生命科学最新文献

{"title":"Moso bamboo sucrose synthase gene SUS3 promotes earlier germination of tiller buds in Dendrocalamus brandisii ‘Manxie Tianzhu’","authors":"Weijie Sun,&nbsp;Muthusamy Ramakrishnan,&nbsp;Long-Hai Zou,&nbsp;Kai-Li Wang,&nbsp;Xiaohong Zhou,&nbsp;Mingbing Zhou","doi":"10.1007/s00468-025-02612-2","DOIUrl":"10.1007/s00468-025-02612-2","url":null,"abstract":"<div><h3>Key message</h3><p><b>Transient overexpression of </b><b><i>PeSUS3</i></b> <b>using a</b> <b><i>BaMV</i></b> <b>vector in</b><b><i> D. brandisii</i></b> <b>‘Manxie Tianzhu’ enhanced tillering bud germination and growth, suggesting a crucial role for sucrose metabolism in bamboo development.</b></p><h3>Abstract</h3><p>Bamboo shoots are highly sought after in China for their nutritional value. <i>Dendrocalamus brandisii</i> ‘Manxie Tianzhu’ (Manxie Sweet Dragon Bamboo) faces supply challenges due to limited distribution, necessitating faster growing, higher yielding varieties. The sucrose synthase gene, particularly <i>PeSUS3</i>, is vital for sucrose metabolism, nutrient transport, and regulating dormancy release and bud germination, yet its role in bamboo shoot production is not well understood. This study used a bamboo mosaic virus vector (BaMV) to overexpress <i>PeSUS3</i> in <i>D. brandisii</i> ‘Manxie Tianzhu’ seedlings. <i>PeSUS3</i> was cloned into the BaMV-P19-EGFP-2 vector, introduced into <i>Agrobacterium tumefaciens</i>, and used to infect tobacco leaves. The resulting virus was mechanically inoculated into the bamboo seedlings. Analysis revealed that <i>PeSUS3</i> overexpression increased the number of tiller buds and accelerated germination by 1–2 days compared to controls. Despite the transient overexpression of <i>PeSUS3</i>, the increased sucrose content in the overexpressing plants suggests a role for sucrose metabolism in these processes. These findings emphasize the importance of the transient overexpression of <i>PeSUS3</i> in promoting tillering bud germination and growth in <i>D. brandisii</i> ‘Manxie Tianzhu’, providing a foundation for future research on its function and mechanisms.</p></div>","PeriodicalId":805,"journal":{"name":"Trees","volume":"39 2","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143489581","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Restoration implications of the germination ecology of six dry-forest woody Fabaceae species in Mexico","authors":"Citlali Aguirre-Salcedo,&nbsp;Susana Adriana Montaño-Arias,&nbsp;Roland Jansson","doi":"10.1007/s00468-025-02606-0","DOIUrl":"10.1007/s00468-025-02606-0","url":null,"abstract":"<div><h3>Key message</h3><p><b>Seed germination responses to variation in temperature and light differed among six dry forest species, results that will inform ecological restoration and climate change adaptation projects.</b></p><h3>Abstract</h3><p>In dry forests, where opportunities for plant establishment occur in a narrow window of opportunity, seeds must respond to cues to germinate when conditions for growth are suitable. Knowledge of the strategies and adaptations of seeds to the seasonal dry-forest ecosystems, being under constant threat, is needed to guide restoration and management actions in the face of climate change. We investigated the effects of scarification, temperature and light in germination percentage, germination time and synchrony of six woody Fabaceae species. The species have ecological potential for restoration and are of cultural or economic importance for the local people in the Tehuacán-Cuicatlán Valley, Mexico. We carried out a multifactorial germination experiment with five temperatures, two light regimes and two scarification conditions for <i>Mimosa luisana</i>, <i>M. polyantha</i>, <i>M. adenantheroides</i>, <i>M. lactiflua</i>, <i>Acaciella angustissima</i> and <i>Vachellia constricta</i>. All germinated in a wide range of temperatures (10–40 °C), and mechanical scarification highly increased the germination percentage. Higher temperature increased and speeded up germination in dark conditions for most of the species, but they exist heterogeneous responses in their germination synchrony. Studied species had high germination percentages in warm temperatures, but their recruitment in nature might be negatively affected by warmer and drier conditions, and by the loss of shade and seed dispersers due to deforestation and changes in land use. It is crucial to study not just germination percentage and time but also other aspects of the germination process such as the germination synchrony, since it might reveal useful information for management actions.</p></div>","PeriodicalId":805,"journal":{"name":"Trees","volume":"39 2","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00468-025-02606-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481028","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Elicitor Specific Mechanisms of Defence Priming in Oak Seedlings Against Powdery Mildew.","authors":"Rosa Sanchez-Lucas, Jack L Bosanquet, James Henderson, Marco Catoni, Victoria Pastor, Estrella Luna","doi":"10.1111/pce.15419","DOIUrl":"https://doi.org/10.1111/pce.15419","url":null,"abstract":"<p><p>Defence priming sensitises plant defences to enable a faster and/or stronger response to subsequent stress. Various chemicals can trigger priming; however, the response remains unexplored in oak. Here, we characterise salicylic acid (SA)-, jasmonic acid (JA)-, and β-aminobutyric acid (BABA)-induced priming of oak seedlings against the causal agent of powdery mildew (Erysiphe alphitoides, PM). Whilst JA had no effects, BABA and SA enhanced resistance by priming callose deposition and SA-dependent gene expression, respectively. Untargeted transcriptome and metabolome analyses revealed genes and metabolites uniquely primed by BABA, SA, and JA. Enrichment analyses demonstrated a limited number of pathways differentiating the three treatments or the resistance-inducing elicitors BABA and SA. However, a similar mode of action between BABA and JA was identified. Moreover, our analyses revealed a lack of crosstalk between SA and JA. Interestingly, priming by BABA was linked to alkaloid, lignan, phenylpropanoid, and indolitic compounds biosynthesis. Moreover, integration of the omics analyses revealed the role of ubiquitination and protein degradation in priming by BABA. Our results confirm the existence of chemical-induced priming in oak and has identified specific molecular markers associated with well-characterised elicitors.</p>","PeriodicalId":222,"journal":{"name":"Plant, Cell & Environment","volume":" ","pages":""},"PeriodicalIF":6.0,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143497741","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":"miR3398-VqMYB15 Regulates the Synthesis of Stilbene in Vitis quinquangularis.","authors":"Yangyang Luo, Yang Feng, Qingqing Xie, Wenjing Lu, Dong Duan","doi":"10.1111/pce.15446","DOIUrl":"https://doi.org/10.1111/pce.15446","url":null,"abstract":"<p><p>Grapevine (Vitis vinifera L.) is an economically important fruit crop grown worldwide. Grapevine is cultivated extensively in China, and certain wild grapes exhibit excellent resistance to pathogens and stress. MicroRNAs (miRNAs) act as key regulators of plant growth, development, and immunity; however, their functions in grape stilbene synthesis are poorly understood. We identified an miRNA (miR3398) that negatively regulates the transcription factor MYB15 and participates in the synthesis of stilbene from Vitis quinquangularis (V. quinquangularis). MiR3398 and VqMYB15 showed completely opposite expression patterns after AlCl₃ treatment, and the interaction between miR3398 and VqMYB15 was confirmed using 5'-RACE ligase-mediated rapid amplification of cDNA ends, dual-luciferase reporter gene system, and western blot analysis. VqMYB15 could bind to the VqSTS48 promoter by using yeast one-hybrid and electrophoretic mobility shift assay, and overexpression of VqMYB15 promoted stilbene accumulation in grape leaves. Using an overexpression and silencing system, we found that miR3398 negatively targets VqMYB15 to synthesis of stilbenes. We used Al³⁺ as an elicitor, indicating that miR3398 plays an important role in the plant immunity of V. quinquangularis. We also found that miR3398 is involved in plant immunity by detecting its promoter activity in grape protoplasts, luciferase imaging, and transgenic Arabidopsis thaliana. More importantly, we found that an ethylene transcription factor, ERF057, can bind to the promoter of miR3398 using Y1H and EMSA assays and inhibit its transcription using DLR, luciferase imaging, and β-glucuronidase transcript assays. Overexpression of VqERF057 reduced miR3398 transcript in V. quinquangularis and transgenic grapevine calli, but increased the stilbene content. These findings contribute to the understanding of the biological functions of miR3398 regulates stilbene synthesis in grapevines and clarify the molecular mechanism underlying the interaction between miR3398 and VqMYB15.</p>","PeriodicalId":222,"journal":{"name":"Plant, Cell & Environment","volume":" ","pages":""},"PeriodicalIF":6.0,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481768","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":"Network Architecture of Leaf Trait Correlations Has Shifted Following Crop Domestication.","authors":"Zhangying Lei, Ziliang Li, Ian J Wright, Shubham Chhajed, Wangfeng Zhang, Daohua He, Yali Zhang","doi":"10.1111/pce.15443","DOIUrl":"https://doi.org/10.1111/pce.15443","url":null,"abstract":"<p><p>Domestication of crops with the goal of improving yield has led to spectacular shifts in phenotypic traits and their correlation patterns. However, it is relatively unknown whether domestication has driven variation in the architecture of trait correlation networks to optimise carbon return on construction cost along the leaf economics spectrum (LES). Here, we compiled a data set of leaf functional, biochemical, and anatomical traits of 54 wild and cultivated crops. We found that crops tended to be located at the acquisitive end of global LES, typically having low leaf mass per area (LMA), high photosynthetic rate per mass, and high leaf nitrogen and phosphorus content per mass. Architectural changes in trait networks (module number, hub traits, and number of correlations) aligned with the notion of a divergent domestication syndrome due to artificial selection for faster growth and higher yield in high-resource agricultural fields. Domestication has increased the carbon return on resource investment via selecting trait combinations including higher photosynthesis, greater leaf area and LMA. We highlight that strategy-shifts towards faster photosynthetic return on investments in leaves have been coordinated with divergent trait correlation, which has important implications for understanding patterns of trait covariation under crop domestication.</p>","PeriodicalId":222,"journal":{"name":"Plant, Cell & Environment","volume":" ","pages":""},"PeriodicalIF":6.0,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481868","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}