Phylotranscriptomics reveals the phylogeny of Asparagales and the evolution of allium flavor biosynthesis

Abstract Asparagales, the largest monocot order, is renowned for its ecological, economic, and medicinal significance. Here, we leveraged transcriptome data from 455 Asparagales species to explore the phylogeny of Asparagales. Moreover, we investigated the evolutionary patterns of the genes involved in allium flavor formation. Our analyses not only established a robust bifurcating phylogeny of Asparagales but also explored their reticulate relationships. Notably, we found that eight genes involved in the biosynthesis of allium flavor compounds underwent expansion in Allium species. Furthermore, we observed Allium-specific mutations in one amino acid within alliinase and three within lachrymatory factor synthase. Overall, our findings highlight the role of gene expansion, increased expression, and particularly amino acid mutations in driving the evolution of Allium-specific compounds. These insights not only deepen our understanding of the phylogeny of Asparagales, but also illuminate the genetic mechanisms underpinning specialized compounds.