Wild tobacco genomes reveal the evolution of nicotine biosynthesis

Abstract

Nicotine, the signature alkaloid of Nicotiana species responsible for the addictive properties of human tobacco smoking, functions as a defensive neurotoxin against attacking herbivores. However, the evolution of the genetic features that contributed to the assembly of the nicotine biosynthetic pathway remains unknown. We sequenced and assembled genomes of two wild tobaccos, Nicotiana attenuata (2.5 Gb) and Nicotiana obtusifolia (1.5 Gb), two ecological models for investigating adaptive traits in nature. We show that after the Solanaceae whole-genome triplication event, a repertoire of rapidly expanding transposable elements (TEs) bloated these Nicotiana genomes, promoted expression divergences among duplicated genes, and contributed to the evolution of herbivoryinduced signaling and defenses, including nicotine biosynthesis. The biosynthetic machinery that allows for nicotine synthesis in the roots evolved from the stepwise duplications of two ancient primary metabolic pathways: the polyamine and nicotinamide adenine dinucleotide (NAD) pathways. In contrast to the duplication of the polyamine pathway that is shared among several solanaceous genera producing polyamine-derived tropane alkaloids, we found that lineage-specific duplications within the NAD pathway and the evolution of rootspecific expression of the duplicated Solanaceae-specific ethylene response factor that activates the expression of all nicotine biosynthetic genes resulted in the innovative and efficient production of nicotine in the genus Nicotiana. Transcription factor binding motifs derived from TEs may have contributed to the coexpression of nicotine biosynthetic pathway genes and coordinated the metabolic flux. Together, these results provide evidence that TEs and gene duplications facilitated the emergence of a key metabolic innovation relevant to plant fitness.Nicotiana genomes | genome-wide multiplications | transposable elements | nicotine biosynthesis | expression divergence

Natural variations in the MYB transcription factor MYB31 determine the evolution of extremely pungent peppers

“…Variations and/or chemical modifications in the TF‐coding sequence and/or promoter always alter the transcriptional regulation of target genes (Espley et al ., ; Chagné et al ., ; Hatlestad et al ., ; Sheehan et al ., ; Sun et al ., ; Yuan et al ., ; Li et al ., ). These mutations result in the modulation of coordinated gene expression required for the evolution of adaptive traits (Yuan et al ., ; Li et al ., ; Xu et al ., ). In Petunia , mutations in the MYB‐FL promoter and coding sequence influence flavonol accumulation to control the gain and loss of floral ultraviolet (UV) absorbance and affect pollinator preference (Sheehan et al ., ).…”

Glucosylation of the phytoalexin N‐feruloyl tyramine modulates the levels of pathogen‐responsive metabolites in Nicotiana benthamiana

“…As Nicotiana species are a rich source for bioactive plant secondary metabolites their production and biological activities have been extensively studied including pyridine alkaloids, isoprenoids, aromatic compounds, and volatiles (Nugroho and Verpoorte, ). Therefore, the cultivated tobacco ( Nicotiana tabacum ), with more than 2500 structurally known metabolites, has been chemically very well studied (Xu et al ., ).…”

“…Several Nicotiana species are now extensively used as model organisms in scientific research as the genetic methods established in cultivated tobacco have been applied to, and expanded in, other Nicotiana species (Goodin et al ., ). Therefore, over the last decade, tobacco research has led to significant progress in plant science and biotechnology (Onkokesung et al ., ; Gulati et al ., ; Mhlongo et al ., , b; Xu et al ., ; Zhao et al ., ). Tobacco is currently used in bio‐engineering pharmaceutical laboratories as a manufacturing platform for the production of a wide range of drugs and therapeutic agents (Yao et al ., ).…”

Root‐expressed phytochromes B1 and B2, but not PhyA and Cry2, regulate shoot growth in nature

“…Although irCry2 plants showed a small reduction in NaCry1 transcript accumulations compared with EV plants, the constructs designed for both irCry2 and irPhyB1‐B2 lines (Table S1) did not show any off‐target sites when the sequence fragments used for the transformation constructs were blasted against the entire N . attenuata genome (Xu et al, ). From this, we infer that any nonspecific effects of the constructs result from possible coregulation among the members within the same gene family.…”

“…attenuata virus‐induced gene silencing (VIGS) tool constructed from the Sol Genomics Network (SGN) virus‐induced gene silencing tool designed for the Solanaceae family (http://vigs.solgenomics.net/), but using the N . attenuata genome (Xu et al, ) as the database. Additional stably‐silenced lines were used and previously characterized by Fragoso et al, , namely, lines silenced for NaPhyA ( irPhyA‐200 and irPhyA‐213 ) and crosses made with lines individually silenced for NaPhyB1 and NaPhyB2 , leading to the hemizigous irPhyB1xB2 lines irPhyB1‐178 × irPhyB2‐204 and irPhyB1‐246 × irPhyB2‐171 .…”