The Plant Journal最新文献

{"title":"A chromosome-scale genome of Hippophae neurocarpa provides new insights into serotonin biosynthesis and chlorophyll-derived brown fruit coloration","authors":"Ning Chen,&nbsp;Guo-yun Zhang,&nbsp;Ya-ting Song,&nbsp;Yang Yang,&nbsp;Jian-guo Zhang,&nbsp;Cai-yun He","doi":"10.1111/tpj.70031","DOIUrl":"https://doi.org/10.1111/tpj.70031","url":null,"abstract":"<div>\u0000 \u0000 <p>Sea buckthorn (<i>Hippophae neurocarpa</i>), a plant with both medicinal and edible properties, exhibits high content of serotonin with a unique brown color. Here, we assemble the 1002.54 Mb genome sequence of <i>H. neurocarpa</i> and find that it has evolved from two sequential polyploidizations with four sub-genomes. Based on <i>in vitro</i> enzyme activity and transient overexpression experiments, we confirm that the expression of both <i>HnT5H1</i> and <i>HnT5H2</i> genes from tandem duplication contributes to high accumulation of serotonin in sea buckthorn. Furthermore, we verify that the <i>HnGLK1</i> gene plays a crucial role in continuous chlorophyll accumulation, driving the brown color formation of <i>H. neurocarpa</i> fruit. Collectively, the high-quality genome of <i>H. neurocarpa</i> offers valuable insights into the mechanisms underlying serotonin biosynthesis and abnormal coloration and serves as a valuable resource for further functional genomic studies and molecular breeding efforts in sea buckthorn.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 5","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143530469","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":"Behind phyllotaxis, within the meristem: a REM-ARF complex shapes inflorescence in Arabidopsis thaliana","authors":"Francesca Caselli,&nbsp;Carlotta Ferrario,&nbsp;Veronica Maria Beretta,&nbsp;Sri Amarnadh Gupta Tondepu,&nbsp;Renaud Dumas,&nbsp;Humberto Herrera-Ubaldo,&nbsp;Stefan de Folter,&nbsp;Martin M. Kater,&nbsp;Veronica Gregis","doi":"10.1111/tpj.70041","DOIUrl":"https://doi.org/10.1111/tpj.70041","url":null,"abstract":"<p>Inflorescence architecture is established during the early stages of reproductive development and depends on the activity and identity of meristems. In <i>Arabidopsis thaliana</i>, the floral meristems (FMs), which will develop into flowers, arise with precise spatiotemporal regulation from the inflorescence meristem (IM). The outcome of this process is a geometrically organized structure characterized by a reiterated pattern called phyllotaxis, in which successive organs arise at specific divergence angles of 137.5°. Here we show that REM34 and REM35 transcription factors control phyllotactic patterning through cooperative interaction with ARF7 and ARF19, influencing the cell cycle rate and thus the IM dimension. Our proposed model suggests that ARF7 and ARF19, whose activity is triggered by auxin accumulation, interact with REM34 and REM35 to regulate two auxin-induced genes, <i>LBD18</i> and <i>PUCHI</i>, whose mutants phenocopy the permutated phyllotactic pattern of <i>rem34 rem35</i> and <i>arf7 arf19</i>. This complex also restricts cell cycling activity to specific areas of the meristem, indirectly determining its dimension and ultimately establishing FM positioning and phyllotaxis. Reiterative patterns are found in morphogenetic processes of complex organisms, and phyllotaxis has been employed to understand the mechanisms behind this regularity. Our research broadens the knowledge on this mechanism which is also strictly correlated with yield.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 5","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70041","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143530470","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":"GOLEM: A tool for visualizing the distribution of Gene regulatOry eLEMents within the plant promoters with a focus on male gametophyte","authors":"Lukáš Nevosád,&nbsp;Božena Klodová,&nbsp;Jiří Rudolf,&nbsp;Tomáš Raček,&nbsp;Tereza Přerovská,&nbsp;Alžbeta Kusová,&nbsp;Radka Svobodová,&nbsp;David Honys,&nbsp;Petra Procházková Schrumpfová","doi":"10.1111/tpj.70037","DOIUrl":"https://doi.org/10.1111/tpj.70037","url":null,"abstract":"<p>Gene expression regulation during tissue development is extremely complex. A key mechanism of gene regulation is the recognition of regulatory motifs, also known as cis-regulatory elements (CREs), by various proteins in gene promoter regions. Localization of these motifs near the transcription start site (TSS) or translation start site (ATG) is crucial for transcription initiation and rate. Transcription levels of individual genes, regulated by these motifs, can vary significantly across tissues and developmental stages, especially in processes like sexual reproduction. However, the precise localization and visualization of these motifs in relation to gene expression in specific tissues can be challenging. Here, we introduce a freely available tool called GOLEM (Gene regulatOry eLEMents; https://golem.ncbr.muni.cz), which enables users to precisely locate any motif of interest with respect to TSS or ATG within the relevant plant genomes across the plant Tree of Life (<i>Chara</i>, <i>Marchantia</i>, <i>Physcomitrium</i>, <i>Azolla</i>, <i>Ceratopteris</i>, <i>Amborella</i>, <i>Oryza</i>, <i>Zea</i>, <i>Solanum</i> and <i>Arabidopsis</i>). The visualization of the motifs is performed with respect to the transcript levels of particular genes in leaves and male reproductive tissues and can be compared with genome-wide distribution regardless of the transcription level. Additionally, genes with specific CREs at defined positions and high expression in selected tissues can be exported for further analysis. GOLEM's functionality is illustrated by its application to conserved motifs (e.g. TATA-box, ABRE, I-box, and TC-element), hormone-responsive elements (GCC-box, ARR10_binding motif), as well as to male gametophyte-related motifs (e.g., LAT52, MEF2, and DOF_core).</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 5","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70037","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143530471","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":"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":"&lt;p&gt;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 &amp; Gardner, &lt;span&gt;2021&lt;/span&gt;). 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., &lt;span&gt;2022&lt;/span&gt;).&lt;/p&gt;&lt;p&gt;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 &amp; Gardner, &lt;span&gt;2021&lt;/span&gt;). Phototropins form dimers, suggesting that autophosphorylation can occur both in &lt;i&gt;cis&lt;/i&gt; (by the molecule's own kinase domain) and in &lt;i&gt;trans&lt;/i&gt; (by its dimer partner). Arabidopsis phototropin 1 (Atphot1) was shown to undergo trans-autophosphorylation (Kaiserli et al., &lt;span&gt;2009&lt;/span&gt;; Petersen et al., &lt;span&gt;2017&lt;/span&gt;), but such mechanistic insight remains scarce for phototropins of other species.&lt;/p&gt;&lt;p&gt;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 &lt;i&gt;Marchantia polymorpha&lt;/i&gt; (Marchantia).&lt;/p&gt;&lt;p&gt;Marchantia harbours a single copy phototropin gene (&lt;i&gt;MpPHOT&lt;/i&gt;) that mediates chloroplast accumulation and avoidance responses under weak and strong light, respectively (Komatsu et al., &lt;span&gt;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}