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Germplasm Bank of Wild Species
LI Dezhu's Group
YANG Yongping's Group
HU Xiangyang's Group
LI Weiqi's Group
GAO Lizhi's Group
YI Tingshuang's Group
GUO Zhenhua's Group
Jeff Bennetzen's Group
ZHANG Chengjun's Group
Location: Home > Germplasm Bank of Wild Species > Jeff Bennetzen's Group > Publications
Selective Publications

1. Estep, M.C., J.D. DeBarry and J.L. Bennetzen. 2013. The dynamics of LTR retrotransposon accumulation across 35 million years of panicoid grass evolution. Heredity 110: 194-204.

2. 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.

3. 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.

4. 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.

5. 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.

6. 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.

7. 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.

8. 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)

9. 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.

10. 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.

11. 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.

12. 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.

13. 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.

14. 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.

15. 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.

16. Lisch, D. and J.L. Bennetzen. 2011. Transposable element origins of epigenetic gene regulation. Curr. Opin. Plant Biol. 14: 156-161.

17. 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.

18. 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.

19. Vitte, C., T. Peterson and J.L. Bennetzen. 2011. Transposable elements in 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.

20. 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).

21. 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.

22. 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.

23. 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.

24. 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.

25. 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.

26. 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.

27. 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).

28. 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.

29. 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.

30. 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).

31. 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.

32. 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.

33. 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.

34. 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

35. 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.

36.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.

37.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.

38.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

39.DeBarry, J., R. Liu, and J.L. Bennetzen. 2008. Discovery and assembly of repeat family pseudomolecules from sparse genomic sequence data using the Assisted Automated Assembler of Repeat Families (AAARF) algorithm. BMC Bioinformatics 9: 235.

40.Conner, J.A., S. Goel, G. Gunawan, M.-M. Cordonnier-Pratt, V.E. Johnson, C. Liang, H. Wang, L.H. Pratt, J.E. Mullet, J. DeBarry, L. Yang, J.L. Bennetzen, P.E. Klein and P. Ozias-Akins. 2008. Sequence analysis of BAC clones from the apospory-specific genomic regions (ASGR) of Pennisetum and Cenchrus. Plant Physiol. 147: 1396-1411.

41.Dida, M.M., N. Wanyera, M.L. Harrison Dunn, J.L. Bennetzen and K.M. Devos. 2008. Population structure and diversity in finger millet (Eleusine coracana) germplasm. Tropical Plant Biol. 1: 131-141.

42.Nagy, E.D. and J.L. Bennetzen. 2008. Pathogen corruption and site-directed recombination at a plant disease resistance gene cluster. Genome Res. 18: 1918-1923.

43.Nelson, W.M., M. Luo, J. Ma, M. Estep, J. Estill, R. He, J. Talag, N. Cisneros, D. Kudrna, H. Kim, J.S.S. Ammiraju, K. Collura, A.K. Bharti, J. Messing, R.A. Wing, P. SanMiguel, J.L. Bennetzen and C. Soderlund. 2008. Methylation-sensitive linking libraries enhance gene-enriched sequencing of complex genomes and map DNA methylation domains. BMC Genomics, in press, published on line.

44.Ammiraju, J.S.S., F. Lu, A. Sanyal, Y. Yu, X. Song, N. Jiang, A.C. Pontaroli, T. Rambo, J. Currie, K. Collura, J. Talag, C. Fan, J.L. Goicoechea, A. Zuccolo, J.L. Bennetzen, M. Chen, S. Jackson and R.A. Wing. 2008. Dynamic evolution of Oryza genomes revealed by comparative genomic analysis of a genus-wide vertical dataset. Plant Cell, in press, published on line.

45.Rensing, S.A., D. Lang, A. Zimmer, A. Terry, A. Salamov, H. Shapiro, T. Nishiyama, P.-F. Perroud, E. Lindquist, Y. Kamisugi, T. Tanahashi, K. Sakakibara, T. Fujita, K. Oishi, T. Shin, Y. Kruoki, A. Toyoda, Y. Suzuki, S. Hashimoto, K. Yamaguchi, S. Sugano, Y. Kohara, A. Fujiyama, A. Anterola, S. Aoki, N. Ashton, W.B. Barbazuk, E. Barker, J.L. Bennetzen, R. Blankenship, S.H. Cho, S. Dutcher, M. Estelle, J.A. Fawcett, H. Gundlach, K. Hanada, A. Heyl, K.A. Hicks, J. Hughes, M. Lohr, K. Mayer, A. Melkozernov, T. Murata, D. Nelson, B. Pils, M. Prigge, B. Reiss, T. Renner, S. Rombauts, P. Rushton, A. Sanderfoot, G. Schween, S.-H. Shiu, K. Stueber, F.L. Theodoulou, H. Tu, Y. Van de Peer, P.J. Verrier, E. Waters, A. Wood, L. Yang, D. Cove, A.C. Cuming, M. Hasebe, S. Lucas, B.D. Mishler, R. Reski, I. Grigoriev, R.S. Quatrano and J.L. Boore. 2008. The genome of the moss Physcomitrella patens reveals evolutionary insights into the conquest of land by plants. Science 319: 64-6

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