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Many plants naturally synthesize and secrete secondary metabolites that exert an allelopathic effect, offering compelling alternatives to chemical herbicides. These natural herbicides are highly important for sustainable agricultural practices. Ailanthone is the chemical responsible for the herbicidal effect of Ailanthus altissima, or “tree of heaven”. The molecular studies involving ailanthone’s effect on plant growth are limited. In the current study, we combined whole-transcriptome and physiology analysis of three Arabidopsis thaliana ecotypes treated with ailanthone to identify the effect of this allelopathic chemical on genes and plant growth. Our physiology results showed 50% reduced root growth, high proline accumulation, and high reactive-oxygen-species accumulation in response to ailanthone stress. Deep transcriptome analysis revealed 528, 473, and 482 statistically significant differentially expressed genes for Col-0, Cvi-0, and U112-3 under ailanthone stress, including 131 genes shared among the three accessions. The common genes included 82 upregulated and 42 downregulated genes and varied in expression at least twofold. The study also revealed that 34 of the 131 genes had a similar expression pattern when Arabidopsis seedlings were subjected to other herbicides. Differentially expressed genes significantly induced in response to ailanthone included DTXL1, DTX1, ABCC3, NDB4, UGT74E2, and AZI1. Pathways of stress, development and hormone metabolism were significantly altered under ailanthone stress. These results suggest that ailanthone triggers a significant stress response in multiple pathways similar to other herbicides.

The habanero pepper (Capsicum chinense) is an increasingly important spice and vegetable crop worldwide because of its high capsaicin content and pungent flavor. Diets supplemented with the phytochemicals found in habanero peppers might cause shifts in an organism’s metabolism and gene expression. Thus, understanding how these interactions occur can reveal the potential health effects associated with such changes. We performed transcriptomic and metabolomic analyses of Drosophila melanogaster adult flies reared on a habanero pepper diet. We found 539 genes/59 metabolites that were differentially expressed/accumulated in flies fed a pepper versus control diet. Transcriptome results indicated that olfactory sensitivity and behavioral responses to the pepper diet were mediated by olfactory and nutrient-related genes including gustatory receptors (Gr63a, Gr66a, and Gr89a), odorant receptors (Or23a, Or59a, Or82a, and Orco), and odorant-binding proteins (Obp28a, Obp83a, Obp83b, Obp93a, and Obp99a). Metabolome analysis revealed that campesterol, sitosterol, and sucrose were highly upregulated and azelaic acid, ethyl phosphoric acid, and citric acid were the major metabolites downregulated in response to the habanero pepper diet. Further investigation by integration analysis between transcriptome and metabolome data at gene pathway levels revealed six unique enriched pathways, including phenylalanine metabolism; insect hormone biosynthesis; pyrimidine metabolism; glyoxylate, and dicarboxylate metabolism; glycine, serine, threonine metabolism; and glycerolipid metabolism. In view of the transcriptome and metabolome findings, our comprehensive analysis of the response to a pepper diet in Drosophila have implications for exploring the molecular mechanism of pepper consumption.