Norman and Doris Giles Professor Georgia Research Alliance Eminent Scholar Ph.D. (1980) University of Washington Member, National Academy of Sciences 1000 Talents Award, Chinese Academy of Sciences, 2012 Guggenheim Fellow, 2008 Elected Fellow, American Association for the Advancement of Science, 2005 Grant Support - Sequencing of the Aegilops tauschii Genome, NSF “Analysis of the Genetic and Environmental Inputs into Accurate and Inaccurate Double Strand Break Repair in Plants," NSF "Molecular Analysis of Unequal Recombination and Instability at the Pc Toxin Susceptibility Locus," USDA-NIFA Bioenergy Science Center, DOE "Unraveling the Genetics of Two Key Biomass Traits that Differentiate Upland and Lowland Tetraploid Switchgrass Ecotypes, Colonization by Mycorrhizal Fungi and Frost Tolerance," DOE Research Interests - 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. Research Research Areas: Biotechnology Genomics and Bioinformatics Molecular Genetics Selected Publications Selected Publications: Varshney, R. K., and 53 other authors, including J. L. Bennetzen (2021) A global reference for chickpea genetic variation based on the sequencing of 3,366 genomes. Nature 599:622-627. Wang, L. and 25 others, including H. Zhou and J. L. Bennetzen (2021) Aegilops tauschii genome assembly Aet v5.0 features greater sequence continuity and improved annotation. G3 (11, jkab325). Tong, W., J. Yu, Q. Wu, L. Hu, D. Tabys, Y. Wang, C. Wei, T. Ling, M. A. Inayat and J. L. Bennetzen (2021) Black tea quality is highly affected during processing by its leaf surface microbiome. J. Agric. Food Chem. 69:7115-7126. Bahulikar, R. A., S. R. Chaluvadi, I. Torres-Jerez, J. Mosali, J. L. Bennetzen and M. K. Udvardi (2020) Nitrogen fertilization reduces nitrogen fixation activity of diverse diazotrophs in switchgrass roots. Phytobiomes J. DOI:10.1094/PBIOMES-09-19-0050-FI. Park, M., P. Christin, J. L. Bennetzen. (2021) Sample sequence analysis of panicoid grass genomes uncovers episodic amplification and frequent horizontal transfer of LTR-retrotransposons. G3 Mol. Biol. Evol. May 8;msab133. DOI: 10.1093/molbev/msab133. Govindarajulu, R., A. N. Hostetler, Y. Xiao, S. R. Chaluvadi, M. Mauro-Herrera, M. L. Siddoway, C. Whipple, J. L. Bennetzen, K. M. Devos, A. N. Doust, J. S. Hawkins. (2021) Integration of high-density genetic mapping with transcriptome analysis uncovers numerous agronomic QTL and reveals candidate genes for the control of tillering in sorghum. G3 Feb 9;11(2):jkab024. DOI: 10.1093/g3journal/jkab024. Wang, X., S. Chen, X. Ma, A. E. J. Yssel, S. R. Chaluvadi, M. S. Johnson, P. Gangashetty, F. Hamidou, M. D. Sanogo, A. Zwaenepoel, J. Wallace, Y. V. Peer, J. L. Bennetzen, A. V. Deynze. (2021) Genome sequence and genetic diversity analysis of an under-domesticated orphan crop, white fonio (Digitaria exilis). GigaScience. Volume 10, Issue 3, March 2021, giab013. DOI: 10.1093/gigascience/giab013 Varshney, R. K., P. Sinha, V. K. Singh, A. Kumar, Q. Zhang and J. L. Bennetzen (2020) 5Gs for crop improvement. Curr. Opin. Plant Biol., 56, 190-196. DOI:10.1016/j.pbi.2019.12.004. Dai, X., Y. Liu, J. Zhuang, S. Yao, L. Liu, X. Jiang, K. Zhou, D. Xie, J. L. Bennetzen, L. Gao and T. Xia (2020) Discovery and characterization of tannase genes in plants: Roles for hydrolysis of tannins. New Phytol.226(4), 1104-1116. DOI:10.1111/nph.16425. Johnen, L., T. Boldieri de Souza, D. R. Rocha, L. M. Parteka, M. S. González-Elizondo, R. Trevisan, S. R. Chaluvadi, J. L. Bennetzen, and A. L. Laforga Vanzela (2020) Allopolyploidy and genomic differentiation in the holocentric species of Eleocharis montana complex (Cyperaceae). Plant Syst. Evol. 306:1-17. DOI:10.1007/s00606-020-01666-8. Zhang, S., S. R. Chaluvadi, and J. L. Bennetzen (2020) Genome sequence analysis of Enterobacter sp. C6 found in the pitcher fluids of Sarracenia rosea. Microbiol. Resour. Announc., 9:e01214-19. DOI:10.1128/MRA.01214-19. Zhang, S., S. R. Chaluvadi, and J. L. Bennetzen (2020) Draft genome sequence of a Serratia marcescens strain isolated from the pitcher fluids of a Sarracenia pitcher plant. Microbiol. Resour. Announc. 9:e01216-19.DOI:10.1128/MRA.01216-19. VanBuren, R., C. M. Wai, X. Wang, J. Pardo, A. E. Yocca, H. Wang, S. R. Chaluvadi, G. Han, D. Bryant, P. P. Edger, W. Zhang, J. Messing, M. E. Sorrells, T. C. Mockler, J. L. Bennetzen, and T. P. Michael (2020) Exceptional subgenome stability and functional divergence in allotetraploid teff, the primary cereal crop in Ethiopia. Nature Comm. 11:1-11. DOI:10.1038/s41467-020-14724-z. VanBuren, R. V., C. M. Wai, J. Pardo, A. El Yocca, X. Wang, H. Wang, S. R. Chaluvadi, D. Bryant, P. P. Edger, J. L. Bennetzen, T. C. Mockler and T. P. Michael (2019) Exceptional subgenome stability and functional divergence in allotetraploid teff, the primary cereal crop in Ethiopia. Nature Comm 580720. Li, Y., X. Wang, Q. Ban, X. Zhu, C. Jiang, C. Wei and J. L. Bennetzen (2019) Comparative transcriptomic analysis reveals gene expression associated with cold adaptation in the tea plant Camellia sinensis. BMC Genomics 20: article #624. Chen, L.-Y. and 44 others, including H. Zhou, H. Wang and J. L. Bennetzen (2019) The bracteatus pineapple genome and domestication of clonally propagated crops. Nature Genetics 51:1549-1558. Xia, E. and 44 others including T. Wei and J. L. Bennetzen (2019) The tea plant reference genome and improved gene annotation using long-read and paired-end sequencing data. Sequence Data 6: 122 pages. Xu, C.-Q. and 19 others, including X. Wang and J. L. Bennetzen (2019) Genome sequence of Malania oleifera, a threatened tree with great value for nervonic acid production. GigaScience 8. DOI: 10.1093/gigascience/giy164. Dunning, L. T., J. K. Olofsson, C. Parisod, R. Choudhury, J. J. Moreno-Villena, T. Handasyde, Y. Yang, J. Dionora, W. P. Quick, M. Park, J. L. Bennetzen, P. Nosil, C. P. Osborne and P.-A. Christin (2019) Lateral transfers of large DNA fragments spread functional genes among eukaryotes. Proc. Natl. Acad. Sci., USA 116:4416-4425. Bennetzen, J. L. (2019) Better research for better tea. Nature 566:S5. Chaluvadi, S. R., P. Young, K. Thompson, B. A. Barhi, B. Gajera, S. Narayanan, R. Krueger and J. L. Bennetzen (2019) Phoenix phylogeny, and analysis of genetic diversity in a diverse collection of date palm (Phoenix dactylifera) and its wild relatives. Plant Diversity DOI:10.1016/j.pld.2018.11.005. Frailey, D. C., S. R. Chaluvadi, J. N. Vaughn, C. G. Coatney, and J. L. Bennetzen (2018) Gene loss and genome rearrangement in the plastids of five hemiparasites in the family Orobanchaceae. BMC Plant Biol. 18:30. DOI: 10.1186/s12870-018-1249-x. Wuyun, T. and 30 other authors, including X. Wang and J. L. Bennetzen (2018) The hardy rubber tree genome reveals the evolution of polyisoprene biosynthesis. Mol. Plant 5:429-442. DOI: 10.1016/jmolp.2017.11.014. Hoffbert, S. L., N. J. Troendle, T. C. Glenn, O. Mahmud, D. Chalopin, J. L. Bennetzen and R. Mauricio (2018) A high-quality reference genome for the invasive mosquitofish Gambusia affinis using a Chicago library. G3 8:1855-1861. Wei, C. and 42 others, including W. Tong and J. L. Bennetzen (2018) Draft genome sequence of Camellia sinensis var. sinensis provides insights into the evolution of the tea genome and tea quality. Proc. Natl. Acad. Sci. USA 115:E4151-E4158. Bennetzen, J. L. and M. Park (2018) Distinguishing friends, foes and freeloaders in giant genomes. Curr. Opin. Gen. Dev. 49:49-55. Bennetzen, J. L. and X. Wang (2018) Relationships between gene structure and genome instability in flowering plants. Mol. Plant DOI: 10.1016/jmolp.2018.02.003. Arthur, R. A. and J. L. Bennetzen (2018) Discovery of lineage-specific genome change in rice through analysis of resequencing data. Genetics 209:617-626. Souza, T. B., S. R. Chaluvadi, L. Johnen, A. Marques, M. S. Gonzalez-Elizondo, J. L. Bennetzen and A. L. L. Vanzela (2018) Analysis of retrotransposon abundance, diversity and distribution in holocentric Eleocharis (Cyperaceae) genomes. Annals Bot., 122:279-290. Wang, X., S. Yang, Y. Chen, S. Zhang, Q. Zhao, M. Li, Y. Gao, L. Yang and J. L. Bennetzen (2018) Comparative genome-wide characterization leading to simple sequence repeat marker development for Nicotiana. BMC Genomics, 19:500. Manski, C. and >310 other NAS Members, including J. Bennetzen (2018) Statement to restore science-based policy in government by concerned members of the U.S. National Academy of Sciences. Open letter, reproduced at several internet and press sites, including https://scientistsforsciencebasedpolicy.org/. Dai, X., H. Wang, H. Zhou, J. Dvořák, J. L. Bennetzen and H.-G. Müller (2018) Birth and death of LTR-retrotransposons in Aegilops tauschii. Genetics, 210:1039-1051. Chaluvadi, S. R. and J. L. Bennetzen (2018) Species-associated differences in the below-ground microbiomes of wild and domesticated Setaria. Frontiers Plant Sci., 9: 1183 DOI:10.3389/fpls.2018.01183. Wei, T., J. Yu, Y. Hou, Q. Zhou, F. Li, X. Wang, C. Wei, and J. L. Bennetzen (2018) Circular RNA architecture and differentiation during leaf bud to young leaf development in tea (Camellia sinensis). Planta, 248:1417-1429. Bennetzen, J., S. Flint-Garcia, C. Hirsch, and R. Tuberosa (eds.) (2018) The Maize Genome, Springer Nature, Switzerland. Bennetzen, J. L. (2018) Maize transposable element dynamics. In: The Maize Genome (eds. J. Bennetzen, S. Flint-Garcia, C. Hirsch, and R. Tuberosa), Springer Nature, Switzerland, pp. 49-58. Varshney, R. K. and 65 other authors, including H. Wang and J. L. Bennetzen (2017) Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments. Nature Biotech. 35:969-976. Chen, Y., J. Dong, J. L. Bennetzen, M. Zhong, J. Yang, J. Zhang, S. Li, X. Hao, Z. Zhang, and X. Wang (2017) Integrating transcriptome and microRNA analysis identifies genes and microRNAs for AHO-induced systemic acquired resistance in N. tabacum. Scientific Reports 7: DOI: 10.1038/s41598-017-12249-y. Kim, S. and 40 other authors, including M. Park and J. L. Bennetzen (2017) New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication. Genome Biol. 18:210 DOI: 10.1186/s13059-017-1341-9. Luo, M.-C. and 45 other authors, including H. Wang and J. L. Bennetzen (2017) Genome sequence of the progenitor of the wheat D genome Aegilops tauschii. Nature 551:498-502. Wolpe, P. R. and 81 other authors, including J. L. Bennetzen (2017) Ethical principles for the use of cellular biotechnologies. Nature Biotech. 35:1050-1058. Nelson, R. S. and 29 other authors, including R. Percifield and J. L. Bennetzen (2017) Development and use of a switchgrass (Panicum virgatum L.) transformation pipeline by the BioEnergy Science Center to evaluate plants for reduced cell wall recalcitrance. Biotech. Biofuels 10:309 DOI: 10.1186/s13068-017-0991-x.
