Revealing evolution of tropane alkaloid biosynthesis by analyzing two genomes in the Solanaceae family

Abstract

Tropane alkaloids (TAs) are widely distributed in the Solanaceae, while some important medicinal tropane alkaloids (mTAs), such as hyoscyamine and scopolamine, are restricted to certain species/tribes in this family. Little is known about the genomic basis and evolution of TAs biosynthesis and specialization in the Solanaceae. Here, we present chromosome-level genomes of two representative mTAs-producing species: Atropa belladonna and Datura stramonium. Our results reveal that the two species employ a conserved biosynthetic pathway to produce mTAs despite being distantly related within the nightshade family. A conserved gene cluster combined with gene duplication underlies the wide distribution of TAs in this family. We also provide evidence that branching genes leading to mTAs likely have evolved in early ancestral Solanaceae species but have been lost in most of the lineages, with A. belladonna and D. stramonium being exceptions. Furthermore, we identify a cytochrome P450 that modifies hyoscyamine into norhyoscyamine. Our results provide a genomic basis for evolutionary insights into the biosynthesis of TAs in the Solanaceae and will be useful for biotechnological production of mTAs via synthetic biology approaches.

The chromosome-scale genome and the genetic resistance machinery against insect herbivores of the Mexican toloache, Datura stramonium

“…Assessing the quality of our assembly, we found that the Datura genome encompassed 97.25% of complete single-copy orthologs (BUSCOs) out of the 255 total BUSCOs searched. Only 5 single-copy orthologs exhibited fragmentation, a level of completeness consistent with both the initial Mexican draft genome and the newly published Chinese D. stramonium genome ( De-la-Cruz et al 2021 ; Zhang et al 2023 ). This consistency in quality assembly statistics emphasizes the robustness and completeness of our assembly.…”

“…Through the implementation of our workflow, incorporating Omni-C and HiRise scaffolding sequences, we were able to join 18,023 contigs. L90 statistics resulted in 12 scaffolds, each corresponding to the known chromosomes of D. stramonium ( Satina et al 1941 ; Zhang et al 2023 ).…”

“…This consistency in quality assembly statistics emphasizes the robustness and completeness of our assembly. Furthermore, we constructed a dense linkage map that aligns with the expected haploid number of chromosomes in Datura ( Satina et al 1941 ; Zhang et al 2023 ).…”

Tomato root specialized metabolites evolved through gene duplication and regulatory divergence within a biosynthetic gene cluster

“…Using proteomes as input, OrthoFinder separates genes into orthogroups or sets of genes descended from a single gene in the common ancestor of the species under consideration, which includes all orthologs and paralogs. We included 14 sequenced genomes— S. lycopersicum M82_MAS2.0 ( 87 ), S. pimpinellifolium ( 119 ) S. pennellii ( 120 ), S. lycopersicoides ( 121 ), S. tuberosum v6.1 ( 122 ), S. melongena v4.1 ( 123 ), I. cyaneum ( 124 ), Datura stramonium ( 125 ), Lycium barbarum ( 126 ), N. attenuata ( 127 ), P. axillaris ( 128 ), I. trifida ( 129 ), C. canephora ( 130 ), and V. vinifera ( 131 )—and two transcriptomes— S. nigrum ( 55 ) and S. quitoense ( 55 ).…”

Eye Diseases: When the Solution Comes from Plant Alkaloids

“…Third, while microorganisms release metabolites into the media, plants tend to store them into the cells, making the recovery of metabolites more difficult. Fourth, the alkaloid synthesis in plants is often tissue-specific, for example, many biosynthetic enzymes for tropane alkaloids biosynthesis are expressed in roots [114]. To overcome this issue it is possible to use differentiated cultures, such as hairy roots.…”