A reference genome for Nicotiana tabacum enables map-based cloning of homeologous loci implicated in nitrogen utilization efficiency

Abstract

BackgroundTobacco (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.ResultsHere 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.ConclusionsDevelopment 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3791-6) contains supplementary material, which is available to authorized users.

A complex eIF4E locus impacts the durability of va resistance to Potato virus Y in tobacco

“…). The Blast function available on the Sol Genomics Network server (https://solgenomics.net/) (Edwards et al , ) showed a localization of the eIF4E‐2, 3 and 4 genes on chromosome 14 of the tobacco genotype K326 (PI552505), starting, respectively, at positions 109418388, 109399608 and 109292645, indicating these genes are located within a ca. 132 kbp region (Fig.…”

Plant Glandular Trichomes: Natural Cell Factories of High Biotechnological Interest

“…The (draft) genome sequences of a number of plant species with glandular trichomes are now available. A nonexhaustive list includes different tomato species (Solanum lycopersicum and Solanum pimpinellifolium [Tomato Genome Consortium, 2012] and Solanum pennellii [Bolger et al, 2014]), potato (Solanum tuberosum [Xu et al, 2011]), cucumber (Cucumis sativus [Huang et al, 2009]), tobacco (Nicotiana tabacum [Sierro et al, 2014;Edwards et al, 2017]) and its related species (Nicotiana sylvestris and Nicotiana tomentosiformis [Sierro et al, 2013]), hot pepper (Capsicum annuum ), mint (Mentha longifolia [Vining et al, 2017]), cannabis (Cannabis sativa [van Bakel et al, 2011]), and hop (Humulus lupulus [Natsume et al, 2015]). …”

Metabolome and molecular basis for carbohydrate increase and nitrate reduction in burley tobacco seedlings by glycerol through upregulating carbon and nitrogen metabolism

“…Nitrogen fertilizer application in burley tobacco is normally 4–5 fold higher than other tobacco types to produce the same levels of biomass, which resulted in low nitrogen use efficiency and more than 100 times higher of nitrate content in burley tobacco, further contributing to much more TSNA formation during both leaf curing and storage 2,3 . Transcriptomic analysis showed that expression of genes involved in photosynthesis were decreased by reducing nitrogen application, resulting in decreased leaf biomass accumulation and carbohydrates formation in burley tobacco 25 .…”

“…Nitrate is largely accumulated and carbohydrates are extremely low in burley tobacco, which are associated with one double recessive genes mutation 2 . In this study, nitrate content was significantly decreased and leaf biomass was significantly increased by spraying glycerol ( P  < 0.01), and the effect of 20% nitrogen reduction with spraying glycerol was the most effective in decreasing nitrate content in burley tobacco seedlings.…”

“…Burley tobacco is one type of chlorophyll deficiency, and is well known as yellow-green leaf tobacco with reduced chlorophyll content and lower carbohydrate accumulation 1,2 . This mutations is correlated with one double homozygous recessive genotypes at Yellow Burley 1 ( YB1 ) and Yellow Burley 2 ( YB2 ) loci, and has been reported that the changes resulted in low nitrogen use efficiency and high levels of nitrate accumulation which is one of the important precursors of tobacco-specific nitrosamines (TSNAs) 3,4 .…”