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.
Highlights
Tobacco (Nicotiana tabacum) is an important plant model system that has played a key role in the early development of molecular plant biology
* Correspondence: Kieron_edwards@bat.com; Kieron.edwards@cantab.net 1Plant Biotechnology Division, British American Tobacco, Cambridge, UK Full list of author information is available at the end of the article events are highly prevalent in the Nicotiana genus [7], including the relatively young allotetraploid N. tabacum (2n = 4 × = 48), which arose less than 0.2 Ma ago through the hybridisation of the ancestral parents N. sylvestris (2n = 24; maternal S genome donor) and N. tomentosiformis (2n = 24; paternal T genome donor) [8,9,10]. Efforts such as the Tobacco Genome Initiative (TGI) provided sequence data for a low coverage of Bacterial Artificial Chromosomes (BACs) and active parts of the N. tabacum genome (Gene-space Sequence Reads [GSRs]), which allowed for genome-scale characterisation of gene families such as transcription factors [11]
The low level of missed or fragmented single-copy orthologs in the N. tabacum assembly is comparable to, or lower than the level shown by the tomato and potato genome assemblies respectively (Fig. 2a), supporting the quality of this current genome assembly for tobacco
Summary
Tobacco (Nicotiana tabacum) is an important plant model system that has played a key role in the early development of molecular plant biology. Improved tobacco genomic resources are necessary to facilitate such applications, but genome size and complexity has slowed their development. The TGI and other efforts generated Expressed Sequence Tags (ESTs), which provided insight into the gene content of N. tabacum and facilitated studies of Edwards et al BMC Genomics (2017) 18:448 gene expression in the species [12]. The emergence of Generation Sequencing (NGS) technologies over the past-decade (reviewed in [13]) has reduced these barriers and made sequencing efforts in species with complex genomes like N. tabacum more feasible
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