Tobacco genomic resources for gene discovery
As one of the most widely cultivated non-food crops grown in around 120 countries worldwide, Nicotiana tabacum holds significance as both an economically important crop and also as a model organism. Historically it has played a key role in the development of tissue culture and transformation techniques now widely used across all branches of plant molecular biology. As an allotetraploid formed by the recent interspecific hybridisation of diploid parents N. sylvestris and N. tomentosiformis, its genome is large and complex: approximately 4.5 Gb in size and comprised of around 70 % repeat elements. As a result of such genomic complexity, production of a genome sequence with sufficient quality to anchor to chromosomes has been a challenge.
We have recently published an assembly of the K326 cultivar that has been produced through the combination of optical mapping and next generation sequencing technologies. This assembly achieves an N50 size of 2.17 Mb and enables anchoring of 64 % of the genome to chromosomal locations, dramatically increasing the utility of the genome to the community.
In support of the public release of the sequence, a number of tools have been made available via the Solanaceae Genomics Network to enable the use of the genome as a resource for gene discovery (www.sgn.cornell.edu/organism/Nicotiana_tabacum/genome). These include a JBrowse genome browser, a BLAST facility and a VIGS design tool. In this talk, we will demonstrate the utility of these resources in the discovery and characterisation of gene function in the tobacco plant.