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<jats:title>SUMMARY</jats:title><jats:p><jats:italic>Rhus chinensis</jats:italic> Mill., an economically valuable Anacardiaceae species, is parasitized by the galling aphid <jats:italic>Schlechtendalia chinensis</jats:italic>, resulting in the formation of the Chinese gallnut (CG). Here, we report a chromosomal‐level genome assembly of <jats:italic>R. chinensis</jats:italic>, with a total size of 389.40 Mb and scaffold N50 of 23.02 Mb. Comparative genomic and transcriptome analysis revealed that the enhanced structure of CG and nutritional metabolism contribute to improving the adaptability of <jats:italic>R. chinensis</jats:italic> to <jats:italic>S. chinensis</jats:italic> by supporting CG and galling aphid growth. CG was observed to be abundant in hydrolysable tannins (HT), particularly gallotannin and its isomers. Tandem repeat clusters of dehydroquinate dehydratase/shikimate dehydrogenase (DQD/SDH) and serine carboxypeptidase‐like (SCPL) and their homologs involved in HT production were determined as specific to HT‐rich species. The functional differentiation of <jats:italic>DQD/SDH</jats:italic> tandem duplicate genes and the significant contraction in the phenylalanine ammonia‐lyase (<jats:italic>PAL</jats:italic>) gene family contributed to the accumulation of gallic acid and HT while minimizing the production of shikimic acid, flavonoids, and condensed tannins in CG. Furthermore, we identified one UDP glucosyltransferase (<jats:italic>UGT84A</jats:italic>), three carboxylesterase (<jats:italic>CXE</jats:italic>), and six <jats:italic>SCPL</jats:italic> genes from conserved tandem repeat clusters that are involved in gallotannin biosynthesis and hydrolysis in CG. We then constructed a regulatory network of these genes based on co‐expression and transcription factor motif analysis. Our findings provide a genomic resource for the exploration of the underlying mechanisms of plant‐galling insect interaction and highlight the importance of the functional divergence of tandem duplicate genes in the accumulation of secondary metabolites.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p><jats:italic>Arabidopsis thaliana</jats:italic> WRKY proteins are potential targets of pathogen‐secreted effectors. RESISTANT TO RALSTONIA SOLANACEARUM 1 (RRS1; AtWRKY52) is a well‐studied Arabidopsis nucleotide‐binding and leucine‐rich repeat (NLR) immune receptor carrying a C‐terminal WRKY domain that functions as an integrated decoy. RRS1‐R recognizes the effectors AvrRps4 from <jats:italic>Pseudomonas syringae</jats:italic> pv. <jats:italic>pisi</jats:italic> and PopP2 from <jats:italic>Ralstonia pseudosolanacearum</jats:italic> by direct interaction through its WRKY domain. AvrRps4 and PopP2 were previously shown to interact with several AtWRKYs. However, how these effectors selectively interact with their virulence targets remains unknown. Here, we show that several members of subgroup IIIb of the AtWRKY family are targeted by AvrRps4 and PopP2. We demonstrate that several AtWRKYs induce cell death when transiently expressed in <jats:italic>Nicotiana benthamiana</jats:italic>, indicating the activation of immune responses. AtWRKY54 was the only cell death‐inducing AtWRKY that interacted with both AvrRps4 and PopP2. We found that AvrRps4 and PopP2 specifically suppress AtWRKY54‐induced cell death. We also demonstrate that the amino acid residues required for the avirulence function of AvrRps4 and PopP2 are critical for suppressing AtWRKY54‐induced cell death. AtWRKY54 residues predicted to form a binding interface with AvrRps4 were predominantly located in the DNA binding domain and necessary for inducing cell death. Notably, one AtWRKY54 residue, E164, contributes to affinity with AvrRps4 and is exclusively present among subgroup IIIb AtWRKYs, yet is located outside of the DNA‐binding domain. Surprisingly, AtWRKY54 mutated at E164 evaded AvrRps4‐mediated cell death suppression. Taking our observations together, we propose that AvrRp4 and PopP2 specifically target AtWRKY54 to suppress plant immune responses.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>The indole alkaloid gramine, 3‐(dimethylaminomethyl)indole, is a defensive specialized metabolite found in some barley cultivars. In its biosynthetic process, the tryptophan (Trp) side chain is shortened by two carbon atoms to produce 3‐(aminomethyl)indole (AMI), which is then methylated by <jats:italic>N</jats:italic>‐methyltransferase (HvNMT) to produce gramine. Although side chain shortening is one of the crucial scaffold formation steps of alkaloids originating from aromatic amino acids, the gene and enzyme involved in the Trp–AMI conversion reactions are unknown. In this study, through RNA‐seq analysis, 35 transcripts were shown to correlate with gramine production; among them, an uncharacterized cytochrome P450 (CYP) gene, <jats:italic>CYP76M57</jats:italic>, and <jats:italic>HvNMT</jats:italic> were identified as candidate genes for gramine production. Transgenic <jats:italic>Arabidopsis thaliana</jats:italic> and rice overexpressing <jats:italic>CYP</jats:italic> and <jats:italic>HvNMT</jats:italic> accumulate AMI, <jats:italic>N</jats:italic>‐methyl‐AMI, and gramine. CYP76M57, heterologously expressed in <jats:italic>Pichia pastoris</jats:italic>, was able to act on Trp to produce AMI. Furthermore, the amino group nitrogen of Trp was retained during the CYP76M57‐catalyzed reaction, indicating that the C<jats:sub>2</jats:sub> shortening of Trp proceeds with an unprecedented biosynthetic process, the removal of the carboxyl group and C<jats:sub>α</jats:sub> and the rearrangement of the nitrogen atom to C<jats:sub>β</jats:sub>. In some gramine‐non‐accumulating barley cultivars, arginine 104 in CYP76M57 is replaced by threonine, which abolished the catalytic activity of CYP76M57 to convert Trp into AMI. These results uncovered the missing committed enzyme of gramine biosynthesis in barley and contribute to the elucidation of the potential functions of CYPs in plants and undiscovered specialized pathways.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>The secretory pathway is essential for plant immunity, delivering diverse antimicrobial molecules into the extracellular space. <jats:italic>Arabidopsis thaliana</jats:italic> soluble N‐ethylmaleimide‐sensitive‐factor attachment protein receptor SNAP33 is a key actor of this process. The <jats:italic>snap33</jats:italic> mutant displays dwarfism and necrotic lesions, however the molecular determinants of its macroscopic phenotypes remain elusive. Here, we isolated several new <jats:italic>snap33</jats:italic> mutants that exhibited constitutive cell death and H<jats:sub>2</jats:sub>O<jats:sub>2</jats:sub> accumulation, further defining <jats:italic>snap33</jats:italic> as an autoimmune mutant. We then carried out quantitative transcriptomic and proteomic analyses showing that numerous defense transcripts and proteins were up‐regulated in the <jats:italic>snap33</jats:italic> mutant, among which genes/proteins involved in defense hormone, pattern‐triggered immunity, and nucleotide‐binding domain leucine‐rich‐repeat receptor signaling. qRT‐PCR analyses and hormone dosages supported these results. Furthermore, genetic analyses elucidated the diverse contributions of the main defense hormones and some nucleotide‐binding domain leucine‐rich‐repeat receptor signaling actors in the establishment of the <jats:italic>snap33</jats:italic> phenotype, emphasizing the preponderant role of salicylic acid over other defense phytohormones. Moreover, the accumulation of pattern‐triggered immunity and nucleotide‐binding domain leucine‐rich‐repeat receptor signaling proteins in the <jats:italic>snap33</jats:italic> mutant was confirmed by immunoblotting analyses and further shown to be salicylic acid‐dependent. Collectively, this study unveiled molecular determinants underlying the Arabidopsis <jats:italic>snap33</jats:italic> mutant phenotype and brought new insights into autoimmunity signaling.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Endoreduplication, during which cells increase their DNA content through successive rounds of full genome replication without cell division, is the major source of endopolyploidy in higher plants. Endoreduplication plays pivotal roles in plant growth and development and is associated with the activation of specific transcriptional programmes that are characteristic of each cell type, thereby defining their identity. In plants, endoreduplication is found in numerous organs and cell types, especially in agronomically valuable ones, such as the fleshy fruit (pericarp) of tomato presenting high ploidy levels. We used the tomato pericarp tissue as a model system to explore the transcriptomes associated with endoreduplication progression during fruit growth. We confirmed that expression globally scales with ploidy level and identified sets of differentially expressed genes presenting only developmental‐specific, only ploidy‐specific expression patterns or profiles resulting from an additive effect of ploidy and development. When comparing ploidy levels at a specific developmental stage, we found that non‐endoreduplicated cells are defined by cell division state and cuticle synthesis while endoreduplicated cells are mainly defined by their metabolic activity changing rapidly over time. By combining this dataset with publicly available spatiotemporal pericarp expression data, we proposed a map describing the distribution of ploidy levels within the pericarp. These transcriptome‐based predictions were validated by quantifying ploidy levels within the pericarp tissue. This <jats:italic>in situ</jats:italic> ploidy quantification revealed the dynamic progression of endoreduplication and its cell layer specificity during early fruit development. In summary, the study sheds light on the complex relationship between endoreduplication, cell differentiation and gene expression patterns in the tomato pericarp.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Animals and insects communicate using vibrations that are frequently too low or too high for human ears to detect. Plants and trees can communicate and sense sound. Khait et al. used a dependable recording system to capture airborne sounds produced by stressed plants. In addition to allowing plants to communicate their stress, sound aids in plant defense, development, and resilience. It also serves as a warning that danger is approaching. Demey et al. and others discussed the audit examinations that were conducted to investigate sound discernment in plants at the atomic and biological levels. The biological significance of sound in plants, the morphophysiological response of plants to sound, and the airborne noises that plants make and can hear from a few meters away were all discussed.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Crops often have to face several abiotic stresses simultaneously, and under these conditions, the plant's response significantly differs from that observed under a single stress. However, up to the present, most of the molecular markers identified for increasing plant stress tolerance have been characterized under single abiotic stresses, which explains the unexpected results found when plants are tested under real field conditions. One important regulator of the plant's responses to abiotic stresses is abscisic acid (ABA). The ABA signaling system engages many stress‐responsive genes, but many others do not respond to ABA treatments. Thus, the ABA‐independent pathway, which is still largely unknown, involves multiple signaling pathways and important molecular components necessary for the plant's adaptation to climate change. In the present study, ABA‐deficient tomato mutants (<jats:italic>flacca</jats:italic>, <jats:italic>flc)</jats:italic> were subjected to salinity, heat, or their combination. An in‐depth RNA‐seq analysis revealed that the combination of salinity and heat led to a strong reprogramming of the tomato transcriptome. Thus, of the 685 genes that were specifically regulated under this combination in our <jats:italic>flc</jats:italic> mutants, 463 genes were regulated by ABA‐independent systems. Among these genes, we identified six transcription factors (TFs) that were significantly regulated, belonging to the R2R3‐MYB family. A protein–protein interaction network showed that the TFs SlMYB50 and SlMYB86 were directly involved in the upregulation of the flavonol biosynthetic pathway‐related genes. One of the most novel findings of the study is the identification of the involvement of some important ABA‐independent TFs in the specific plant response to abiotic stress combination. Considering that ABA levels dramatically change in response to environmental factors, the study of ABA‐independent genes that are specifically regulated under stress combination may provide a remarkable tool for increasing plant resilience to climate change.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>RNA‐Sequencing is widely used to investigate changes in gene expression at the transcription level in plants. Most plant RNA‐Seq analysis pipelines base the normalization approaches on the assumption that total transcript levels do not vary between samples. However, this assumption has not been demonstrated. In fact, many common experimental treatments and genetic alterations affect transcription efficiency or RNA stability, resulting in unequal transcript abundance. The addition of synthetic RNA controls is a simple correction that controls for variation in total mRNA levels. However, adding spike‐ins appropriately is challenging with complex plant tissue, and carefully considering how they are added is essential to their successful use. We demonstrate that adding external RNA spike‐ins as a normalization control produces differences in RNA‐Seq analysis compared to traditional normalization methods, even between two times of day in untreated plants. We illustrate the use of RNA spike‐ins with 3' RNA‐Seq and present a normalization pipeline that accounts for differences in total transcriptional levels. We evaluate the effect of normalization methods on identifying differentially expressed genes in the context of identifying the effect of the time of day on gene expression and response to chilling stress in sorghum.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>In plants so‐called plasma membrane intrinsic proteins (PIPs) are major water channels governing plant water status. Membrane trafficking contributes to functional regulation of major PIPs and is crucial for abiotic stress resilience. Arabidopsis PIP2;1 is rapidly internalised from the plasma membrane in response to high salinity to regulate osmotic water transport, but knowledge of the underlying mechanisms is fragmentary. Here we show that PIP2;1 occurs in complex with SYNTAXIN OF PLANTS 132 (SYP132) together with the plasma membrane H<jats:sup>+</jats:sup>‐ATPase AHA1 as evidenced through <jats:italic>in vivo</jats:italic> and <jats:italic>in vitro</jats:italic> analysis. SYP132 is a multifaceted vesicle trafficking protein, known to interact with AHA1 and promote endocytosis to impact growth and pathogen defence. Tracking native proteins in immunoblot analysis, we found that salinity stress enhances SYP132 interactions with PIP2;1 and PIP2;2 isoforms to promote redistribution of the water channels away from the plasma membrane. Concurrently, AHA1 binding within the SYP132‐complex was significantly reduced under salinity stress and increased the density of AHA1 proteins at the plasma membrane in leaf tissue. Manipulating SYP132 function in <jats:italic>Arabidopsis thaliana</jats:italic> enhanced resilience to salinity stress and analysis in heterologous systems suggested that the SNARE influences PIP2;1 osmotic water permeability. We propose therefore that SYP132 coordinates AHA1 and PIP2;1 abundance at the plasma membrane and influences leaf hydraulics to regulate plant responses to abiotic stress signals.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Shade avoidance syndrome (SAS) is triggered by a low ratio of red (R) to far‐red (FR) light (R/FR ratio), which is caused by neighbor detection and/or canopy shade. In order to compete for the limited light, plants elongate hypocotyls and petioles by deactivating phytochrome B (phyB), a major R light photoreceptor, thus releasing its inhibition of the growth‐promoting transcription factors PHYTOCHROME‐INTERACTING FACTORs. Under natural conditions, plants must cope with abiotic stresses such as drought, soil salinity, and extreme temperatures, and biotic stresses such as pathogens and pests. Plants have evolved sophisticated mechanisms to simultaneously deal with multiple environmental stresses. In this review, we will summarize recent major advances in our understanding of how plants coordinately respond to shade and environmental stresses, and will also discuss the important questions for future research. A deep understanding of how plants synergistically respond to shade together with abiotic and biotic stresses will facilitate the design and breeding of new crop varieties with enhanced tolerance to high‐density planting and environmental stresses.</jats:p>