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Abstract Arabidopsis thaliana (hereafter Arabidopsis) is a small plant with a fast generation time and a well-annotated genome, which makes it ideal for research labs. It is arguably the most used model species in basic plant sciences. Over the past half century, studies in Arabidopsis have generated enormous insight into fundamental principles of plant life, ranging from mechanistic molecular biology to the complexities of interacting ecosystems. Based on research in Arabidopsis, we now understand that while basic cellular metabolism is generally conserved across species, variation in specialized metabolite enzymes gives rise to complex bouquets of chemical weapons that are tightly interwoven with the environment. Understanding how these are produced, regulated, and—especially—how they are deployed remains a key research area for plant immunity. The breadth of work in Arabidopsis provides a unique window into this complicated aspect of life as a plant. We are happy to have an opportunity to share our common interest in these aspects in this review. Due to space constraints, we focus on compounds produced by Arabidopsis with demonstrated antimicrobial properties. We hope that this focus (despite our eagerness to write more) will inspire new avenues of research that will contribute to a more complete understanding of immunity. 

Abstract Diversity in plant specialized metabolites plays critical roles in plant–environment interactions. In longer evolutionary scales, e.g. between families or orders, this diversity arises from whole-genome and tandem duplication events. Less is known about the evolutionary patterns that shape chemical diversity at shorter scales, e.g. within a family. Utilizing the aliphatic glucosinolate pathway, we explored how the genes encoding the terminal structural modification enzyme GSL-OH evolved across the Brassicaceae and the genomic processes that control presence–absence variation of its products (R)-2-hydroxy-but-3-enyl and (S)-2-hydroxy-but-3-enyl glucosinolate. We implemented a phylo-functional approach to functionally validate GSL-OH orthologs across the Brassicaceae and used that information to map the genomic origin and trajectory of the locus. This uncovered a complex mechanism involving at least 3 ancestral loci with extensive gene loss across all species, creating unequal retention across the phylogenetic relationships. Convergent evolution in enantiomeric specificity was observed, where several independent species had tandem duplicates that diverged toward producing the R or S enantiomers. To explore potential biological differences between the enantiomers, we performed Trichoplusia ni larval choice assays and tested resistance against Botrytis cinerea in a detached leaf assay. We found that plants with the S-enantiomer were more susceptible to B. cinerea infection than to T. ni larval herbivory, while plants with the R-enantiomer seemed more susceptible to T. ni larval herbivory when compared to B. cinerea. Ultimately, we observed recurrent GSL-OH loss, uncovered a complex origin story for the gene, and measured the bioactivity of the enzyme's metabolic products. 

Abstract Organisms regulate gene expression in response to environmental cues, a process known as plasticity, to adjust to changing environments. Research into natural variation and the evolution of plasticity frequently studies cis-regulatory elements with theory suggesting they are more important evolutionarily than trans-regulatory elements. Genome-wide association (GWA) studies have supported this idea, observing a predominance of cis-loci affecting plasticity. However, studies in structured populations provide a contrasting image, raising questions about the genetic architecture of natural variation in plasticity. To circumvent potential statistical difficulties present in GWA studies, we mapped loci underlying transcriptomic plasticity in response to salicylic acid (SA) using recombinant inbred lines generated from 2 random Arabidopsis thaliana accessions. We detected extensive transgressive segregation in the SA response, suggesting that plasticity to salicylate in Arabidopsis is polygenic. Most loci (>75%) underlying this variation act in trans, especially for loci influencing plasticity. Trans-acting loci were enriched in genome hotspots, with predominantly small-effect sizes distributed across many genes. This could potentially explain their under-discovery in GWA studies. This work reveals a potentially important role for trans-acting loci in plastic expression responses, with implications for understanding plant adaptation to different environments.