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Certain cultivars of maize show increased tolerance to water deficit conditions by maintenance of root growth. To better understand the molecular mechanisms related to this adaptation, nodal root growth zone samples were collected from the reference inbred line B73 and inbred line FR697, which exhibits a relatively greater ability to maintain root elongation under water deficits. Plants were grown under various water stress levels in both field and controlled environment settings. FR697-specific RNA-Seq datasets were generated and used for a de novo transcriptome assembly to characterize any genotype-specific genetic features. The assembly was aided by an Iso-Seq library of transcripts generated from various FR697 plant tissue samples. The Necklace pipeline was used to combine a Trinity de novo assembly along with a reference guided assembly and the Viridiplantae proteome to generate an annotated consensus “SuperTranscriptome” assembly of 47,915 transcripts with a N50 of 3152 bp in length. The results were compared by Blastn to maize reference genes, a Benchmarking Universal Single-Copy Orthologs (BUSCO) genome completeness report and compared with three maize reference genomes. The resultant ‘SuperTranscriptome’ was demonstrated to be of high-quality and will serve as an important reference for analysis of the maize nodal root transcriptomic response to environmental perturbations.

GacS/GacA is a conserved two‐component system that functions as a master regulator of virulence‐associated traits in many bacterial pathogens, includingPseudomonasspp., that collectively infect both plant and animal hosts. Among many GacS/GacA‐regulated traits, type III secretion of effector proteins into host cells plays a critical role in bacterial virulence. In the opportunistic plant and animal pathogenPseudomonas aeruginosa, GacS/GacA negatively regulates the expression of type III secretion system (T3SS)‐encoding genes. However, in the plant pathogenic bacteriumPseudomonas syringae, strain‐to‐strain variation exists in the requirement of GacS/GacA for T3SS deployment, and this variability has limited the development of predictive models of how GacS/GacA functions in this species. In this work we re‐evaluated the function of GacA inP. syringaepv.tomatoDC3000. Contrary to previous reports, we discovered that GacA negatively regulates the expression of T3SS genes in DC3000, and that GacA is not required for DC3000 virulence insideArabidopsisleaf tissue. However, our results show that GacA is required for full virulence of leaf surface‐inoculated bacteria. These data significantly revise current understanding of GacS/GacA in regulatingP. syringaevirulence.

A key remit of theNSF‐funded “Arabidopsis Research and Training for the 21^stCentury” (ART‐21) Research Coordination Network has been to convene a series of workshops with community members to explore issues concerning research and training in plant biology, including the role that research usingArabidopsis thalianacan play in addressing those issues. A first workshop focused on training needs for bioinformatic and computational approaches in plant biology was held in 2016, and recommendations from that workshop have been published (Friesner et al.,Plant Physiology, 175, 2017, 1499). In this white paper, we provide a summary of the discussions and insights arising from the secondART‐21 workshop. The second workshop focused on experimental aspects of omics data acquisition and analysis and involved a broad spectrum of participants from academics and industry, ranging from graduate students through post‐doctorates, early career and established investigators. Our hope is that this article will inspire beginning and established scientists, corporations, and funding agencies to pursue directions in research and training identified by this workshop, capitalizing on the reference speciesArabidopsis thalianaand other valuable plant systems.