title: Reference genomes and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis.
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.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Sierro
authors.forename: James N D
authors.initials: JN
authors.lastname: Battey
authors.forename: Sonia
authors.initials: S
authors.lastname: Ouadi
authors.forename: Lucien
authors.initials: L
authors.lastname: Bovet
authors.forename: Simon
authors.initials: S
authors.lastname: Goepfert
authors.forename: Nicolas
authors.initials: N
authors.lastname: Bakaher
authors.forename: Manuel C
authors.initials: MC
authors.lastname: Peitsch
authors.forename: Nikolai V
authors.initials: NV
authors.lastname: Ivanov
mesh_terms: D000470:Alkaloids / Q000096:biosynthesis; D002874:Chromosome Mapping; D035264:Flowers / Q000235:genetics / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D049810:Genetic Speciation; D059646:Genome Size; D018745:Genome, Plant; D017136:Ion Transport; D019216:Metals, Heavy / Q000378:metabolism; D058977:Molecular Sequence Annotation; D009538:Nicotine / Q000096:biosynthesis; D016366:Open Reading Frames; D018515:Plant Leaves / Q000235:genetics / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics / Q000378:metabolism; D018626:Retroelements; D013729:Terpenes / Q000378:metabolism; D014026:Nicotiana / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D059467:Transcriptome
chemical_list: D000470:Alkaloids; D019216:Metals, Heavy; D010940:Plant Proteins; D018626:Retroelements; D013729:Terpenes; D009538:Nicotine