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<jats:title>SUMMARY</jats:title><jats:p>The final step in secretion is membrane fusion facilitated by SNARE proteins that reside in opposite membranes. The formation of a trans‐SNARE complex between one R and three Q coiled‐coiled SNARE domains drives the final approach of the membranes providing the mechanical energy for fusion. Biological control of this mechanism is exerted by additional domains within some SNAREs. For example, the N‐terminal Longin domain (LD) of R‐SNAREs (also called Vesicle‐associated membrane proteins, VAMPs) can fold back onto the SNARE domain blocking interaction with other cognate SNAREs. The LD may also determine the subcellular localization via interaction with other trafficking‐related proteins. Here, we provide cell‐biological and genetic evidence that phosphorylation of the Tyrosine57 residue regulates the functionality of VAMP721. We found that an aspartate mutation mimics phosphorylation, leading to protein instability and subsequent degradation in lytic vacuoles. The mutant SNARE also fails to rescue the defects of <jats:italic>vamp721vamp722</jats:italic> loss‐of‐function lines in spite of its wildtype‐like localization within the secretory pathway and the ability to interact with cognate SNARE partners. Most importantly, it imposes a dominant negative phenotype interfering with root growth, normal secretion and cytokinesis in wildtype plants generating large aggregates that mainly contain secretory vesicles. Non‐phosphorylatable VAMP721<jats:sup>Y57F</jats:sup> needs higher gene dosage to rescue double mutants in comparison to native VAMP721 underpinning that phosphorylation modulates SNARE function. We propose a model where short‐lived phosphorylation of Y57 serves as a regulatory step to control VAMP721 activity, favoring its open state and interaction with cognate partners to ultimately drive membrane fusion.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Perennial monocarpic mass flowering represents as a key developmental innovation in flowering time diversity in several biological and economical essential families, such as the woody bamboos and the shrubby <jats:italic>Strobilanthes</jats:italic>. However, molecular and genetic mechanisms underlying this important biodiversity remain poorly investigated. Here, we generated a full‐length transcriptome resource incorporated into the <jats:italic>BlueOmics</jats:italic> database (<jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="http://blueomics.iflora.cn">http://blueomics.iflora.cn</jats:ext-link>) for two <jats:italic>Strobilanthes</jats:italic> species, which feature contrasting flowering time behaviors. Using about 112 and 104 Gb Iso‐seq reads together with ~185 and ~75 Gb strand‐specific RNA seq data, we annotated 80 971 and 79 985 non‐redundant full‐length transcripts for the perennial polycarpic <jats:italic>Strobilanthes tetrasperma</jats:italic> and the perennial monocarpic <jats:italic>Strobilanthes biocullata</jats:italic>, respectively. In <jats:italic>S. tetrasperma</jats:italic>, we identified 8794 transcripts showing spatiotemporal expression in nine tissues. In leaves and shoot apical meristems at two developmental stages, 977 and 1121 transcripts were differentially accumulated in <jats:italic>S. tetrasperma</jats:italic> and <jats:italic>S. biocullata</jats:italic>, respectively. Interestingly, among the 33 transcription factors showing differential expression in <jats:italic>S. tetrasperma</jats:italic> but without differential expression in <jats:italic>S. biocullata</jats:italic>, three were involved potentially in the photoperiod and circadian‐clock pathway of flowering time regulation (<jats:italic>FAR1 RELATED SEQUENCE 12</jats:italic>, <jats:italic>FRS12</jats:italic>; <jats:italic>NUCLEAR FACTOR Y A1</jats:italic>, <jats:italic>NFYA1</jats:italic>; <jats:italic>PSEUDO‐RESPONSE REGULATOR 5</jats:italic>, <jats:italic>PRR5</jats:italic>), hence provides an important clue in deciphering the flowering diversity mechanisms. Our data serve as a key resource for further dissection of molecular and genetic mechanisms underpinning key biological innovations, here, the perennial monocarpic mass flowering.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Centromeres are the chromosomal domains, where the kinetochore protein complex is formed, mediating proper segregation of chromosomes during cell division. Although the function of centromeres has remained conserved during evolution, centromeric DNA is highly variable, even in closely related species. In addition, the composition of the kinetochore complexes varies among organisms. Therefore, it is assumed that the centromeric position is determined epigenetically, and the centromeric histone H3 (CENH3) serves as an epigenetic marker. The loading of CENH3 onto centromeres depends on centromere‐licensing factors, chaperones, and transcription of centromeric repeats. Several proteins that regulate CENH3 loading and kinetochore assembly interact with the centromeric transcripts and DNA in a sequence‐independent manner. However, the functional aspects of these interactions are not fully understood. This review discusses the variability of centromeric sequences in different organisms and the regulation of their transcription through the RNA Pol II and RNAi machinery. The data suggest that the interaction of proteins involved in CENH3 loading and kinetochore assembly with centromeric DNA and transcripts plays a role in centromere, and possibly neocentromere, formation in a sequence‐independent manner.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Plant height (PH) is an important plant architectural trait targeted during Green Revolution to enhance crop yields. Identification of genes and natural alleles governing plant height without compromising agronomic performance can fill the lacuna of knowledge connecting ideal plant architecture with maximum achievable yield in chickpea. Through coherent strategy involving genome‐wide association study, QTL/fine mapping, map‐based cloning, molecular haplotyping, and downstream functional genomics, the current study identified two Mediator subunit genes namely, <jats:italic>CaMED23</jats:italic> and <jats:italic>CaMED5b</jats:italic> and their derived natural alleles/haplotypes underlying the major QTLs and <jats:italic>trans</jats:italic>‐acting eQTLs regulating plant height in chickpea. Differential accumulation of haplotype‐specific transcripts of these two Mediator genes in corresponding haplotype‐introgressed near‐isogenic lines (NILs) correlates negatively with the plant height trait. Quantitative as well as qualitative estimation based on histology, scanning electron microscopy, and histochemical assay unraveled the reduced lengths and cell sizes of internodes along with compromised lignin levels in dwarf/semi‐dwarf chickpea NILs introgressed with superior <jats:italic>CaMED23</jats:italic> and <jats:italic>CaMED5b</jats:italic> gene haplotypes. This observation, supported by global transcriptome profiling‐based diminished expression of various phenylpropanoid pathway genes upstream of lignin biosynthesis in dwarf/semi‐dwarf NILs, essentially links plant height with lignin accumulation. The identified molecular signatures in the Mediator subunit genes can be efficiently utilized to develop desirable dwarf/semi‐dwarf‐type chickpea cultivars without affecting their yield per plant via modulating lignin/phenylpropanoid biosynthesis.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Seed protein localization in seed storage protein bodies (SSPB) and their significance in germination are well recognized. SSPB are spherical and contain an assembly of water‐soluble and salt‐soluble proteins. Although the native structures of some SSPB proteins are explored, their structural arrangement to the functional correlation in SSPB remains unknown. SSPB are morphologically analogous to electron‐dense amyloid‐containing structures reported in other organisms. Here, we show that wheat, mungbean, barley, and chickpea SSPB exhibit a speckled pattern of amyloids interspersed in an amyloid‐like matrix along with native structures, suggesting the composite nature of SSPB. This is confirmed by multispectral imaging methods, electron microscopy, infrared, and X‐ray diffraction analysis, using <jats:italic>in situ</jats:italic> tissue sections, <jats:italic>ex vivo</jats:italic> protoplasts, and <jats:italic>in vitro</jats:italic> SSPB. Laser capture microdissection coupled with peptide fingerprinting has shown that globulin 1 and 3 in wheat, and 8S globulin and conglycinin in mungbean are the major amyloidogenic proteins. The amyloid composites undergo a sustained degradation during germination and seedling growth, facilitated by an intricate interplay of plant hormones and proteases. These results would lay down the foundation for understanding the amyloid composite structure during SSPB biogenesis and its evolution across the plant kingdom and have implications in both basic and applied plant biology.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Peyote (<jats:italic>Lophophora williamsii</jats:italic>) is an entheogenic and medicinal cactus native to the Chihuahuan desert. The psychoactive and hallucinogenic properties of peyote are principally attributed to the phenethylamine derivative mescaline. Despite the isolation of mescaline from peyote over 120 years ago, the biosynthetic pathway in the plant has remained undiscovered. Here, we use a transcriptomics and homology‐guided gene discovery strategy to elucidate a near‐complete biosynthetic pathway from <jats:sc>l</jats:sc>‐tyrosine to mescaline. We identified a cytochrome P450 that catalyzes the 3‐hydroxylation of <jats:sc>l</jats:sc>‐tyrosine to <jats:sc>l</jats:sc>‐DOPA, a tyrosine/DOPA decarboxylase yielding dopamine, and four substrate‐specific and regiospecific substituted phenethylamine <jats:italic>O</jats:italic>‐methyltransferases. Biochemical assays with recombinant enzymes or functional analyses performed by feeding putative precursors to engineered yeast (<jats:italic>Saccharomyces cerevisiae</jats:italic>) strains expressing candidate peyote biosynthetic genes were used to determine substrate specificity, which served as the basis for pathway elucidation. Additionally, an <jats:italic>N</jats:italic>‐methyltransferase displaying broad substrate specificity and leading to the production of <jats:italic>N</jats:italic>‐methylated phenethylamine derivatives was identified, which could also function as an early step in the biosynthesis of tetrahydroisoquinoline alkaloids in peyote.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p><jats:italic>Populus</jats:italic> species play a foundational role in diverse ecosystems and are important renewable feedstocks for bioenergy and bioproducts. Hybrid aspen <jats:italic>Populus tremula</jats:italic> × <jats:italic>P. alba</jats:italic> INRA 717‐1B4 is a widely used transformation model in tree functional genomics and biotechnology research. As an outcrossing interspecific hybrid, its genome is riddled with sequence polymorphisms which present a challenge for sequence‐sensitive analyses. Here we report a telomere‐to‐telomere genome for this hybrid aspen with two chromosome‐scale, haplotype‐resolved assemblies. We performed a comprehensive analysis of the repetitive landscape and identified both tandem repeat array‐based and array‐less centromeres. Unexpectedly, the most abundant satellite repeats in both haplotypes lie outside of the centromeres, consist of a 147 bp monomer PtaM147, frequently span &gt;1 megabases, and form heterochromatic knobs. PtaM147 repeats are detected exclusively in aspens (section <jats:italic>Populus</jats:italic>) but PtaM147‐like sequences occur in LTR‐retrotransposons of closely related species, suggesting their origin from the retrotransposons. The genomic resource generated for this transformation model genotype has greatly improved the design and analysis of genome editing experiments that are highly sensitive to sequence polymorphisms. The work should motivate future hypothesis‐driven research to probe into the function of the abundant and aspen‐specific PtaM147 satellite DNA.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Root hairs are crucial in the uptake of essential nutrients and water in plants. This study showed that a zinc finger protein, GIS3 is involved in root hair growth in Arabidopsis. The loss‐of‐function <jats:italic>gis3</jats:italic> and GIS3 RNAi transgenic line exhibited a significant reduction in root hairs compared to the wild type. The application of 1‐aminocyclopropane‐1‐carboxylic acid (ACC), an exogenous ethylene precursor, and 6‐benzyl amino purine (BA), a synthetic cytokinin, significantly restored the percentage of hair cells in the epidermis in <jats:italic>gis3</jats:italic> and induced <jats:italic>GIS3</jats:italic> expression in the wild type. More importantly, molecular and genetic studies revealed that GIS3 acts upstream of <jats:italic>ROOT HAIR DEFECTIVE 2</jats:italic> (<jats:italic>RHD2</jats:italic>) and <jats:italic>RHD4</jats:italic> by binding to their promoters. Furthermore, exogenous ACC and BA application significantly induced the expression of <jats:italic>RHD2</jats:italic> and <jats:italic>RHD4</jats:italic>, while root hair phenotype of <jats:italic>rhd2‐1</jats:italic>, <jats:italic>rhd4‐1</jats:italic>, and <jats:italic>rhd4‐3</jats:italic> was insensitive to ACC and BA treatment. We can therefore conclude that <jats:italic>GIS3</jats:italic> modulates root hair development by directly regulating <jats:italic>RHD2</jats:italic> and <jats:italic>RHD4</jats:italic> expression through ethylene and cytokinin signals in Arabidopsis.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Plants have evolved a sophisticated immune system to defend against invasion by pathogens. In response, pathogens deploy copious effectors to evade the immune responses. However, the molecular mechanisms used by pathogen effectors to suppress plant immunity remain unclear. Herein, we report that an effector secreted by <jats:italic>Ralstonia solanacearum</jats:italic>, RipAK, modulates the transcriptional activity of the ethylene‐responsive factor ERF098 to suppress immunity and dehydration tolerance, which causes bacterial wilt in pepper (<jats:italic>Capsicum annuum</jats:italic> L.) plants. Silencing <jats:italic>ERF098</jats:italic> enhances the resistance of pepper plants to <jats:italic>R. solanacearum</jats:italic> infection not only by inhibiting the host colonization of <jats:italic>R. solanacearum</jats:italic> but also by increasing the immunity and tolerance of pepper plants to dehydration and including the closure of stomata to reduce the loss of water in an abscisic acid signal‐dependent manner. In contrast, the ectopic expression of <jats:italic>ERF098</jats:italic> in <jats:italic>Nicotiana benthamiana</jats:italic> enhances wilt disease. We also show that RipAK targets and inhibits the ERF098 homodimerization to repress the expression of salicylic acid‐dependent <jats:italic>PR1</jats:italic> and dehydration tolerance‐related <jats:italic>OSR1</jats:italic> and <jats:italic>OSM1</jats:italic> by <jats:italic>cis</jats:italic>‐elements in their promoters. Taken together, our study reveals a regulatory mechanism used by the <jats:italic>R. solanacearum</jats:italic> effector RipAK to increase virulence by specifically inhibiting the homodimerization of ERF098 and reprogramming the transcription of <jats:italic>PR1</jats:italic>, <jats:italic>OSR1</jats:italic>, and <jats:italic>OSM1</jats:italic> to boost susceptibility and dehydration sensitivity. Thus, our study sheds light on a previously unidentified strategy by which a pathogen simultaneously suppresses plant immunity and tolerance to dehydration by secreting an effector to interfere with the activity of a transcription factor and manipulate plant transcriptional programs.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Seed color is one of the key target traits of domestication and artificial selection in chickpeas due to its implications on consumer preference and market value. The complex seed color trait has been well dissected in several crop species; however, the genetic mechanism underlying seed color variation in chickpea remains poorly understood. Here, we employed an integrated genomics strategy involving QTL mapping, high‐density mapping, map‐based cloning, association analysis, and molecular haplotyping in an inter‐specific RIL mapping population, association panel, wild accessions, and introgression lines (ILs) of <jats:italic>Cicer</jats:italic> gene pool. This delineated a MATE gene, <jats:italic>CaMATE23</jats:italic>, encoding a <jats:italic>Transparent Testa</jats:italic> (<jats:italic>TT</jats:italic>) and its natural allele (8‐bp insertion) and haplotype underlying a major QTL governing seed color on chickpea chromosome 4. Signatures of selective sweep and a strong purifying selection reflected that <jats:italic>CaMATE23</jats:italic>, especially its 8‐bp insertion natural allelic variant, underwent selection during chickpea domestication. Functional investigations revealed that the 8‐bp insertion containing the third <jats:italic>cis</jats:italic>‐regulatory RY‐motif element in the <jats:italic>CaMATE23</jats:italic> promoter is critical for enhanced binding of CaFUSCA3 transcription factor, a key regulator of seed development and flavonoid biosynthesis, thereby affecting <jats:italic>CaMATE23</jats:italic> expression and proanthocyanidin (PA) accumulation in the seed coat to impart varied seed color in chickpea. Consequently, overexpression of <jats:italic>CaMATE23</jats:italic> in Arabidopsis <jats:italic>tt12</jats:italic> mutant partially restored the seed color phenotype to brown pigmentation, ascertaining its functional role in PA accumulation in the seed coat. These findings shed new light on the seed color regulation and evolutionary history, and highlight the transcriptional regulation of <jats:italic>CaMATE23</jats:italic> by <jats:italic>CaFUSCA3</jats:italic> in modulating seed color in chickpea. The functionally relevant InDel variation, natural allele, and haplotype from <jats:italic>CaMATE23</jats:italic> are vital for translational genomic research, including marker‐assisted breeding, for developing chickpea cultivars with desirable seed color that appeal to consumers and meet global market demand.</jats:p>