The Plant Journal最新文献

{"title":"Phosphorylation in two acts: Marchantia phototropin undergoes sequential cis- and trans-autophosphorylation","authors":"Martin Balcerowicz","doi":"10.1111/tpj.70072","DOIUrl":"https://doi.org/10.1111/tpj.70072","url":null,"abstract":"<p>Plants optimise photosynthetic performance and protect themselves from light-induced damage by sensing the intensity, periodicity, composition and direction of light. Consequently, plants have evolved several sets of photoreceptors to monitor their light environment. Phototropins are UV-A and blue light receptors that regulate responses such as phototropism, leaf flattening, chloroplast positioning and stomatal opening (Hart & Gardner, <span>2021</span>). Among these, light-induced chloroplast movement is one of the most conserved processes and can be observed not only in seed plants, but also in green algae, mosses and liverworts. Under low light conditions, chloroplasts accumulate at cell walls and orient perpendicular to the incoming light, maximising photosynthetic efficiency. Strong light intensities instead elicit an avoidance response where chloroplasts reorient parallel to the incoming light. This is generally thought of as a photoprotective mechanism, avoiding light-induced damage to the photosynthetic apparatus, but also allowing light to penetrate into deeper tissues (Łabuz et al., <span>2022</span>).</p><p>Phototropins contain two light-sensing LOV (Light, Oxygen, or Voltage-sensing) domains and a C-terminal serine/threonine kinase domain. In darkness, the LOV2 domain represses the kinase activity. Upon light absorption, this repression is relieved, triggering autophosphorylation of the kinase domain at multiple serine and threonine residues – an essential step in phototropin signalling (Hart & Gardner, <span>2021</span>). Phototropins form dimers, suggesting that autophosphorylation can occur both in <i>cis</i> (by the molecule's own kinase domain) and in <i>trans</i> (by its dimer partner). Arabidopsis phototropin 1 (Atphot1) was shown to undergo trans-autophosphorylation (Kaiserli et al., <span>2009</span>; Petersen et al., <span>2017</span>), but such mechanistic insight remains scarce for phototropins of other species.</p><p>Yutaka Kodama got interested in phototropins because of their major role in chloroplast movement. He worked on chloroplast biology during his postdoc in the lab of Masamitsu Wada at the National Institute for Biology and Kyushu University, after which he gained further expertise in bioimaging with Chang-Deng Hu at Purdue University. He started his own lab at Utsunomiya University in 2011, where his research focuses on organelle biology and developing innovative imaging technology. Studying chloroplast dynamics in response to external stimuli led him to explore phototropin function. Minoru Noguchi, currently a PhD candidate in the group, is particularly interested in phototropin signalling pathways and has been studying phototropin function in the liverwort <i>Marchantia polymorpha</i> (Marchantia).</p><p>Marchantia harbours a single copy phototropin gene (<i>MpPHOT</i>) that mediates chloroplast accumulation and avoidance responses under weak and strong light, respectively (Komatsu et al., <span>20","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 4","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70072","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143513540","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Role of methyltransferase 1-dependent DNA methylation in affecting maize kernel development","authors":"Xiaosong Li,&nbsp;Xuqing Tong,&nbsp;Bin Wang,&nbsp;Menglin Pu,&nbsp;Guangming Zheng,&nbsp;Bohui Wang,&nbsp;Jun Li,&nbsp;Xiaofei He,&nbsp;Zhilong Liu,&nbsp;Haiping Ding,&nbsp;Zhiming Zhang,&nbsp;Xiansheng Zhang,&nbsp;Chao Zhou,&nbsp;Xiangyu Zhao","doi":"10.1111/tpj.17250","DOIUrl":"https://doi.org/10.1111/tpj.17250","url":null,"abstract":"<div>\u0000 \u0000 <p>DNA methylation plays an essential role in plant growth and development, however, its specific influence on maize kernel development remains uncertain. In this study, we investigated the gene responsible for the maize kernel mutant <i>smk313</i> and identified it as the DNA methyltransferase ZmMET1. The <i>smk313</i> mutants displayed a distinct small kernel phenotype and exhibited developmental abnormalities in the basal endosperm transfer layer (BETL), the endosperm adjacent to the scutellum cell (EAS), and the starchy endosperm cells (SEs). Compared with that of the wild-type (WT), we found that the mutants had lower CG methylation density across the whole genome through whole genome methylation sequencing (WGBS), and there were many accessible chromatin regions (ACRs) through assay for targeting accessible chromatin with high-throughout sequencing (ATAC-seq). Combining these findings with the transcriptome analysis revealed a cascade of effects caused by the loss of <i>ZmMET1</i> function. This deficiency leads to alterations in genomic methylation and chromatin accessibility, which in turn influences the expression of genes related to starch and protein synthesis, as well as material transport processes. These alterations were consistent with the delayed development and dysplasia observed in EAS and BETLs of <i>smk313</i> kernels. Consequently, our investigation emphasizes the vital role of <i>ZmMET1</i> in maize seed development.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 4","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143490031","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcription factor KUA1 positively regulates tomato resistance against Phytophthora infestans by fine-tuning reactive oxygen species accumulation","authors":"Zhicheng Wang,&nbsp;Ruili Lv,&nbsp;Yuhui Hong,&nbsp;Chenglin Su,&nbsp;Zhengjie Wang,&nbsp;Jiaxuan Zhu,&nbsp;Ruirui Yang,&nbsp;Ruiming Wang,&nbsp;Yan Li,&nbsp;Jun Meng,&nbsp;Yushi Luan","doi":"10.1111/tpj.70007","DOIUrl":"https://doi.org/10.1111/tpj.70007","url":null,"abstract":"<div>\u0000 \u0000 <p>Tomato is a horticultural crop of global significance. However, the pathogen <i>Phytophthora infestans</i> causing the late blight disease imposes a severe threat to tomato production and quality. Many transcription factors (TFs) are known to be involved in responses to plant pathogens, however, the key TFs in tomato resistant to <i>P. infestans</i> remain to be explored. Here, we identified six TFs related to tomato responses to <i>P. infestans</i> infection. In particular, we found overexpression of <i>SlKUA1</i> could significantly improve tomato resistance to <i>P. infestans</i>; moreover, reactive oxygen species (ROS) accumulation was significantly increased in OE-<i>SlKUA1</i> compared with WT after <i>P. infestans</i> infection along with higher expression of <i>SlRBOHD</i>. Surprisingly, we found that SlKUA1 could not bind to the promoter of <i>SlRBOHD</i>. Further experiments revealed that <i>SlKUA1</i> inhibited the expression of <i>SlPrx1</i> by binding to its promoter region, thereby decreasing POD enzyme abundance and causing compromised ROS scavenge. Meanwhile, we identified that SlKUA1 also binds to the promoter region of two plant immune-related genes, <i>SlMAPK7</i> and <i>SlRLP4</i>, promoting their expression and enhancing tomato disease resistance. Together, our results have unraveled that <i>SlKUA1</i> can boost tomato resistance against <i>P. infestans</i> through quantitatively regulating ROS accumulation and related immune gene expression, thus, providing promising new targets for breeding late blight resistance tomatoes.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 4","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481431","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The COP1W467 tryptophan residue in the WD40 domain is essential for light- and temperature-mediated hypocotyl growth and flowering in Arabidopsis","authors":"Bidhan Chandra Malakar,&nbsp;Cristian M. Escudero,&nbsp;Vishmita Sethi,&nbsp;Gouranga Upadhyaya,&nbsp;Sreeramaiah N. Gangappa,&nbsp;Javier F. Botto","doi":"10.1111/tpj.70051","DOIUrl":"https://doi.org/10.1111/tpj.70051","url":null,"abstract":"<div>\u0000 \u0000 <p>COP1 is the essential protein that integrates various environmental and hormonal cues to control plant growth and development at multiple levels. COP1 is a RING-finger-type E3 ubiquitin ligase that acts as a potent repressor of photomorphogenesis and flowering by targeting numerous substrates for ubiquitination and promoting their proteolysis via the 26S proteasome system. The WD40 repeat domain with conserved amino acid residues was shown to be essential for interacting with its targets. However, the role of these amino acids in regulating hypocotyl growth and flowering in response to varying light and temperatures remains unknown. Here, we show that tryptophan amino acid at the position 467 residue (COP1^W467) is relevant in mediating the interaction with its targets to regulate the COP1-mediated proteolysis. The COP1^W467 plays a critical role in inducing growth responses in shade light by interacting and degrading HY5, a crucial negative regulator of shade-avoidance response (SAR). Moreover, COP1^W467 integrates warm ambient temperature signals to promote hypocotyl growth by increasing PIF4 and decreasing HY5 protein stability. Finally, we found that COP1^W467 is important in inhibiting flowering under a short-day photoperiod, likely through interacting with CO for degradation. Together, this study highlights that the COP1^W467 residue is essential to regulate seedling photomorphogenesis, SAR, thermomorphogenesis and flowering for the fine adjustment of plant growth and development under dynamic light and temperature conditions.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 4","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481571","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A self-amplifying NO-H2S loop mediates melatonin-induced CBF-responsive pathway and cold tolerance in watermelon","authors":"Yanliang Guo,&nbsp;Jiayue Li,&nbsp;Lingling Liu,&nbsp;Jiahe Liu,&nbsp;Wanbang Yang,&nbsp;Yi Chen,&nbsp;Chao Li,&nbsp;Li Yuan,&nbsp;Chunhua Wei,&nbsp;Jianxiang Ma,&nbsp;Yong Zhang,&nbsp;Jianqiang Yang,&nbsp;Feishi Luan,&nbsp;Xian Zhang,&nbsp;Hao Li","doi":"10.1111/tpj.70025","DOIUrl":"https://doi.org/10.1111/tpj.70025","url":null,"abstract":"<div>\u0000 \u0000 <p>Melatonin is a pivotal bioactive molecule that enhances plant cold stress tolerance, but the precise mechanisms remain enigmatic. Here, we have discovered that overexpressing melatonin biosynthetic gene <i>ClCOMT1</i> or applying exogenous melatonin activates the C-repeat binding factor (CBF)-responsive pathway and enhances watermelon cold tolerance. This enhancement is accompanied by elevated levels of nitric oxide (NO) and hydrogen sulfide (H₂S), along with upregulation of <i>nitrate reductase 1</i> (<i>ClNR1</i>) and <i>L-cysteine desulfhydrase</i> (<i>ClLCD</i>) genes involved in NO and H₂S generation respectively. Conversely, knockout of <i>ClCOMT1</i> exhibits contrasting effects compared to its overexpression. Furthermore, application of sodium nitroprusside (SNP, a NO donor) and NaHS (a H₂S donor) promotes the accumulation of H₂S and NO, respectively, activating the CBF pathway and enhancing cold tolerance. However, knockout of <i>ClNR1</i> or <i>ClLCD</i> abolished melatonin-induced H₂S or NO production respectively and abrogated melatonin-induced CBF pathway and cold tolerance. Conversely, supplementation with SNP and NaHS restored the diminished cold response caused by <i>ClCOMT1</i> deletion. Additionally, deletion of either <i>ClNR1</i> or <i>ClLCD</i> eliminated NaHS- or SNP-induced cold response, respectively. Overall, these findings suggest a reciprocal positive-regulatory loop between <i>ClNR1</i>-mediated NO and <i>ClLCD</i>-mediated H₂S, which plays a crucial role in mediating the melatonin-induced enhancement of cold tolerance.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 4","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481575","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The mixed auto-/allooctoploid genome of Japanese knotweed (Reynoutria japonica) provides insights into its polyploid origin and invasiveness","authors":"Fanhong Wang,&nbsp;Minghao Li,&nbsp;Ze Liu,&nbsp;Wei Li,&nbsp;Qiang He,&nbsp;Longsheng Xing,&nbsp;Yao Xiao,&nbsp;Meijia Wang,&nbsp;Yu Wang,&nbsp;Cailian Du,&nbsp;Hongyu Zhang,&nbsp;Yue Zhou,&nbsp;Huilong Du","doi":"10.1111/tpj.70005","DOIUrl":"https://doi.org/10.1111/tpj.70005","url":null,"abstract":"<div>\u0000 \u0000 <p><i>Reynoutria japonica</i> Houtt. (Polygonaceae), a traditional Chinese medicine, is one of the top 100 most destructive invasive species worldwide due to its aggressive growth and strong adaptability. Here, we report an 8.04 Gb chromosome-scale assembly of <i>R. japonica</i> with 88 chromosomes across eight homologous sets. Through a combined phylogenetic and genomic analysis, we demonstrate that <i>R. japonica</i> is a mixed auto-/allooctoploid (AAAABBBB). Subgenome A (SubA) exhibited a close phylogenetic relationship with the related species <i>Fallopia multiflora</i>. We also unveiled the origin and evolutionary history of octoploid <i>R. japonica</i> based on resequencing data from <i>Reynoutria</i> species with different ploidy. Comparative genomics analysis revealed the genetic basis of <i>R. japonica</i>'s invasivity and adaptability. The <i>auxin response factor</i> (<i>ARF</i>) gene family was significantly expanded in <i>R. japonica</i>, and these genes were highly expressed in rhizomes. We also investigated the collaboration and differentiation of the duplicated genes resulting from auto- and allo-polyploidization at the genomic variation, gene family evolution, and gene expression levels in <i>R. japonica</i>. Transcriptomic analysis of stem internodes and apices at different developmental stages revealed that the octuplication and significant expansion of the SAUR19 and SAUR63 subfamilies due to tandem replication in SubA, and the high expression of these genes in stems, likely contribute to the rapid growth of <i>R. japonica</i>. Our study provides important clues into adaptive evolution and polyploidy dominant traits in invasive plants, and will also provide important guidance for the breeding of polyploid crops.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 4","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481429","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chromosome-level assemblies of Amaranthus palmeri, Amaranthus retroflexus, and Amaranthus hybridus allow for genomic comparisons and identification of a sex-determining region","authors":"Damilola A. Raiyemo,&nbsp;Jacob S. Montgomery,&nbsp;Luan Cutti,&nbsp;Fatemeh Abdollahi,&nbsp;Victor Llaca,&nbsp;Kevin Fengler,&nbsp;Alexander J. Lopez,&nbsp;Sarah Morran,&nbsp;Christopher A. Saski,&nbsp;David R. Nelson,&nbsp;Eric L. Patterson,&nbsp;Todd A. Gaines,&nbsp;Patrick J. Tranel","doi":"10.1111/tpj.70027","DOIUrl":"https://doi.org/10.1111/tpj.70027","url":null,"abstract":"<p><i>Amaranthus palmeri</i> (Palmer amaranth), <i>Amaranthus retroflexus</i> (redroot pigweed), and <i>Amaranthus hybridus</i> (smooth pigweed) are troublesome weeds that are economically damaging to several cropping systems. Collectively referred to as “pigweeds,” these species are incredibly adaptive and have become successful competitors in diverse agricultural settings. The development of genomic resources for these species promises to facilitate the elucidation of the genetic basis of traits such as biotic and abiotic stress tolerance (e.g., herbicide resistance) and sex determination. Here, we sequenced and assembled chromosome-level genomes of these three pigweeds. By combining the haplotype-resolved assembly of <i>A. palmeri</i> with existing restriction site-associated DNA sequencing data, we identified an approximately 2.84 Mb region on chromosome 3 of Hap1 that is male-specific and contains 37 genes. Transcriptomic analysis revealed that two genes, <i>RESTORER OF FERTILITY 1</i> (<i>RF1</i>) and <i>TLC DOMAIN-CONTAINING PROTEIN</i> (<i>TLC</i>), within the male-specific region were upregulated in male individuals across the shoot apical meristem, the floral meristem, and mature flowers, indicating their potential involvement in sex determination in <i>A. palmeri</i>. In addition, we rigorously classified cytochrome P450 genes in all three pigweeds due to their involvement in non-target-site herbicide resistance. Finally, we identified contiguous extrachromosomal circular DNA (eccDNA) in <i>A. palmeri</i>, a critical component of glyphosate resistance in this species. The findings of this study advance our understanding of sex determination in <i>A. palmeri</i> and provide genomic resources for elucidating the genetic basis and evolutionary origins of adaptive traits within the genus.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 4","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70027","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481577","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ubiquitin-mediated degradation of the inhibitor FvMYB1 and the activator FvBBX20 by FvCSN5 balances anthocyanin biosynthesis in strawberry fruit","authors":"Yuxin Nie,&nbsp;Yingying Lei,&nbsp;Hongbo Jiao,&nbsp;Zhuo Zhang,&nbsp;Jinxiang Yao,&nbsp;He Li,&nbsp;Hongyan Dai,&nbsp;Zhihong Zhang,&nbsp;Junxiang Zhang","doi":"10.1111/tpj.70021","DOIUrl":"https://doi.org/10.1111/tpj.70021","url":null,"abstract":"<div>\u0000 \u0000 <p>Plant CSN5 is widely recognized as the subunit of the COP9 signalosome and CSN5 is mainly involved in plant growth and development, and tolerance to biotic and abiotic stresses. However, the molecular mechanism of CSN5 regulating anthocyanin biosynthesis in plants is still largely unknown. Here, we identified FvCSN5 from the woodland strawberry yeast two-hybrid library using the anthocyanin pathway inhibitor MYB1 as bait. We demonstrated the interaction of FvCSN5 and FvMYB1 by H2Y, Pull-down, LCI, and BiFC assays. FvCSN5 was expressed in all test tissues and localized in the nucleus and cytosol with self-activation activity. Stable overexpression of <i>FvCSN5</i> in woodland strawberries reduced anthocyanin accumulation in fruits. The protein level of FvMYB1 greatly decreased in overexpressing <i>FvCSN5</i> plants compared with wild-type plants. Protein degradation assay and MG-132 treatment (a proteasome inhibitor blocking 26S proteasome activity) revealed FvCSN5 degraded FvMYB1 through the ubiquitination pathway. In addition, FvCSN5 also interacted with the anthocyanin activator FvBBX20 and FvBBX20 could be degraded by FvCSN5. Moreover, transient expression analysis showed the expression of anthocyanin biosynthetic genes <i>FvCHS</i> and <i>FvF3H</i> was greatly increased and decreased when FvCSN5 was co-expressed with FvMYB1 and FvBBX20, respectively. These results indicate that FvMYB1-FvCSN5-FvBBX20 is a novel ternary complex that regulates anthocyanin biosynthesis by the ubiquitination pathway.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 4","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481430","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Haplotype-resolved genome assembly of Ficus carica L. reveals allele-specific expression in the fruit","authors":"Gabriele Usai,&nbsp;Tommaso Giordani,&nbsp;Alberto Vangelisti,&nbsp;Marco Castellacci,&nbsp;Samuel Simoni,&nbsp;Emanuele Bosi,&nbsp;Lucia Natali,&nbsp;Flavia Mascagni,&nbsp;Andrea Cavallini","doi":"10.1111/tpj.70012","DOIUrl":"https://doi.org/10.1111/tpj.70012","url":null,"abstract":"<p>In this study, we produced a haplotype-phased genome sequence of the fig tree (<i>Ficus carica</i> L.), a non-Rosaceae fruit tree model species, providing a systematic overview of the organization of a heterozygous diploid genome and, for the first time in a fruit tree, evidence of allelic expression direction-shifting among haplotypes. The genome was used for whole genome analysis of heterozygosis, allelic cytosine methylation, and expression profiles in peel and pulp fruit tissues. The two pseudo-haplotypes spanned approximately 355 and 346 Mbp, respectively, and 97% of the sequences were associated with 13 chromosome pairs of the fig tree. Overall, the methylation profile in peel and pulp tissues showed no variations between the homologous chromosomes. However, we detected differential DNA methylation within defined heterozygous allelic gene regions, particularly in upstream regions. Among 6768 heterozygous coding sequences identified, 4024 exhibited allele-specific expression, with approximately 18% specific to the peel and 14% to the pulp. Specifically, 2715 genes were consistent, with one allele always more expressed than the other in both peel and pulp. On the contrary, 22 allele-specific expressed genes switched allele expression among the fig fruit peel and pulp tissues, indicating evidence of overdominance and suggesting that the genome can express one of the two alleles higher or lower depending on developmental or environmental triggers. Notably, these genes were associated with key biological processes, including fruit maturation regulation, seed maturation, and stress response, highlighting their potential role in the plant's developmental and adaptive functions in view of gene editing-based breeding.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 4","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70012","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481569","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Growth and survival strategies of oilseed rape (Brassica napus L.) leaves under potassium deficiency stress: trade-offs in potassium ion distribution between vacuoles and chloroplasts","authors":"Hehe Gu,&nbsp;Ziyao He,&nbsp;Zhifeng Lu,&nbsp;Shipeng Liao,&nbsp;Yangyang Zhang,&nbsp;Xiaokun Li,&nbsp;Rihuan Cong,&nbsp;Tao Ren,&nbsp;Jianwei Lu","doi":"10.1111/tpj.70009","DOIUrl":"https://doi.org/10.1111/tpj.70009","url":null,"abstract":"<div>\u0000 \u0000 <p>Potassium (K) is a prevalent limiting factor in terrestrial ecosystems, with approximately one-eighth of the world's soils undergoing K⁺ deficiency stress. Upon encountering K⁺ deficiency stress, leaf area (LA) declines before the net photosynthetic rate (<i>A</i>_n). The sequential alterations fundamentally represent the adaptive trade-off between survival and growth in plants subjected to K⁺ deficiency stress. This trade-off is hypothesized to be linked to the differences in the subcellular distribution of limited K⁺ resources. Thus, the K⁺ distribution and apparent concentration in subcellular compartments, along with the LA and <i>A</i>_n characteristics of rapeseed leaves at various developmental stages and K⁺ supply conditions were quantified to elucidate the mechanisms by which subcellular K⁺ regulates leaf growth and survival. The results revealed that during the early stages of K⁺ deficiency, leaves actively downregulate growth to sustain normal physiological functions. This is primarily accomplished by lowering the K⁺ distribution and apparent concentration in vacuoles, restricting LA expansion, and enhancing K⁺ distribution to chloroplasts to ensure <i>A</i>_n. Prolonged K⁺ deficiency decreased the apparent K⁺ concentration in chloroplasts below the critical threshold (37.8 m<span>m</span>), disrupting chloroplast structure and function, impairing <i>A</i>_n, and ultimately threatening the survival of rapeseed. Hence, sustaining an adequate concentration of K⁺ within chloroplasts is crucial for preserving leaf photosynthetic efficiency and ensuring survival under K⁺ deficiency stress. In conclusion, under K⁺ deficiency stress, leaves regulate LA and <i>A</i>_n by trade-offs in the K⁺ distribution between vacuoles and chloroplasts to coordinate growth and survival.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 4","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481364","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}