@article{edwards_fernandez-pozo_drake-stowe_humphry_evans_bombarely_allen_hurst_white_kernodle_et al._2017, title={A reference genome for Nicotiana tabacum enables map-based cloning of homeologous loci implicated in nitrogen utilization efficiency}, volume={18}, ISSN={["1471-2164"]}, DOI={10.1186/s12864-017-3791-6}, abstractNote={Tobacco (Nicotiana tabacum) is an important plant model system that has played a key role in the early development of molecular plant biology. The tobacco genome is large and its characterisation challenging because it is an allotetraploid, likely arising from hybridisation between diploid N. sylvestris and N. tomentosiformis ancestors. A draft assembly was recently published for N. tabacum, but because of the aforementioned genome complexities it was of limited utility due to a high level of fragmentation.Here we report an improved tobacco genome assembly, which, aided by the application of optical mapping, achieves an N50 size of 2.17 Mb and enables anchoring of 64% of the genome to pseudomolecules; a significant increase from the previous value of 19%. We use this assembly to identify two homeologous genes that explain the differentiation of the burley tobacco market class, with potential for greater understanding of Nitrogen Utilization Efficiency and Nitrogen Use Efficiency in plants; an important trait for future sustainability of agricultural production.Development of an improved genome assembly for N. tabacum enables what we believe to be the first successful map-based gene discovery for the species, and demonstrates the value of an improved assembly for future research in this model and commercially-important species.}, journal={BMC GENOMICS}, author={Edwards, K. D. and Fernandez-Pozo, N. and Drake-Stowe, K. and Humphry, M. and Evans, A. D. and Bombarely, A. and Allen, F. and Hurst, R. and White, B. and Kernodle, S. P. and et al.}, year={2017}, month={Jun} }
 @article{drake-stowe_bakaher_goepfert_philippon_mark_peterson_lewis_2017, title={Multiple Disease Resistance Loci Affect Soilborne Disease Resistance in Tobacco (Nicotiana tabacum)}, volume={107}, ISSN={["1943-7684"]}, DOI={10.1094/phyto-03-17-0118-r}, abstractNote={ Phytophthora nicotianae and Ralstonia solanacearum are two of the most important pathogens affecting tobacco worldwide. Greater insight regarding genetic systems controlling resistance to these two soilborne pathogens, as well as identification of DNA markers associated with genomic regions controlling this resistance, could aid in variety development. An evaluation of 50 historical tobacco lines revealed a high positive correlation between resistances to the two pathogens, preliminarily suggesting that some genomic regions may confer resistance to both pathogens. A quantitative trait loci (QTL) mapping experiment designed to investigate the genetic control of soilborne disease resistance of highly resistant ‘K346’ tobacco identified four QTL significantly associated with resistance to P. nicotianae (explaining 60.0% of the observed phenotypic variation) and three QTL to be associated with R. solanacearum resistance (explaining 50.3% of the observed variation). The two QTL with the largest effect on Phytophthora resistance were also found to be the QTL with the greatest effects on resistance to Ralstonia. This finding partially explains previously observed associations between resistances to these two pathogens among U.S. current cultivars and within breeding populations. Further study is needed to determine whether these relationships are due to the same genes (i.e., pleiotropy) or favorable coupling-phase linkages that have been established over time. }, number={9}, journal={PHYTOPATHOLOGY}, author={Drake-Stowe, Katherine and Bakaher, Nicolas and Goepfert, Simon and Philippon, Berangere and Mark, Regis and Peterson, Paul and Lewis, Ramsey S.}, year={2017}, month={Sep}, pages={1055–1061} }
 @article{drake_moore_bertrand_fortnum_peterson_lewis_2015, title={Black Shank Resistance and Agronomic Performance of Flue-Cured Tobacco Lines and Hybrids Carrying the Introgressed Nicotiana rustica Region, Wz}, volume={55}, ISSN={["1435-0653"]}, DOI={10.2135/cropsci2014.02.0164}, abstractNote={ABSTRACT}, number={1}, journal={CROP SCIENCE}, author={Drake, Katherine E. and Moore, J. Michael and Bertrand, Paul and Fortnum, Bruce and Peterson, Paul and Lewis, Ramsey S.}, year={2015}, pages={79–86} }
 @article{drake_lewis_2013, title={An Introgressed Nicotiana rustica Genomic Region Confers Resistance to Phytophthora nicotianae in Cultivated Tobacco}, volume={53}, ISSN={["1435-0653"]}, DOI={10.2135/cropsci2012.10.0605}, abstractNote={ABSTRACT}, number={4}, journal={CROP SCIENCE}, author={Drake, Katherine and Lewis, Ramsey S.}, year={2013}, pages={1366–1374} }