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<jats:title>SUMMARY</jats:title><jats:p>Specific ecological conditions in the high mountain environment exert a selective pressure that often leads to convergent trait evolution. Reticulations induced by incomplete lineage sorting and introgression can lead to discordant trait patterns among gene and species trees (hemiplasy/xenoplasy), providing a false illusion that the traits under study are homoplastic. Using phylogenetic species networks, we explored the effect of gene exchange on trait evolution in <jats:italic>Soldanella</jats:italic>, a genus profoundly influenced by historical introgression. At least three features evolved independently multiple times: the single‐flowered dwarf phenotype, dysploid cytotype, and ecological generalism. The present analyses also indicated that the recurring occurrence of stoloniferous growth might have been prompted by an introgression event between an ancestral lineage and a still extant species, although its emergence via convergent evolution cannot be completely ruled out. Phylogenetic regression suggested that the independent evolution of larger genomes in snowbells is most likely a result of the interplay between hybridization events of dysploid and euploid taxa and hostile environments at the range margins of the genus. The emergence of key intrinsic and extrinsic traits in snowbells has been significantly impacted not only by convergent evolution but also by historical and recent introgression events.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Acyl‐acyl carrier protein (ACP) thioesterases (FAT) hydrolyze acyl‐ACP complexes to release FA in plastids, which ultimately affects FA biosynthesis and profiles. Soybean <jats:italic>GmFATA1</jats:italic> and <jats:italic>GmFATA2</jats:italic> are homoeologous genes encoding oleoyl‐ACP thioesterases whose role in seed oil accumulation and plant growth has not been defined. Using CRISPR/Cas9 gene editing mutation of <jats:italic>Gmfata1</jats:italic> or <jats:italic>2</jats:italic> led to reduced leaf FA content and growth defect at the early seedling stage. In contrast, no homozygous double mutants were obtained. Combined this indicates that <jats:italic>GmFATA1</jats:italic> and <jats:italic>GmFATA2</jats:italic> display overlapping, but not complete functional redundancy. Combined transcriptomic and lipidomic analysis revealed a large number of genes involved in FA synthesis and FA chain elongation are expressed at reduced level in the <jats:italic>Gmfata1</jats:italic> mutant, accompanied by a lower triacylglycerol abundance at the early seedling stage. Further analysis showed that the <jats:italic>Gmfata1 or 2</jats:italic> mutants had increased composition of the beneficial FA, oleic acid. The growth defect of Gm<jats:italic>fata1</jats:italic> could be at least partially attributed to reduced acetyl‐CoA carboxylase activity, reduced abundance of five unsaturated monogalactosyldiacylglycerol lipids, and altered chloroplast morphology. On the other hand, overexpression of <jats:italic>GmFATA</jats:italic> in soybean led to significant increases in leaf FA content by 5.7%, vegetative growth, and seed yield by 26.9%, and seed FA content by 23.2%. Thus, overexpression of <jats:italic>GmFATA</jats:italic> is an effective strategy to enhance soybean oil content and yield.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p><jats:italic>Prunella vulgaris</jats:italic> is one of the bestselling and widely used medicinal herbs. It is recorded as an ace medicine for cleansing and protecting the liver in <jats:italic>Chinese Pharmacopoeia</jats:italic> and has been used as the main constitutions of many herbal tea formulas in China for centuries. It is also a traditional folk medicine in Europe and other countries of Asia. Pentacyclic triterpenoids are a major class of bioactive compounds produced in <jats:italic>P. vulgaris</jats:italic>. However, their biosynthetic mechanism remains to be elucidated. Here, we report a chromosome‐level reference genome of <jats:italic>P. vulgaris</jats:italic> using an approach combining Illumina, ONT, and Hi‐C technologies. It is 671.95 Mb in size with a scaffold N50 of 49.10 Mb and a complete BUSCO of 98.45%. About 98.31% of the sequence was anchored into 14 pseudochromosomes. Comparative genome analysis revealed a recent WGD in <jats:italic>P. vulgaris</jats:italic>. Genome‐wide analysis identified 35 932 protein‐coding genes (PCGs), of which 59 encode enzymes involved in 2,3‐oxidosqualene biosynthesis. In addition, 10 <jats:italic>PvOSC</jats:italic>, 358 <jats:italic>PvCYP</jats:italic>, and 177 <jats:italic>PvUGT</jats:italic> genes were identified, of which five <jats:italic>PvOSCs</jats:italic>, 25 <jats:italic>PvCYPs</jats:italic>, and 9 <jats:italic>PvUGTs</jats:italic> were predicted to be involved in the biosynthesis of pentacyclic triterpenoids. Biochemical activity assay of PvOSC2, PvOSC4, and PvOSC6 recombinant proteins showed that they were mixed amyrin synthase (MAS), lupeol synthase (LUS), and β‐amyrin synthase (BAS), respectively. The results provide a solid foundation for further elucidating the biosynthetic mechanism of pentacyclic triterpenoids in <jats:italic>P. vulgaris</jats:italic>.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Citrus bacterial canker (CBC) is a serious bacterial disease caused by <jats:italic>Xanthomonas citri</jats:italic> subsp. <jats:italic>citri</jats:italic> (<jats:italic>Xcc</jats:italic>) that adversely impacts the global citrus industry. In a previous study, we demonstrated that overexpression of an <jats:italic>Xcc</jats:italic>‐inducible apetala 2/ethylene response factor encoded by <jats:italic>Citrus sinensis</jats:italic>, CsAP2‐09, enhances CBC resistance. The mechanism responsible for this effect, however, is not known. In the present study, we showed that CsAP2‐09 targeted the promoter of the <jats:italic>Xcc‐</jats:italic>inducible WRKY transcription factor coding gene <jats:italic>CsWRKY25</jats:italic> directly, activating its transcription. CsWRKY25 was found to localize to the nucleus and to activate transcriptional activity. Plants overexpressing <jats:italic>CsWRKY25</jats:italic> were more resistant to CBC and showed higher expression of the respiratory burst oxidase homolog (RBOH) CsRBOH2, in addition to exhibiting increased RBOH activity. Transient overexpression assays in citrus confirmed that CsWRKY25 and CsRBOH2 participated in the generation of reactive oxygen species (ROS) bursts, which were able to restore the ROS degradation caused by CsAP2‐09 knockdown. Moreover, CsWRKY25 was found to bind directly to W‐box elements within the <jats:italic>CsRBOH2</jats:italic> promoter. Notably, <jats:italic>CsRBOH2</jats:italic> knockdown had been reported previously to reduce the CBC resistance, while demonstrated in this study, CsRBOH2 transient overexpression can enhance the CBC resistance. Overall, our results outline a pathway through which CsAP2‐09‐CsWRKY25 transcriptionally reprograms CsRBOH2‐mediated ROS homeostasis in a manner conducive to CBC resistance. These data offer new insight into the mechanisms and regulatory pathways through which CsAP2‐09 regulates CBC resistance, highlighting its potential utility as a target for the breeding of CBC‐resistant citrus varieties.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Ginger is cultivated in tropical and subtropical regions and is one of the most crucial spices worldwide owing to its special taste and scent. Here, we present a high‐quality genome assembly for ‘Small Laiwu Ginger’, a famous cultivated ginger in northern China. The ginger genome was phased into two haplotypes, haplotype A (1.55Gb), and haplotype B (1.44Gb). Analysis of Ty1/Copia and Ty3/Gypsy LTR retrotransposon families revealed that both have undergone multiple retrotransposon bursts about 0–1 million years ago. In addition to a recent whole‐genome duplication event, there has been a lineage‐specific expansion of genes involved in stilbenoid, diarylheptanoid, and gingerol biosynthesis, thereby enhancing 6‐gingerol biosynthesis. Furthermore, we focused on the biosynthesis of 6‐gingerol, the most important gingerol, and screened key transcription factors ZoMYB106 and ZobHLH148 that regulate 6‐gingerol synthesis by transcriptomic and metabolomic analysis in the ginger rhizome at four growth stages. The results of yeast one‐hybrid, electrophoretic mobility shift, and dual‐luciferase reporter gene assays showed that both ZoMYB106 and ZobHLH148 bind to the promoters of the key rate‐limiting enzyme genes <jats:italic>ZoCCOMT1</jats:italic> and <jats:italic>ZoCCOMT2</jats:italic> in the 6‐gingerol synthesis pathway and promote their transcriptional activities. The reference genome, transcriptome, and metabolome data pave the way for further research on the molecular mechanism underlying the biosynthesis of 6‐gingerol. Furthermore, it provides precious new resources for the study on the biology and molecular breeding of ginger.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Phosphate (Pi) is essential for plant growth and development. One strategy to improve Pi use efficiency is to enhance Pi remobilization among leaves. Using transcriptome analysis with first (top) and fourth (down) leaf blades from rice (<jats:italic>Oryza sativa</jats:italic>) in Pi‐sufficient and deficient conditions, we identified 1384 genes differentially expressed among these leaf blades. These genes were involved in physiological processes, metabolism, transport, and photosynthesis. Moreover, we identified the Pi efflux transporter gene, <jats:italic>OsPHO1;3</jats:italic>, responding to Pi‐supplied conditions among these leaf blades. <jats:italic>OsPHO1;3</jats:italic> is highly expressed in companion cells of phloem, but not xylem, in leaf blades and induced by Pi starvation. Mutation of <jats:italic>OsPHO1;3</jats:italic> led to Pi accumulation in second to fourth leaves under Pi‐sufficient conditions, but enhanced Pi levels in first leaves under Pi‐deficient conditions. These Pi accumulations in leaves of <jats:italic>Ospho1;3</jats:italic> mutants resulted from induction of <jats:italic>OsPHT1;2</jats:italic> and <jats:italic>OsPHT1;8</jats:italic> in root and reduction of Pi remobilization in leaf blades, revealed by the decreased Pi in phloem of leaves. Importantly, lack of <jats:italic>OsPHO1;3</jats:italic> caused growth defects under a range of Pi‐supplied conditions. These results demonstrate that Pi remobilization is essential for Pi homeostasis and plant growth irrespective of Pi‐supplied conditions, and <jats:italic>OsPHO1;3</jats:italic> plays an essential role in Pi remobilization for normal plant growth.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>Members of the glycosyltransferase (GT)43 and GT47 families have been associated with heteroxylan synthesis in both dicots and monocots and are thought to assemble into central cores of putative xylan synthase complexes (XSCs). Currently, it is unknown whether protein–protein interactions within these central cores are specific, how many such complexes exist, and whether these complexes are functionally redundant. Here, we used gene association network and co‐expression approaches in rice to identify four <jats:italic>Os</jats:italic>GT43s and four <jats:italic>Os</jats:italic>GT47s that assemble into different GT43/GT47 complexes. Using two independent methods, we showed that (i) these GTs assemble into at least six unique complexes through specific protein–protein interactions and (ii) the proteins interact directly <jats:italic>in vitro</jats:italic>. Confocal microscopy showed that, when alone, all <jats:italic>Os</jats:italic>GT43s were retained in the endoplasmic reticulum (ER), while all <jats:italic>Os</jats:italic>GT47s were localized in the Golgi. co‐expression of <jats:italic>Os</jats:italic>GT43s and <jats:italic>Os</jats:italic>GT47s displayed complexes that form in the ER but accumulate in Golgi. ER‐to‐Golgi trafficking appears to require interactions between <jats:italic>Os</jats:italic>GT43s and <jats:italic>Os</jats:italic>GT47s. Comparison of the central cores of the three putative rice <jats:italic>Os</jats:italic>XSCs to wheat, asparagus, and Arabidopsis XSCs, showed great variation in GT43/GT47 combinations, which makes the identification of orthologous central cores between grasses and dicots challenging. However, the emerging picture is that all central cores from these species seem to have at least one member of the IRX10/IRX10‐L clade in the GT47 family in common, suggesting greater functional importance for this family in xylan synthesis. Our findings provide a new framework for future investigation of heteroxylan biosynthesis and function in monocots.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>The cytosol‐facing outer membrane (OM) of organelles communicates with other cellular compartments to exchange proteins, metabolites, and signaling molecules. Cellular surveillance systems also target OM‐resident proteins to control organellar homeostasis and ensure cell survival under stress. However, the OM proximity proteomes have never been mapped in plant cells since using traditional approaches to discover OM proteins and identify their dynamically interacting partners remains challenging. In this study, we developed an OM proximity labeling (OMPL) system using biotin ligase‐mediated proximity biotinylation to identify the proximity proteins of the OMs of mitochondria, chloroplasts, and peroxisomes in living Arabidopsis (<jats:italic>Arabidopsis thaliana</jats:italic>) cells. Using this approach, we mapped the OM proximity proteome of these three organelles under normal conditions and examined the effects of the ultraviolet‐B (UV‐B) or high light (HL) stress on the abundances of OM proximity proteins. We demonstrate the power of this system with the discovery of cytosolic factors and OM receptor candidates potentially involved in local protein translation and translocation. The candidate proteins that are involved in mitochondrion–peroxisome, mitochondrion–chloroplast, or peroxisome–chloroplast contacts, and in the organellar quality control system are also proposed based on OMPL analysis. OMPL‐generated OM proximity proteomes are valuable sources of candidates for functional validation and suggest directions for further investigation of important questions in cell biology.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>The model moss species <jats:italic>Physcomitrium patens</jats:italic> has long been used for studying divergence of land plants spanning from bryophytes to angiosperms. In addition to its phylogenetic relationships, the limited number of differential tissues, and comparable morphology to the earliest embryophytes provide a system to represent basic plant architecture. Based on plant–fungal interactions today, it is hypothesized these kingdoms have a long‐standing relationship, predating plant terrestrialization. Mortierellaceae have origins diverging from other land fungi paralleling bryophyte divergence, are related to arbuscular mycorrhizal fungi but are free‐living, observed to interact with plants, and can be found in moss microbiomes globally. Due to their parallel origins, we assess here how two Mortierellaceae species, <jats:italic>Linnemannia elongata</jats:italic> and <jats:italic>Benniella erionia</jats:italic>, interact with <jats:italic>P. patens</jats:italic> in coculture. We also assess how <jats:italic>Mollicute</jats:italic>‐related or <jats:italic>Burkholderia</jats:italic>‐related endobacterial symbionts (MRE or BRE) of these fungi impact plant response. Coculture interactions are investigated through high‐throughput phenomics, microscopy, RNA‐sequencing, differential expression profiling, gene ontology enrichment, and comparisons among 99 other <jats:italic>P. patens</jats:italic> transcriptomic studies. Here we present new high‐throughput approaches for measuring <jats:italic>P. patens</jats:italic> growth, identify novel expression of over 800 genes that are not expressed on traditional agar media, identify subtle interactions between <jats:italic>P. patens</jats:italic> and Mortierellaceae, and observe changes to plant–fungal interactions dependent on whether MRE or BRE are present. Our study provides insights into how plants and fungal partners may have interacted based on their communications observed today as well as identifying <jats:italic>L. elongata</jats:italic> and <jats:italic>B. erionia</jats:italic> as modern fungal endophytes with <jats:italic>P. patens</jats:italic>.</jats:p>

<jats:title>SUMMARY</jats:title><jats:p>As sessile organisms, plants experience variable environments and encounter diverse stresses during their growth and development. Adventitious rooting, orchestrated by multiple coordinated signaling pathways, represents an adaptive strategy evolved by plants to adapt to cope with changing environmental conditions. This study uncovered the role of the miR159a‐<jats:italic>PeMYB33</jats:italic> module in the formation of adventitious roots (ARs) synergistically with abscisic acid (ABA) signaling in poplar. Overexpression of <jats:italic>miR159a</jats:italic> increased the number of ARs and plant height while reducing sensitivity to ABA in transgenic plants. In contrast, inhibition of miR159a (using Short Tandem Target Mimic) or overexpression of <jats:italic>PeMYB33</jats:italic> decreased the number of ARs in transgenic plants. Additionally, miR159a targets and cleaves transcripts of <jats:italic>PeMYB33</jats:italic> using degradome analysis, which was further confirmed by a transient expression experiment of poplar protoplast. We show the miR159a‐<jats:italic>PeMYB33</jats:italic> module controls ARs development in poplar through ABA signaling. In particular, we demonstrated that miR159a promotes the expression of genes in the ABA signaling pathway. The findings from this study shed light on the intricate regulatory mechanisms governing the development of ARs in poplar plants. The miR159a‐<jats:italic>PeMYB33</jats:italic> module, in conjunction with ABA signaling, plays a crucial role in modulating AR formation and subsequent plant growth.</jats:p>