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Reference genomes and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis

Nicolas Sierro, James ND Battey, Sonia Ouadi, Lucien Bovet, Simon Goepfert, Nicolas Bakaher, Manuel C Peitsch and Nikolai V Ivanov*

Author Affiliations

Philip Morris International R&D, Philip Morris Products SA, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland

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Genome Biology 2013, 14:R60  doi:10.1186/gb-2013-14-6-r60

Published: 17 June 2013

Abstract

Background

Nicotiana sylvestris and Nicotiana tomentosiformis are members of the Solanaceae family that includes tomato, potato, eggplant and pepper. These two Nicotiana species originate from South America and exhibit different alkaloid and diterpenoid production. N. sylvestris is cultivated largely as an ornamental plant and it has been used as a diploid model system for studies of terpenoid production, plastid engineering, and resistance to biotic and abiotic stress. N. sylvestris and N. tomentosiformis are considered to be modern descendants of the maternal and paternal donors that formed Nicotiana tabacum about 200,000 years ago through interspecific hybridization. Here we report the first genome-wide analysis of these two Nicotiana species.

Results

Draft genomes of N. sylvestris and N. tomentosiformis were assembled to 82.9% and 71.6% of their expected size respectively, with N50 sizes of about 80 kb. The repeat content was 72-75%, with a higher proportion of retrotransposons and copia-like long terminal repeats in N. tomentosiformis. The transcriptome assemblies showed that 44,000-53,000 transcripts were expressed in the roots, leaves or flowers. The key genes involved in terpenoid metabolism, alkaloid metabolism and heavy metal transport showed differential expression in the leaves, roots and flowers of N. sylvestris and N. tomentosiformis.

Conclusions

The reference genomes of N. sylvestris and N. tomentosiformis represent a significant contribution to the SOL100 initiative because, as members of the Nicotiana genus of Solanaceae, they strengthen the value of the already existing resources by providing additional comparative information, thereby helping to improve our understanding of plant metabolism and evolution.