The N gene protects tomato plants from tomato brown rugose fruit virus infection.

The tobamovirus tomato brown rugose fruit virus (ToBRFV) has recently emerged, causing significant damage to the tomato industry in various regions worldwide, including the US. ToBRFV evades the widely used Tm-2 resistance gene, which encodes a nucleotide-binding leucine-rich repeat (NLR) class immune receptor with an N-terminal coiled-coil (CC) domain that confers resistance to the tomato mosaic virus (ToMV). In this study, we tested a transgenic tomato line (tomato) expressing the Nicotiana glutinosa N gene, which encodes an NLR with a Toll-Interleukin 1 homology domain (TIR) at the N-terminus, for resistance to ToBRFV.

Holo-omics disentangle drought response and biotic interactions among plant, endophyte and pathogen.

Holo-omics provide a novel opportunity to study the interactions among fungi from different functional guilds in host plants in field conditions. We address the entangled responses of plant pathogenic and endophytic fungi associated with sorghum when droughted through the assembly of the most abundant fungal, endophyte genome from rhizospheric metagenomic sequences followed by a comparison of its metatranscriptome with the host plant metabolome and transcriptome. The rise in relative abundance of endophytic Acremonium persicinum (operational taxonomic unit 5 (OTU5)) in drought co-occurs with a rise in fungal membrane dynamics and plant metabolites, led by ethanolamine, a key phospholipid membrane component.

Comparative mutant analyses reveal a novel mechanism of ARF regulation in land plants.

The plant hormone auxin regulates a wide variety of transcriptional responses depending on the cell type, environment and species. How this diversity is achieved may be related to the specific complement of auxin-signalling components in each cell. The levels of activators (class-A AUXIN RESPONSE FACTORS) and repressors (class-B ARFs) are particularly important.

Regulatory variation controlling architectural pleiotropy in maize.

An early event in plant organogenesis is establishment of a boundary between the stem cell containing meristem and differentiating lateral organ. In maize (Zea mays), evidence suggests a common gene network functions at boundaries of distinct organs and contributes to pleiotropy between leaf angle and tassel branch number, two agronomic traits. To uncover regulatory variation at the nexus of these two traits, we use regulatory network topologies derived from specific developmental contexts to guide multivariate genome-wide association analyses.

Genome-wide identification of novel flagellar motility genes in pv. DC3000.

pv. DC3000 ( DC3000) is a plant pathogenic bacterium that possesses complicated motility regulation pathways including a typical chemotaxis system. A significant portion of our understanding about the genes functioning in DC3000 motility is based on comparison to other bacteria.

Sorghum rhizosphere bacteriome studies and generation of multistrain beneficial bacterial consortia.

The plant rhizosphere microbiome plays a crucial role in plant growth and health. Within this microbiome, bacteria dominate, exhibiting traits that benefit plants, such as facilitating nutrient acquisition, fixing nitrogen, controlling pathogens, and promoting root growth. This study focuses on designing synthetic bacterial consortia using key bacterial strains which have been mapped and then isolated from the sorghum rhizosphere microbiome.

A regulatory network controlling developmental boundaries and meristem fates contributed to maize domestication.

During domestication, early farmers selected different vegetative and reproductive traits, but identifying the causative loci has been hampered by their epistasis and functional redundancy. Using chromatin immunoprecipitation sequencing combined with genome-wide association analysis, we uncovered a developmental regulator that controls both types of trait while acting upstream of multiple domestication loci. tasselsheath4 (tsh4) is a new maize domestication gene that establishes developmental boundaries and specifies meristem fates despite not being expressed within them.

CLAVATA3 Signaling Buffers Arabidopsis Shoot Apical Meristem Activity in Response to Photoperiod.

Land plants grow throughout their life cycle via the continuous activity of stem cell reservoirs contained within their apical meristems. The shoot apical meristem (SAM) of Arabidopsis and other land plants responds to a variety of environmental cues, yet little is known about the response of meristems to seasonal changes in day length, or photoperiod. Here, the vegetative and reproductive growth of Arabidopsis wild-type and plants in different photoperiod conditions was analyzed.

Defined synthetic microbial communities colonize and benefit field-grown sorghum.

The rhizosphere constitutes a dynamic interface between plant hosts and their associated microbial communities. Despite the acknowledged potential for enhancing plant fitness by manipulating the rhizosphere, the engineering of the rhizosphere microbiome through inoculation has posed significant challenges. These challenges are thought to arise from the competitive microbial ecosystem where introduced microbes must survive, and the absence of adaptation to the specific metabolic and environmental demands of the rhizosphere.

Transcription factor binding site divergence across maize inbred lines drives transcriptional and phenotypic variation.

Regulatory elements are important constituents of plant genomes that have shaped ancient and modern crops. Their identification, function, and diversity in crop genomes however are poorly characterized, thus limiting our ability to harness their power for further agricultural advances using induced or natural variation. Here, we use DNA affinity purification-sequencing (DAP-seq) to map transcription factor (TF) binding events for 200 maize TFs belonging to 30 distinct families and heterodimer pairs in two distinct inbred lines historically used for maize hybrid plant production, providing empirical binding site annotation for 5.

Rhythmic lipid and gene expression responses to chilling in panicoid grasses.

Chilling stress threatens plant growth and development, particularly affecting membrane fluidity and cellular integrity. Understanding plant membrane responses to chilling stress is important for unraveling the molecular mechanisms of stress tolerance. Whereas core transcriptional responses to chilling stress and stress tolerance are conserved across species, the associated changes in membrane lipids appear to be less conserved, as which lipids are affected by chilling stress varies by species.

Molecular dissection of the pseudokinase ZED1 expands effector recognition to the tomato immune receptor ZAR1.

The highly conserved angiosperm immune receptor HOPZ-ACTIVATED RESISTANCE 1 (ZAR1) is a bacterial pathogen recognition hub that mediates resistance by guarding host kinases for modification by pathogen effectors. The pseudokinase HOPZ-ETI DEFICIENT 1 (ZED1) is the only known ZAR1-guarded protein that interacts directly with a pathogen effector, HopZ1a, from the bacterial pathogen Pseudomonas syringae, making it a promising system for rational design of effector recognition for plant immunity. Here, we conducted an in-depth molecular analysis of ZED1.

Phylogenetic distribution and experimental characterization of corrinoid production and dependence in soil bacterial isolates.

Soil microbial communities impact carbon sequestration and release, biogeochemical cycling, and agricultural yields. These global effects rely on metabolic interactions that modulate community composition and function. However, the physicochemical and taxonomic complexity of soil and the scarcity of available isolates for phenotypic testing are significant barriers to studying soil microbial interactions.

Streptomyces umbrella toxin particles block hyphal growth of competing species.

Streptomyces are a genus of ubiquitous soil bacteria from which the majority of clinically utilized antibiotics derive. The production of these antibacterial molecules reflects the relentless competition Streptomyces engage in with other bacteria, including other Streptomyces species. Here we show that in addition to small-molecule antibiotics, Streptomyces produce and secrete antibacterial protein complexes that feature a large, degenerate repeat-containing polymorphic toxin protein.

High-quality assembled and annotated genomes of Nicotiana tabacum and Nicotiana benthamiana reveal chromosome evolution and changes in defense arsenals.

Nicotiana tabacum and Nicotiana benthamiana are widely used models in plant biology research. However, genomic studies of these species have lagged. Here we report the chromosome-level reference genome assemblies for N.

The trxG protein ULT1 regulates Arabidopsis organ size by interacting with TCP14/15 to antagonize the LIM peptidase DA1 for H3K4me3 on target genes.

Plant organ size is an important agronomic trait that makes a significant contribution to plant yield. Despite its central importance, the genetic and molecular mechanisms underlying organ size control remain to be fully clarified. Here, we report that the trithorax group protein ULTRAPETALA1 (ULT1) interacts with the TEOSINTE BRANCHED1/CYCLOIDEA/PCF14/15 (TCP14/15) transcription factors by antagonizing the LIN-11, ISL-1, and MEC-3 (LIM) peptidase DA1, thereby regulating organ size in Arabidopsis.

Identification of transcriptional networks controlling leaf sheath growth in Sorghum bicolor.

Objectives: The objective of this data set was to identify transcriptional networks that control elongation of seedling leaf sheaths in the C4 grass Sorghum bicolor. One motivation was that leaf sheaths are a primary constituent of stems in grass seedlings; therefore, genes that control growth of this organ are important contributors to successful transition from the seedling stage to the mature plant stage and, ultimately, crop success. Since diurnal rhythms contribute to regulation of signaling networks responsible for growth, a time course representing the late afternoon and early evening was anticipated to pinpoint important control genes for stem growth.

is a conserved primary regulator of flowering.

Introduction: A fundamental developmental switch for plants is transition from vegetative to floral growth, which integrates external and internal signals. INDETERMINATE1 (Id1) family proteins are zinc finger transcription factors that activate flowering in grasses regardless of photoperiod. Mutations in maize and rice () cause very late flowering.

Chromosome-level genome of the transformable northern wattle, Acacia crassicarpa.

The genus Acacia is a large group of woody legumes containing an enormous amount of morphological diversity in leaf shape. This diversity is at least in part the result of an innovation in leaf development where many Acacia species are capable of developing leaves of both bifacial and unifacial morphologies. While not unique in the plant kingdom, unifaciality is most commonly associated with monocots, and its developmental genetic mechanisms have yet to be explored beyond this group.

Stem Cells: Engines of Plant Growth and Development.

The development of both animals and plants relies on populations of pluripotent stem cells that provide the cellular raw materials for organ and tissue formation. Plant stem cell reservoirs are housed at the shoot and root tips in structures called meristems, with the shoot apical meristem (SAM) continuously producing aerial leaf, stem, and flower organs throughout the life cycle. Thus, the SAM acts as the engine of plant development and has unique structural and molecular features that allow it to balance self-renewal with differentiation and act as a constant source of new cells for organogenesis while simultaneously maintaining a stem cell reservoir for future organ formation.

The CLAVATA3/ESR-related peptide family in the biofuel crop pennycress.

CLAVATA3/ESR-related (CLE) peptides perform a variety of important functions in plant development and historically have been targeted during the domestication of existing crops. Pennycress () is an emerging biofuel crop currently undergoing domestication that offers novel monetary and environmental incentives as a winter cover crop during an otherwise fallow period of the corn/soybean farming rotation. Here we report the characterization of the gene family in pennycress through homology comparison of the CLE motif with other dicot species by conducting a homology comparison and maximum likelihood phylogenetic analysis supplemented with manual annotation.

Genetic and Phenotypic Analysis of Shoot Apical and Floral Meristem Development.

The shoot apical and floral meristems (SAM and FM, respectively) of Arabidopsis thaliana contain reservoirs of self-renewing stem cells that function as sources of progenitor cells for organ formation during development. The primary SAM produces all the aerial structures of the adult plant, while the FMs generate the four types of floral organs. Consequently, aberrant SAM and FM activity can profoundly affect vegetative and reproductive plant morphology.