant, D.G. Peterson, D. Pollock, N. Pourmand, B.J. Raney, K.A. Roessler, J.R. Sanford, R.H. Sawyer, C.J. Schmidt, E.W. Triplett, T.D. Tuberville, M. Venegas-Anaya. 2012. Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biology and Evolution 13:415. Download
  • Moolhuijzen, P., A. Ala Lew-Tabor, J. Morgan, V.M. Rodriguez, D.G. Peterson, S.E. Dowd, F.D. Guerrero, M. Bellgard, R. Appels. 2011. The complexity of Rhipicephalus (Boophilus) microplus genome characterised through detailed analysis of two BAC clones. BioMed Central Genomics 4:254. Download
  • Guerrero, F.D., P. Moolhuijzen, D.G. Peterson, S. Bidwell, E. Caler, R. Appels, M. Bellgard, V.M. Nene, A. Djikeng. 2010. Reassociation kinetics-based approach for partial genome sequencing of the cattle tick, Rhipicephalus (Boophilus) microplus. BioMed Central Genomics 11:374. Download
  • Lin, L., G.J Pierce, J.E. Bowers, J.C. Estill, R.O. Compton, L.K. Rainville, C. Kim, C. Lemke, J. Rong, H. Tang, X. Wang, M. Braidotti, A.H. Chen, K. Chicola, K. Collura, E. Epps, W. Golser, C. Grover, J. Ingles, S. karunakaran, D. Kudrna, J. Olive, N. Tabassum, E. um, M. Wissotski, Y. Yu, A. Zuccolo, M.U. Rahman, D.G. Peterson, R.A. Wing, J.F. Wendel, A.H. Paterson. 2010. A draft physical map of a D-genome cotton species (Gossypium raimondii). BMC Genomics 11:395. Download
  • Paterson, A.H., J. Rong, A.R. Gingle, P.W. Chee, E.S. Dennis, D. Llewellyn, L.S. Dure, C. Haigler, G.O. Myers, D.G. Peterson, M.Rahman, Y. Zafar, U. Reddy, Y. Saranga, J.M. Stewart, J.A. Udall, V.N. Waghmare, J.F. Wendel, T.A. Wilkins, R.J. Wright, E. Zaki, E.E. Hafex, J. Zhu. 2010. Sequencing and utilization of the Gossypium genomes. Tropical Plant Biology 3(2):71-74. Download
  • Bunge, J., P. Chouvarine, D.G. Peterson. 2009. CotQuest: Improved algorithm and software for nonlinear regression analysis of DNA reassociation kinetics data. Analytical Biochemistry 388(2):322-330. Download
  • Morse, A.M., D.G. Peterson, M.N. Islam-Faridi, K.E. Smith, Z.V. Magbanua, S.A. Garcia, T.L. Kubisiak, H.V. Amerson, J.E. Carlson, C.D. Nelson, J.M. Davis. 2009. Evolution of genome size and complexity in Pinus. PLoS ONE 4(2):e4332. Download
  • Shan, X., D.A. Ray, J. Bunge,D.G. Peterson. 2009. A bacterial chromosome library for the Australian saltwater crocodile (Crocodylus porosus) and its utilization in gene isolation and genome characterization. BMC Genomic 10(Suppl 2):S9. Download
  • Chouvarine, P., S. Saha, D.G. Peterson. 2008. An automated, high-throughput sequence read classification pipeline for preliminary genome characterization. Analytical Biochemistry 373:78-87. Download
  • Saha, S., S. Bridges, Z.V. Magbanua, D.G. Peterson. 2008. Computational approaches and tools used in identification of dispersed repetitive DNA sequences. Tropical Plant Biology 1(1):85-96. Download
  • Saha, S., S. Bridges, Z.V. Magbanua, D.G. Peterson. 2008. Discovering relationships among dispersed repeats using spatial association rule mining. BMC Bioinformatics 9(Suppl 10):04. Download
  • Saha, S., S. Bridges, Z.V. Magbanua, D.G. Peterson. 2008. Empirical comparison of ab initio repeat finding programs. Nucleic Acids Research 36(7):2284-2294. Download
  • Bunge, J., S.S. Epstein, D.G. Peterson. 2006. Comment on "Computations improvements reveal great bacterial diversity and high metal toxicity in soil. Science 313(5789):918. Download
  • Dennis, J.H., H. Fan, S.M. Reynolds, G. Yuan, J.C. Meldrim, D.J. Richter, D.G. Peterson, O.J. Rando, W.S. Noble, R.E. Kingston. 2007. Independent and complementary methods for large-scale structural analysis of mammalian chromatin. Genome Research 17:928-939. Download
  • Plomion, C., D. Chagne, D. Pot, S. Kumar, P.L. Wilcox, R.D. Burdon, D. Prat, D.G. Peterson, J. Paiva, P. Chaumeil, G.G. Vendramin, F. Sebastiani, C.D. Nelson, C.S. Echt, O. Savolainen, T.L. Kubisiak, M.T. Cervera, N. de Maria, M.N. Islam-Faridi. 2007. Pines. Chapter 2, Pages 29-78 in C. Kole, editor, Forest Trees. Genome Mapping and Molecular Breeding in Plants, Volume 7. Springer.
  • Lamoureux, D., D.G. Peterson, W. Li, J.P. Fellers, B.S. Gill. 2005. The efficacy of Cot-based gene enrichment in wheat (Triticum aestivum L.). Genome 48(6):1120-1126. Download
  • Peterson, D.G. 2005. Reduced representation strategies and their application to plant genomes. The Handbook of Plant Genome Mapping: Genetic and Physical Mapping (eds K. Meksem and G. Kahl), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, FRG. Download
  • Wicker, T., J.S. Robertson, S.R. Schulze, F.A. Feltus, V. Magrini, J.A. Morrison, E.R. Mardis, R.K. Wilson, D.G. Peterson, A.H. Paterson, R. Ivarie. 2005. The repetitive landscape of the chicken genome. Genome Research 15(1):126-136. Download