show Abstracthide AbstractIn this study, we present the first draft genomes of two plants of the annual herb Datura stramonium (Solanaceae). This species produces tropane alkaloids and terpenoids that are widely used in the pharmaceutic industry. Likewise, these compounds have been related as defenses against herbivores and pathogens. Comparative genomics was carried out with other 11 Solanaceae species to provide insights into the genome evolution of D. stramonium within the Solanaceae family and to provide evidence into the adaptation of this plant to biotic and abiotic stresses. We also studied the evolution of eight genes of D. stramonium involved in the production of the main tropane alkaloids. A notable finding is that the D. stramonium genomes show expansion, physicochemical divergence and/or positive selection on terpenoids, tropanes, R defensive genes, and proteins related with biotic and abiotic stresses such as defense against natural enemies and drought. Non-model species such as D. stramonium could be of wide interest because they offer new modes of investigating the ecological and evolutionary processes that plants undergone in their natural environments and how they respond to pollution, human disturbance and climate change. With the availability of these genomic data, subsequent development of genetic markers for further genetic selection and molecular breeding of D. stramonium can be realized. Also, this genomic data would allow us to elucidate the genetic basis of complex phenotypes such as resistance to herbivores and to shed new light on how plants defend themselves and create new strategies for pest control.