Source: http://genetics.uga.edu/directory/jeffrey-bennetzen
Timestamp: 2019-04-21 22:48:45+00:00

Document:
My lab is interested in plant genome structure and evolution, especially the nature of rearrangements and the contributions of transposable elements. We also study the relationship between genome structure, evolution and gene function. We have long-standing interestes in genetic diversity and its use in under-utilized crops of the developing world, the rapid evolution of complex disease resistance loci in plants, fine structure recombinational analysis, epigenetic gene regulation, biomass improvement for bioenergy, and the coevolution of plant/microbe and plant/parasite interactions.
Chaluvadi, S. R., S. Khanam, M. Aly and J. L. Bennetzen (2014) Diversity and population structure of native and introduced date palm (Phoenix dactylifera) germplasm in the United Arab Emirates, Trop. Plant Biol. 7:30-41.
Vaughn, J. N. and J. L. Bennetzen (2014) Natural insertions in rice commonly form tandem duplications indicative of patch-mediated double-strand break induction and repair. Proc. Natl. Acad. Sci. USA 111:6684-6689.
Hawkins, J. S., V. Delgado, L. Feng, M. Carlisle, H. K. Dooner and J. L. Bennetzen (2014) Variation in allelic expression associated with a recombination hotspot in Zea mays. Plant J. 79:375-384.
Vaughn, J. N., S. R. Chaluvadi, Tushar, L. Rangan and J. L. Bennetzen (2014) Whole plastome sequences from five ginger species facilitate marker development and define limits to barcode methodology. PLoS ONE 9: e108581 (doi: 10.1371/journal.pone.0108581).
Zhang, Q.-J, T. Zhu, E.-H. Xia, C. Shi, Y.-L. Liu, Y. Zhang, Y. Liu, W.-K. Jiang, Y.-J Zhao, S.-Y. Mao, L.-P. Zhang, H. Huang, J.-Y. Jiao, P.-Z. Xu, Q.-Y. Yao, F.-C. Zeng, L.-L. Yang, J. Gao, D.-Y. Tao, Y.-J. Wang, J. L. Bennetzen and L.-Z. Gao (2014) Rapid diversification of five Oryza AA genomes associated with rice adaptation. Proc. Natl. Acad. Sci. USA doi:10.1073/pnas.1418307111.
Wang, H., K. M. Devos and J. L. Bennetzen (2014) Recurrent loss of specific introns during angiosperm evolution. PLoS Genetics (doi:10.1371/journalpgen. 1004843).
Bennetzen, J. L. and H. Wang (2014) The contributions of transposable elements to the structure, function and evolution of plant genomes. Ann. Rev. Plant Biol. 65:505-530.
Diao, X., J. Schnable, J. L. Bennetzen and J. Li (2014) Initiation of Setaria as a model plant. Front. Agr. Sci. Eng. 1:16-20.
Wang, C., X. Shi, L. Liu, H. Li, J. S. S. Ammiraju, D. A. Kudrna, W. Xiong, H. Wang, Z. Dai, Y. Zheng, J. Lai, W. Jin, J. Messing, J. L. Bennetzen, R. A. Wing and M. Luo (2013) Genomic resources for gene discovery, functional genome association and evolutionary studies of maize and its close relatives. Genetics 195:723-727.
Vitte, C., M. Estep, J. Leebens-Mack and J.L. Bennetzen (2013) Young, intact and nested retrotransposons are abundant in the onion and asparagus genomes. Annals Bot. 112:881-889.
Chao, M., H. Wang, D. Chung, J. L. Bennetzen and J. Westpheling (2013) Isolation and bioinformatics analysis of a novel transposable element, ISCbe4, from the hyperthermophilic bacterium, Caldicellulosiruptor bescii. J. Industrial Micro. Biotech. 40:1443-1448.
Wang, C., X. Shi, L. Liu, H. Li, J.S.S. Ammiraju, D.A. Kudrna, W. Xiong, H. Wang, Z. Dai, Y. Zheng, J. Lai, W. Jin, J. Messing, J.L. Bennetzen, R.A. Wing and M. Luo (2013) Genetics 195:723-727.
Zhu, Q., J. L. Bennetzen and S.M. Smith (2013) Isolation and diversity analysis of resistance gene homologues from switchgrass. G3: Genes, Genomes and Genetics 3: 1031-1042.
Estep, M.C., J. D. DeBarry and J. L. Bennetzen (2013) The dnyamics of LTR retrotransposon accumulation across 35 million years of panicoid grass evolution. Heredity 110: 194-204.
Parvathaneni, R. K., V. Jakkula, F. K. Padi, S. Faure, N. Nethra, A. C. Pontaroli, X. Wu, J. L. Bennetzen and K. M. Devos (2013) Fine mapping and identification of a candidate gene underlying the d2 dwarfing phenotype in pearl millet, Cenchrus americanus (L.) Morrone. G3: Genes, Genomes and Genetics 3: 567-572.
Federoff, N. V. and J. L. Bennetzen (2013) Transposons, genomic shock and genome evolution. In: N.V. Fedoroff, ed., Plant Transposons and Genome Dynamics in Evolution, John Wiley & Sons, pp. 181-201.
Wang, H. and J. L. Bennetzen (2012) Centromere retention and loss during the descent of maize from a tetraploid ancestor. Proc. Natl. Acad. Sci. USA 109: 21004-21009.
Bennetzen, J. L., J. Schmutz, H. Wang, R. Percifield, J. Hawkins, A. C. Pontaroli, M. Estep, L. Feng, J. N. Vaughn, J. Grimwood, J. Jenkins, K. Barry, E. Lindquist, U. Hellsten, S. Deshpande, X. Wang, X. Wu, T. Mitros, J. Triplett, X. Yang, C.-Y. Ye, M. Mauro-Herrera, L. Wang, P. Li, M. Sharma, R. Sharma, P. C. Ronald, O. Panaud, E. A. Kellogg, T. Brutnell, A. Doust, G. A. Tuskan, D. Rokhsar and K. M. Devos (2012) Full genome sequence analysis of the model plant Setaria. Nature Biotech. 30: 555-561.
Smith, S. M., Y. Yuan, A. N. Doust and J. L. Bennetzen (2012) Haplotype analysis and linkage disequilibrium at five loci in Eragrostis tef. G3: Genes, Genomes and Genetics 2: 407-419.
Estep, M. C., B. S. Gowda, K. Huang, M. P. Timko and J. L. Bennetzen (2012) Genomic characterization for parasitic weeds of the genus Striga by sample sequence analysis. Plant Genome 5: 30-41.
Urano, D., J. C. Jones, H. Wang, M. Mathew, W. Bradford, J. L. Bennetzen and A. M. Jones (2012) G protein activation without a GEF in the plant kingdom. PLoS Genetics, online (doi: 10.1371/journal.pgen.1002756).
Wu, J., Z. Wang, Z. Shi, S. Zhang, R. Ming, S. Zhu, M. Awais Khan, S. Tao, S. S. Korbans, H. Wang, N. J. Chen, T. Nishio, X. Xu, L. Cong, K. Qui, X. Huang, Y. Wang, X. Zhao, J. Wu, C. Deng, C. Gou, W. Zhou, H. Yin, G. Qin, Y. Sha, Y. Tao, H. Chen, Y. Yang, Y. Song, D. Zhan, J. Wang, L. Li, M. Dai, C. Gu, Y. Wang, D. Shi, X. Wang, H. Yang, L. Zeng, C. Zheng, C. Wang, M. Chen, G. Wang, L. Xie, V. Sovero, S. Sha, W. Huang, S. Zhang, M. Zhang, J. Sun, L. Xu, Y. Li, X. Lui, Q. Li, J. Shen, J. Wang, R. E. Paull, J. L. Bennetzen, J. Wang and S. Zhang (2012) The genome of pear (Pyrus bretschneideri Rhed). Genome Res. 23: 396-408.
Zhu, Q., S. M. Smith, M. Ayele, L. Yang, A. Jogi, S. Chaluvadi and J. L. Bennetzen (2012) High throughput discovery of mutations in tef semi-dwarfing genes by next generation sequence analysis. Genetics 192: 819-829.
Xu, J.-H., J. L. Bennetzen and J. Messing (2012) Dynamic gene copy number variation in collinear regions of grass genomes. Mol. Biol. Evol. 29: 861-871.
Estep, M., T. A. Van Mourik, P. Muth, D. Guindo, H. K. Parzies, O. A. Koita, E. Weltzien and J. L. Bennetzen (2011) Genetic diversity of a parasitic weed, Striga hermonthica, on sorghum and pearl millet in Mali. Tropical Plant Biol. 4: 91-98.
Shulaev, V. et al [66 authors, including H. Wang and J.L. Bennetzen] (2011) The genome of woodland strawberry (Fragaria vesca). Nature Genetics 43: 109-116.
Banks, J. A. et al [103 authors, including J. DeBarry, L. Feng, L. Yang, Q. Zhu and J. L. Bennetzen] (2011) The compact Selaginella genome identifies changes in gene content associated with the evolution of vascular plants. Science 332: 960-963.
Al-Dous, E. K., B. George, M. E. Al-Mahmoud, M. Y. Al-Jaber, H. Wang, Y. M. Salameh, E. K. Al-Azwani, S. Chaluvadi, A. C. Pontaroli, J. DeBarry, J. Ohlrogge, V. Arondel, I. J. Saie, K. M. Suliman-Elmeer, J. L. Bennetzen, R. R. Kruegger and J. A. Malek (2011) De novo genome sequencing and comparative genomics of the date palm (Phoenix dactylifera). Nature Biotech. 29: 521-527.
Lisch, D. and J. L. Bennetzen (2011) Transposable element origins of epigenetic gene regulation. Curr. Opin. Plant Biol. 14: 156-161.
Wusirika, R., K. Li, R. L. Phillips and J. L Bennetzen (2011) Zea. In: C. Kole, ed., Wild Crop Relatives: Genomic and Breeding Resources. Vol 1: Wild Relatives of Cereals. Springer Verlag, Berlin, Heidelberg, pp. 457-488.
Desphande, A., A. C. Pontaroli, S. R. Chaluvadi, F. Lu and J. L. Bennetzen (2011) Plant genetics for study of the roles of root exudates and microbes in soil. In: A. Costa de Oliveira and R.K. Varshney, eds., Root Genomics, Springer, pp. 99-112.
Vitte, C., T. Peterson and J.L. Bennetzen (2011) Transposable elements and the evolving structure of the maize genome. In: J.L. Prioul, ed., Advances in Maize, Taylor and Francis, Soc. Exp. Biol., London, pp. 2-36.
Mann, D.G.J., Z.R. King, W. Liu, B.L. Joyce, R.J. Percifield, J.S. Hawkins, P.R. LaFayette, B.J. Artelt, J.N Burris, M. Mazarei, J.L. Bennetzen, W.A. Parrott and C.N. Stewart, Jr (2011) Switchgrass (Panicum virgatum L.) ubiquitin gene (PvUbi1 and PvUbi2) promoters for use in plant transformation. BMC Biotech. 11: 74 (doi: 10.1186/1472-6750-11-74).
Gleick, P.H. and 254 additional U.S. National Academy of Sciences members (incl. J.L. Bennetzen) (2010) Climate change and the integrity of science. Science 328: 689-690.
Davis, T. M., M. E. Shields, Q. Zhang, D. C. Tombolato, J. L. Bennetzen, A. C. Pontaroli, H. Wang, Q. Yao, P. SanMiguel and K. M. Folta (2010) An examination of targeted gene neighborhoods in strawberry. BMC Plant Biol. 10: 81, publ. online.
Jetty, S., C. Fan, Y. Yu, X. Song, K. Cranston, A.C. Pontaroli, F. Lu, A. Sanyal, N. Jiang, T. Rambo, J. Currie, K. Collura, J. Talag, J. L. Bennetzen, M. Chen, S. Jackson and R.A. Wing (2010) Spatio-temporal patterns of genome evolution in allotetraploid species of the genus Oryza. Plant J. 63: 430-442.
Baucom, R. S., J. C. Estill, J. Leebens-Mack and J. L. Bennetzen (2009) Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome. Genome Res. 19: 243-254.
Lu, F., J. S. S. Ammiraju, A. Sanyal, S. Zhang, R. Song, J. Chen, G. Li, Y. Sui, Z. Cheng, A. C. de Oliveira, J. L. Bennetzen, S. A. Jackson, R. A. Wing and M. Chen (2009) Comparative sequence analysis of MONOCULM1-orthologous regions in fourteen Oryza genomes. Proc. Natl. Acad. Sci. USA 106: 2071-2076.
Pontaroli, A. C., R. L. Rogers, Q. Zhang, M. E. Shields, T. M. Davis, K. M. Folta, P. SanMiguel and J. L. Bennetzen (2009) Gene content and distribution in the nuclear genome of Fragaria vesca. Plant Genome 2: 83-91.
Estill, J. C. and J. L Bennetzen (2009) The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomes. Plant Methods 5:8 (online).
Yang, L. and J. L. Bennetzen (2009) Structure-based discovery and description of plant and animal Helitrons. Proc. Natl. Acad. Sci. USA 106: 12832-12837.
Doust, A. N., E. A. Kellogg, K. M. Devos and J. L. Bennetzen (2009) Foxtail millet (Setaria italica): A sequence-driven grass model. Plant Physiol. 149: 137-141.
Bennetzen, J. L. (2009) Biology and the beasts: Individual investigator-riven research in the megaprojects era. Trends Genet. 25: 57-59. (Inaugural article, Science and Society section).
Yang, L. and J. L. Bennetzen (2009) Distribution, diversity, evolutuion and survival of Helitrons in the maize genome. Proc. Natl. Acad. Sci. USA 106: 19922-19927.
Tian, Z., C. Rizzon, J. Du, B. S. Gaut, J. L. Bennetzen, S. A. Jackson and J. Ma (2009) Genetic recombination shapes the pattern of DNA acquistion and elimination mediated by LTR-retrotransposons in rice. Genome Res. 19: 2221-2230.
Schnable, P. et al.: Maie Genome Sequences Consortium [~160 authors; R. Baucom, J. Estill, L. Yang, J.L. Bennetzen includeded] (2009) The B73 maize genome: Complexity, diversity and dynamics. Science 326: 1112-1115.
Baucom, R. S., J. C. Estill, N. Upshaw, A. Jogi, C. Chapparro, J. M. Deragon, R. R. Westerman, P. J. SanMiguel and J. L. Bennetzen (2009) Exceptional diversity, non-random distribution and rapid evolution of retroelements in the B73 maize genome. PLoS Genetics 5: e1000732 (doi: 10.1371/journal.pgen.1000732).
Bennetzen, J. L (2009) Maize genome structure and evolution. In J. L. Bennezten and S. Hake, eds., The Maize Handbook - Volume II: Genetics and Genomics. Springer, New York, pp. 179-200.
Bennetzen, J. L (2009) The future of maize. In J. L. Bennezten and S. Hake, eds., The Maize Handbook - Volume II: Genetics and Genomics. Springer, New York, pp. 771-780.
Bennetzen, J. L., S. M. Smith, Y. Yuan and D. Groth (2009) Comparative plant biology: Opening new avenues for the improvement of orphan crops in a time of rapid and potentially catastrophic change in worldwide agriculture. In: Z. Tadele, ed., New Approaches to Plant Breeding of Orphan Crops in Africa: Proceedings of an International Conference. Univ. Bern, Stampfli AG, Bern, pp. 11-20.
Wei, F., J. C. Stein, C. Liang, J. Zhang, R. S. Fulton, R. S. Baucom, E. de Paoli, S. Zhou, L. Yang, Y. Han, S. Paternak, A. Narechania, L. Zhang, C.-T. Yeh, K. Ying, D.H. Nagel, K. Collura, D. Kudrna, J. Currie, J. Lin, H. Kim, A. Angelove, G. Scara, M. Wissotski, W. Golser, L. Courtney, S. Kruchowski, T. Graves, S. Rock, S. Adams, L. Fulton, C. Fronick, W. Courtney, M. Kramer, L. Spiegel, L. Nascimento, A. Kalyanaraman, C. Chaparro, J.-M. Deragon, P. SanMiguel, N. Jiang, S.R. Wessler, P. J. Green, Y. Yu, D. C. Schwartz, B. C. Meyers, J. L. Bennetzen, R. Martienssen, W. R. McCombie, S. Aluru, S. W. Clifton, P. S. Schnable, D. Ware, R. K. Wilson and R. A. Wing (2009) Detailed analysis of a contiguous 22-Mb region of the maize genome. PLoS Genetics 5: e1000728 (doi: 10.1371/journal.pgen.1000728).

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