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CsMYB36-mediated ROS homeostasis modulates the switch from cell division to differentiation in cucumber glandular trichome
IF 6.2 1区 生物学
The Plant Journal Pub Date : 2025-02-24 DOI: 10.1111/tpj.70032
Chunhua Wang, Hongxin Yao, Kai Fang, Ting Yang, Xi Shen, Yalin Du, Ning Hao, Jiajian Cao, Tao Wu
{"title":"CsMYB36-mediated ROS homeostasis modulates the switch from cell division to differentiation in cucumber glandular trichome","authors":"Chunhua Wang,&nbsp;Hongxin Yao,&nbsp;Kai Fang,&nbsp;Ting Yang,&nbsp;Xi Shen,&nbsp;Yalin Du,&nbsp;Ning Hao,&nbsp;Jiajian Cao,&nbsp;Tao Wu","doi":"10.1111/tpj.70032","DOIUrl":"https://doi.org/10.1111/tpj.70032","url":null,"abstract":"<div>\u0000 \u0000 <p>Glandular trichomes (GTs) synthesize, store, and secrete diverse specialized metabolites that protect plants against biotic and abiotic stress. The bloom is deposited on the GTs and is perceptible on the surface of the cucumber fruit. Our previous investigation revealed the absence of bloom on the fruit surface in the loss-of-function <i>CsMYB36</i> plants. GTs are formed through a series of cell differentiation events that support compound production. However, the mechanisms governing these events remain unclear. Here, we found GT cells initiate excessive periclinal divisions and fail to differentiate into functional GT cells in the absence of <i>CsMYB36</i> based on the establishment of a detailed developmental process of GT in cucumber. We further found that <i>CsMYB36</i> and <i>CsGL1</i> form a positive feedback loop to regulate the cell differentiation of GT. DNA affinity purification (DAP)-seq, combined with RNA-seq data demonstrated that <i>CsMYB36/CsGL1</i> can regulate the expression of phenylalanine synthesis-related genes, including peroxidase 53 (<i>CsPRX53</i>) which is a reactive oxygen species (ROS)-scavenging enzyme. H<sub>2</sub>O<sub>2</sub> effectively inhibited GT cell division in <i>Csmyb36</i> mutant plants. Collectively, our findings demonstrate that <i>CsMYB36</i> combined with <i>CsGL1</i> balances cell division and differentiation in the GT by mediating ROS homeostasis, thus affecting bloom production in cucumbers.</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":"143481572","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}
引用次数: 0
Emerging frontiers in sorghum genetic engineering
IF 6.2 1区 生物学
The Plant Journal Pub Date : 2025-02-23 DOI: 10.1111/tpj.17244
Deepti Nigam, Vikas Devkar, Pallavi Dhiman, Sana Shakoor, Degao Liu, Gunvant B. Patil, Yinping Jiao
{"title":"Emerging frontiers in sorghum genetic engineering","authors":"Deepti Nigam,&nbsp;Vikas Devkar,&nbsp;Pallavi Dhiman,&nbsp;Sana Shakoor,&nbsp;Degao Liu,&nbsp;Gunvant B. Patil,&nbsp;Yinping Jiao","doi":"10.1111/tpj.17244","DOIUrl":"https://doi.org/10.1111/tpj.17244","url":null,"abstract":"<div>\u0000 \u0000 <p>Sorghum, a climate-resilient cereal, is crucial for meeting the growing demand for food and feed in arid and semi-arid regions, especially amid global population growth and climate change. Despite its natural drought tolerance and adaptability, sorghum faces challenges in increasing yield, enhancing resistance to abiotic and biotic stresses, and improving grain quality. Genetic engineering has emerged as a powerful tool to address these challenges by directly modifying genes associated with desirable traits. Recent advancements have utilized morphogenic regulators to improve transformation and regeneration efficiency in sorghum. This review explores the status of genomic resources and genetic diversity in sorghum, highlighting the advancements and challenges faced in its genetic engineering efforts. Genome editing technologies, particularly CRISPR/Cas systems, have improved key agronomic traits such as stress tolerance, nutrient use efficiency, and grain quality. However, significant obstacles still need to be addressed, including low regeneration rates, high genotype dependency, and labor-intensive transformation processes. We highlight potential strategies to overcome these barriers, such as optimizing transformation protocols, exploring alternative explants, using morphogenic regulators and advancing tissue culture techniques. Additionally, we discuss the biosafety considerations and potential applications of genetically engineered sorghum in global agriculture. This review underscores the need for ongoing innovation to unlock the potential of genetically engineered sorghum in addressing global food security challenges.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 4","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143475570","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}
引用次数: 0
Divergence in the effects of sugar feedback regulation on the major gene regulatory network and metabolism of photosynthesis in leaves between the two founding Saccharum species 糖分反馈调控对两个蔗糖树种叶片光合作用主要基因调控网络和代谢的影响存在差异
IF 6.2 1区 生物学
The Plant Journal Pub Date : 2025-02-22 DOI: 10.1111/tpj.70019
Huihong Shi, Xiuting Hua, Dongxu Zhao, Juanjuan Xu, Min Li, Beiyuan Wan, Zhen Li, Yingying Zhang, Jiayu Yao, Shuangyu Li, Yuhong Lan, Yiying Qi, Ruiting Gao, Yixing Zhang, Kelun Zhang, Yijia Guo, Xianwei Fan, Haibao Tang, Jisen Zhang
{"title":"Divergence in the effects of sugar feedback regulation on the major gene regulatory network and metabolism of photosynthesis in leaves between the two founding Saccharum species","authors":"Huihong Shi,&nbsp;Xiuting Hua,&nbsp;Dongxu Zhao,&nbsp;Juanjuan Xu,&nbsp;Min Li,&nbsp;Beiyuan Wan,&nbsp;Zhen Li,&nbsp;Yingying Zhang,&nbsp;Jiayu Yao,&nbsp;Shuangyu Li,&nbsp;Yuhong Lan,&nbsp;Yiying Qi,&nbsp;Ruiting Gao,&nbsp;Yixing Zhang,&nbsp;Kelun Zhang,&nbsp;Yijia Guo,&nbsp;Xianwei Fan,&nbsp;Haibao Tang,&nbsp;Jisen Zhang","doi":"10.1111/tpj.70019","DOIUrl":"https://doi.org/10.1111/tpj.70019","url":null,"abstract":"<div>\u0000 \u0000 <p>Sugarcane is a crop that accumulates sucrose with high photosynthesis efficiency. Therefore, the feedback regulation of sucrose on photosynthesis is crucial for improving sugarcane yield. <i>Saccharum spontaneum</i> and <i>Saccharum officinarum</i> are the two founding <i>Saccharum</i> species for modern sugarcane hybrids. <i>S. spontaneum</i> exhibits a higher net photosynthetic rate but lower sucrose content than <i>S. officinarum</i>. However, the mechanism underlying the negative feedback regulation of photosynthesis by sucrose remains poorly understood. This study investigates the effects of exogenous sucrose treatment on <i>S. spontaneum</i> and <i>S. officinarum</i>. Exogenous sucrose treatment increases sucrose content in the leaf base but inhibits photosynthetic efficiency and the expression of photosynthesis-related pathway genes (including <i>RBCS</i> and <i>PEPC</i>) in both species. However, gene expression patterns differed significantly, with few differentially expressed genes (DEGs) shared between the two species, indicating a differential response to exogenous sucrose. The expression networks of key genes involved in sugar metabolism, sugar transport, and <i>PEPC</i> and <i>RBCS</i> showed divergence between two species. Additionally, DEGs involved in the pentose phosphate pathway and the metabolism of alanine, aspartate, and glutamate metabolism were uniquely enriched in <i>S. spontaneum</i>, potentially contributing to the differential changes in sucrose content in the tip between the two species. We propose a model of the mechanisms underlying the negative feedback regulation of photosynthesis by sucrose in the leaves of <i>S. spontaneum</i> and <i>S. officinarum</i>. Our findings enhance the understanding of sucrose feedback regulation on photosynthesis and provide insights into the divergent molecular mechanisms of sugar accumulation in <i>Saccharum</i>.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 4","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143471915","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}
引用次数: 0
The gap-free genome assembly and multi-omics analyses illustrate the evolutionary history and the synthesis of medicinal components of Ligustrum lucidum
IF 6.2 1区 生物学
The Plant Journal Pub Date : 2025-02-22 DOI: 10.1111/tpj.70029
Yong Li, Meng-Jie Yuan, Zi-Yan Zhang, Nan-Cai Pei
{"title":"The gap-free genome assembly and multi-omics analyses illustrate the evolutionary history and the synthesis of medicinal components of Ligustrum lucidum","authors":"Yong Li,&nbsp;Meng-Jie Yuan,&nbsp;Zi-Yan Zhang,&nbsp;Nan-Cai Pei","doi":"10.1111/tpj.70029","DOIUrl":"https://doi.org/10.1111/tpj.70029","url":null,"abstract":"<div>\u0000 \u0000 <p><i>Ligustrum lucidum</i>, an important ornamental and medicinal plant in the Oleaceae family, has become a globally notorious invasive species because of its high adaptability. However, the lack of a high quality genome has hindered the understanding of the genetic basis for its broad adaptability and the mechanisms of its medicinal component synthesis. In this study, we successfully assembled a gap free telomere to telomere genome of <i>L. lucidum</i>. Through the reconstruction of the phylogenetic tree, we presented evidence that Jasmineae diverged from Oleaceae earlier than Forsythieae, which challenges the existing phylogenetic relationships within Oleaceae. Comparative genomics has found that two rounds of gene family expansions in <i>L. lucidum</i> significantly increased the number of genes related to its biotic and abiotic stress resistances, which may lay the genetic foundation for its broad adaptability. Among the <i>L. lucidum</i> fruits from January to March in our investigation, the results of metabolome show that March may be the optimal harvesting time. By integrating genomic, transcriptomic, and metabolomic data, we identified candidate genes involved in the synthesis of compounds, such as specnuezhenide, salidroside, and oleanolic acid. This study provides valuable genomic resources for comparative genomics studies within Oleaceae and for the genetic research of <i>L. lucidum</i>.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 4","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143471938","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}
引用次数: 0
Tasselyzer, a machine learning method to quantify maize anther exertion, based on PlantCV Tasselyzer 是一种基于 PlantCV 的机器学习方法,用于量化玉米花药用力情况
IF 6.2 1区 生物学
The Plant Journal Pub Date : 2025-02-22 DOI: 10.1111/tpj.70014
Chong Teng, Noah Fahlgren, Blake C. Meyers
{"title":"Tasselyzer, a machine learning method to quantify maize anther exertion, based on PlantCV","authors":"Chong Teng,&nbsp;Noah Fahlgren,&nbsp;Blake C. Meyers","doi":"10.1111/tpj.70014","DOIUrl":"https://doi.org/10.1111/tpj.70014","url":null,"abstract":"<p>Maize anthers emerge from male-only florets, a process that involves complex genetic programming and is affected by environmental factors. Quantifying anther exertion provides a key indicator of male fertility; however, traditional manual scoring methods are often subjective and labor-intensive. To address this limitation, we developed <i>Tasselyzer</i> — an accessible, cost-effective, and time-saving method for quantifying maize anther exertion. This image-based program uses the PlantCV platform to provide a quantitative assessment of anther exertion by capturing regional differences within the tassel based on the distinct color of anthers. We applied this method to 22 maize lines with six genotypes, showing high precision (F<sub>1</sub> score &gt; 0.8). Furthermore, we demonstrate that customizing the parameters to assay a specific line is straightforward and practical for enhancing precision in additional genotypes. Tasselyzer is a valuable resource for maize research and breeding programs, enabling automated and efficient assessments of anther exertion.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 4","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70014","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143471983","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}
引用次数: 0
SlMYB1R1-SlSWEET12c module synergistically promotes sugar accumulation in tomato fruits SlMYB1R1-SlSWEET12c 模块协同促进番茄果实的糖分积累
IF 6.2 1区 生物学
The Plant Journal Pub Date : 2025-02-22 DOI: 10.1111/tpj.70062
Hui Liu, Jia-Qi Zhang, Rong-Rong Zhang, Chen Chen, Jian-Ping Tao, Jin-Song Xiong, Ai-Sheng Xiong
{"title":"SlMYB1R1-SlSWEET12c module synergistically promotes sugar accumulation in tomato fruits","authors":"Hui Liu,&nbsp;Jia-Qi Zhang,&nbsp;Rong-Rong Zhang,&nbsp;Chen Chen,&nbsp;Jian-Ping Tao,&nbsp;Jin-Song Xiong,&nbsp;Ai-Sheng Xiong","doi":"10.1111/tpj.70062","DOIUrl":"https://doi.org/10.1111/tpj.70062","url":null,"abstract":"<div>\u0000 \u0000 <p>Tomato (<i>Solanum lycopersium</i>), a globally significant vegetable crop prized for its distinctive flavor, relies on efficient sugar allocation for fruit development. Despite this, the molecular module underlying the translocation of sugars from sources to sinks within the tomato remains elusive. Sugar will eventually be exported transporters (SWEETs), a class of proteins known to mediate sugar transport, have been implicated in the process. Here, we discovered that SlSWEET12c, belonged to subfamily III, which was markedly upregulated during the development of tomato fruits. The subcellular localization of SlSWEET12c-GFP to the plasma and vacuolar membrane supported its putative role in apoplasmic sucrose transport. Complementary growth in a yeast (<i>Saccharomyces cerevisiae</i>) mutant strain SUSY7/ura3 confirmed SlSWEET12c with sucrose transport activity. Overexpressing and CRISPR/Cas9-mediated knockdown of SlSWEET12c in tomato plants demonstrated its role in promoting sugar accumulation in fruits. Additionally, the MYB transcription factor SlMYB1R1 was obtained by screening the cDNA library of tomato, which was highly expressed during tomato fruit development with a similar pattern to <i>SlSWEET12c</i>. The SlMYB1R1 could bind to the <i>SlSWEET12c</i> promoter and regulate its activity, thereby positively promoting sugar accumulation in tomato fruits. Collectively, our findings presented a novel role for the SlMYB1R1-<i>SlSWEET12c</i> module in facilitating sugar accumulation and provided a basis for future efforts to breed crops with enhanced sugar content.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 4","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143471939","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}
引用次数: 0
The complex I subunit B22 contains a LYR domain that is crucial for an interaction with the mitochondrial acyl carrier protein SDAP1
IF 6.2 1区 生物学
The Plant Journal Pub Date : 2025-02-21 DOI: 10.1111/tpj.70028
Saurabh Saha, Simge Parlar, Etienne H. Meyer, Monika W. Murcha
{"title":"The complex I subunit B22 contains a LYR domain that is crucial for an interaction with the mitochondrial acyl carrier protein SDAP1","authors":"Saurabh Saha,&nbsp;Simge Parlar,&nbsp;Etienne H. Meyer,&nbsp;Monika W. Murcha","doi":"10.1111/tpj.70028","DOIUrl":"https://doi.org/10.1111/tpj.70028","url":null,"abstract":"<p>Mitochondrial complex I (CI), a large multi-subunit respiratory complex contains two LYR (leucine/tyrosine/arginine) domain-containing subunits, B14 (NDUA6/LYRM6) and B22 (NDUB9/LYRM3). Mitochondrial LYR (LYRM) proteins are soluble matrix-located proteins that have been implicated in diverse functions such as iron–sulphur cluster insertion, OXPHOS complex assembly, and mitoribosome biogenesis. B14 and B22 are unique to other LYRM proteins in that they are integral components of CI. To explore the function of B22, we examined T-DNA insertional knockout and knockdown lines, which displayed a mild growth defect linked to reduced CI activity and abundance. Notably, this defect could not be rescued by complementation with a B22 variant that contained a mutated LYR domain, indicating the domain's critical role in B22's function. Protein interaction assays further revealed that the LYR domain is crucial for B22's interaction with the neighbouring CI subunit, mitochondrial acyl carrier protein SDAP1. Similarly, T-DNA insertional knockdown lines of SDAP1 showed a comparable CI defect, suggesting that the interaction between B22 and SDAP1, mediated by the LYR domain, is important for the function and assembly of CI.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 4","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70028","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143456134","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}
引用次数: 0
Mannose-binding lectin 1.1A interacts with hypersensitive-induced response 4 to promote hypersensitive cell death and defense responses in cotton upon Verticillium dahliae infection
IF 6.2 1区 生物学
The Plant Journal Pub Date : 2025-02-21 DOI: 10.1111/tpj.70018
Leitian Yuan, Min Wu, Deming Tan, Shuling Zhang, Huanyang Zhang, Jing Li, Guixian Xia, Fuxin Wang
{"title":"Mannose-binding lectin 1.1A interacts with hypersensitive-induced response 4 to promote hypersensitive cell death and defense responses in cotton upon Verticillium dahliae infection","authors":"Leitian Yuan,&nbsp;Min Wu,&nbsp;Deming Tan,&nbsp;Shuling Zhang,&nbsp;Huanyang Zhang,&nbsp;Jing Li,&nbsp;Guixian Xia,&nbsp;Fuxin Wang","doi":"10.1111/tpj.70018","DOIUrl":"https://doi.org/10.1111/tpj.70018","url":null,"abstract":"<div>\u0000 \u0000 <p>Increasing evidence indicates that mannose-binding lectins (MBLs) act as a lectin-receptor-like protein in plant immune responses, yet the functional basis remains elusive. In this study, we dissected the functional mechanism of GbMBL1.1A in defense against <i>Verticillium dahliae</i> infection in sea island cotton (<i>Gossypium barbadense</i>). GbMBL1.1A expressed preferentially in cotton roots and significantly upregulated upon <i>V. dahliae</i> infection. Transgenic expression of <i>GbMBL1.1A</i> in upland cotton (<i>Gossypium hirsutum</i>) and Arabidopsis remarkably improved the disease resistance of the plants, while silencing of <i>GbMBL1.1A</i> resulted in an increased susceptibility of cotton plants in response to <i>V. dahliae</i> attack. Protein interaction assays revealed that GbMBL1.1A interacted with the cotton hypersensitive-induced response protein 4 (GbHIR4, a scaffold protein for immune signaling in the plasma membrane microdomain) through PAN domain. <i>GbHIR4</i> expression was upregulated in response to <i>V. dahliae</i> invasion, and silencing of <i>GbHIR4</i> seriously attenuated the disease tolerance of cotton plants. GbMBL1.1A enhanced the cell death phenotype induced by the transient expression of GbHIR4, and meanwhile promoted HR-PCD and GbHIR4-dependent resistance upon <i>V. dahliae</i> infection. The results suggested that GbMBL1.1A employed GbHIR4 as a downstream component to trigger the hypersensitive responses and therefore contributed to cotton resistance against <i>V. dahliae</i>. In addition, we observed that <i>GbMBL1.1A</i> overexpression could alter the phytohormone-mediated defense and growth signaling under both normal and <i>V. dahliae</i> infection conditions. Collectively, these results demonstrated that the lectin receptor-like protein GbMBL1.1A interacts with GbHIR4 in cotton immunity to induce the hypersensitive response, which is associated with phytohormone-mediated defense and growth signaling.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 4","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143466099","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}
引用次数: 0
DNA methylation dynamics in gymnosperm duplicate genes: implications for genome evolution and stress adaptation
IF 6.2 1区 生物学
The Plant Journal Pub Date : 2025-02-21 DOI: 10.1111/tpj.70006
Kai-Yuan Huang, Yuan-Yuan Feng, Hong Du, Chang-Wang Ma, Dan Xie, Tao Wan, Xiu-Yan Feng, Xiao-Gang Dai, Tong-Ming Yin, Xiao-Quan Wang, Jin-Hua Ran
{"title":"DNA methylation dynamics in gymnosperm duplicate genes: implications for genome evolution and stress adaptation","authors":"Kai-Yuan Huang,&nbsp;Yuan-Yuan Feng,&nbsp;Hong Du,&nbsp;Chang-Wang Ma,&nbsp;Dan Xie,&nbsp;Tao Wan,&nbsp;Xiu-Yan Feng,&nbsp;Xiao-Gang Dai,&nbsp;Tong-Ming Yin,&nbsp;Xiao-Quan Wang,&nbsp;Jin-Hua Ran","doi":"10.1111/tpj.70006","DOIUrl":"https://doi.org/10.1111/tpj.70006","url":null,"abstract":"<div>\u0000 \u0000 <p>Duplicate genes are pivotal in driving evolutionary innovation, often exhibiting expression divergence that offers a system to investigate the role of DNA methylation in transcriptional regulation. However, previous studies have predominantly focused on angiosperms, leaving the methylation patterns in major lineages of land plants still unclear. This study explores DNA methylation evolution in duplicate genes across representative gymnosperm species with large genomes, spanning over 300 million years, using genomic, transcriptomic, and high-depth DNA methylomic data. We observed variations in DNA methylation levels along gene bodies, flanking regions, and methylation statuses of coding regions across different duplication types. Biased divergences in DNA methylation and gene expression frequently occurred between duplicate copies. Specifically, methylation divergences in the 2-kb downstream regions negatively correlated with gene expression. Both CG and CHG DNA methylation in gene bodies were positively correlated with gene length, suggesting these methylation types may function as an epigenomic buffer to mitigate the adverse impact of gene length on expression. Duplicate genes exhibiting both methylation and expression divergences were notably enriched in adaptation-related biological processes, suggesting that DNA methylation may aid adaptive evolution in gymnosperms by regulating stress response genes. Changes in expression levels correlated with switches in methylation status within coding regions of transposed duplicates. Specifically, depletion for CG methylation or enrichment for non-CG methylation significantly reduced the expression of translocated copies. This correlation suggests that DNA methylation may reduce genetic redundancy by silencing translocated copies. Our study highlights the significance of DNA methylation in plant genome evolution and stress adaptation.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 4","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143466098","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}
引用次数: 0
Establishment and maintenance of embryogenic cell fate during microspore embryogenesis
IF 6.2 1区 生物学
The Plant Journal Pub Date : 2025-02-21 DOI: 10.1111/tpj.17243
Charlotte Siemons, Sven Jonkers, Redmar Cornelis Vlieg, Patricia Corral-Martínez, John van Noort, Kim Boutilier
{"title":"Establishment and maintenance of embryogenic cell fate during microspore embryogenesis","authors":"Charlotte Siemons,&nbsp;Sven Jonkers,&nbsp;Redmar Cornelis Vlieg,&nbsp;Patricia Corral-Martínez,&nbsp;John van Noort,&nbsp;Kim Boutilier","doi":"10.1111/tpj.17243","DOIUrl":"https://doi.org/10.1111/tpj.17243","url":null,"abstract":"<p>Microspore embryogenesis is a type of <i>in vitro</i> totipotency in which the immature male gametophyte (pollen) develops into a haploid embryo after an abiotic stress treatment. In <i>Brassica napus</i>, heat-stress treatment of male gametophytes induces the development of different types of multicellular embryogenic structures, each with different cellular characteristics and the capacity to form a differentiated embryo. The origin and early development of these different embryogenic structures have not been determined. We used two-photon excitation fluorescence microscopy and time-lapse imaging of cells expressing either a <i>LEAFY COTYLEDON1</i> (<i>LEC1</i>) embryo identity reporter or a <i>DR5v2</i> auxin response reporter to follow the development of embryogenic structures starting at the single- to few-cell stage. We show for the first time that the developmental fate of embryogenic structures is defined by the symmetry of the first embryogenic division and that the division plane also predicts the timing of subsequent pollen wall (exine) rupture: suspensorless embryos develop after a symmetric division and undergo late exine rupture, while suspensor-bearing embryos and embryogenic callus develop after an asymmetric division and undergo early exine rupture. Live imaging also captured previously unknown dynamic <i>LEC1</i> and <i>DR5v2</i> expression patterns that are associated with changes in exine integrity. This study highlights the developmental plasticity of cultured pollen and uncovers new roles for the first embryogenic cell division plane and the exine in defining and maintaining cell fate during microspore embryogenesis.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"121 4","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.17243","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143456133","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}
引用次数: 0
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