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Efficient data filtering with multiple group conditions: a command tool for bioinformatics data analysis. 具有多组条件的高效数据过滤:用于生物信息学数据分析的命令工具。
IF 4.6 4区 农林科学
aBIOTECH Pub Date : 2025-03-13 eCollection Date: 2025-06-01 DOI: 10.1007/s42994-025-00207-6
Wenpeng Deng, Jianye Chang, Alun Li, He Xie, Jue Ruan
{"title":"Efficient data filtering with multiple group conditions: a command tool for bioinformatics data analysis.","authors":"Wenpeng Deng, Jianye Chang, Alun Li, He Xie, Jue Ruan","doi":"10.1007/s42994-025-00207-6","DOIUrl":"https://doi.org/10.1007/s42994-025-00207-6","url":null,"abstract":"<p><p>Bioinformatics analysis often requires the filtering of multi-datasets, based on frequency or frequency of occurrence, for decisions on retention or deletion. Existing tools for this purpose often present a challenge with complex installation, which necessitate custom coding, thereby impeding efficient data processing activities. To address this issue, Filterx, a user-friendly command line tool that written in C language, was developed that supports multi-condition filtering, based on frequency or occurrence. This tool enables users to complete the data processing tasks through a simple command line, greatly reducing both workload and data processing time. In addition, future development of this tool could facilitate its integration into various bioinformatics data analysis pipelines.</p>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 2","pages":"274-277"},"PeriodicalIF":4.6,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12237833/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144610297","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Effects of cultivating biotech maize GG2 and glyphosate treatment on the rhizospheric microbial community structure. 转基因玉米GG2栽培及草甘膦处理对根际微生物群落结构的影响
IF 4.6 4区 农林科学
aBIOTECH Pub Date : 2025-03-12 eCollection Date: 2025-06-01 DOI: 10.1007/s42994-025-00205-8
Yinxiao Wang, Yihe Hao, Shengyan Li, Ning Wen, Mingyuan Yin, Zhihong Lang
{"title":"Effects of cultivating biotech maize GG2 and glyphosate treatment on the rhizospheric microbial community structure.","authors":"Yinxiao Wang, Yihe Hao, Shengyan Li, Ning Wen, Mingyuan Yin, Zhihong Lang","doi":"10.1007/s42994-025-00205-8","DOIUrl":"10.1007/s42994-025-00205-8","url":null,"abstract":"<p><p>In environmental biosafety assessments of glyphosate-tolerant crops, it is essential to evaluate the effects of cultivating these crops and applying glyphosate on the microbial community in the rhizosphere soil, which play a critical role in maintaining soil health, plant growth, and crop productivity. Maize (<i>Zea mays</i>) line GG2 was previously generated by transforming wild-type maize with the <i>gat</i> and <i>gr79-epsps</i> genes, endowing GG2 with both active and passive resistance to glyphosate. However, the ecological risk of introducing these two new glyphosate-tolerance genes into maize, as well as glyphosate treatment, to rhizosphere microorganisms remain unclear. In this study, we used high-throughput sequencing to analyze the diversity and composition of the bacterial and fungal communities in the rhizosphere soil around biotech maize GG2, with (GG2-H) and without glyphosate treatment (GG2-N), compared with the near-isogenic, non-biotech maize line ZD958 at seven stages of growth. The structure and diversity of the bacterial and fungal communities of GG2-H were similar to those of ZD958, whereas glyphosate treatment had temporary effects on bacterial and fungal diversity and richness. The differences in the bacterial and fungal communities were associated with changes in soil properties such as pH, available phosphorus and organic matter, and seasonal changes. These factors, rather than maize lines, made the greatest contributions to the shifts in bacterial and fungal community structure. This study provides a comprehensive analysis of the effects of biotech crop cultivation, glyphosate treatment, soil physicochemical properties of soil, and maize growth stages on soil microbial communities, offering valuable insights for the large-scale adoption of biotech crops in China.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42994-025-00205-8.</p>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 2","pages":"174-188"},"PeriodicalIF":4.6,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12237839/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144610296","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
An accelerated transgene-free genome editing system using microparticle bombardment of sorghum immature embryos. 利用微粒子轰击高粱未成熟胚胎的加速无转基因基因组编辑系统。
IF 4.6 4区 农林科学
aBIOTECH Pub Date : 2025-03-04 eCollection Date: 2025-06-01 DOI: 10.1007/s42994-025-00204-9
Yan Zhang, Ming Cheng, Karen Massel, Ian D Godwin, Guoquan Liu
{"title":"An accelerated transgene-free genome editing system using microparticle bombardment of sorghum immature embryos.","authors":"Yan Zhang, Ming Cheng, Karen Massel, Ian D Godwin, Guoquan Liu","doi":"10.1007/s42994-025-00204-9","DOIUrl":"10.1007/s42994-025-00204-9","url":null,"abstract":"<p><p>The key factors for genome-editing in plants using CRISPR/Cas9, such as the Cas9 nuclease and guide RNA (gRNA) are typically expressed from a construct that is integrated into the plant genome. However, the presence of foreign DNA in the host genome causes genetic and regulatory concerns, particularly for commercialization. To address this issue, we developed an accelerated pipeline for generating transgene-free genome-edited sorghum (<i>Sorghum bicolor</i>) in the T<sub>0</sub> generation. For proof-of-concept, we selected the <i>Phytoene desaturase</i> (<i>PDS</i>) gene as the target due to its visible phenotype (albinism) upon mutation. Following microprojectile-mediated co-transformation with a maize (<i>Zea mays</i>)-optimized Cas9 vector and a guide RNA (gRNA) cassette with a geneticin (G418) resistance gene, we divided tissue derived from immature embryos into two groups (with and without antibiotic selection) and cultured them separately as parallel experiments. In regenerated plants cultured on medium containing MS basal nutrition (to allow albino plants to survive), we detected higher rates of albinism in the non-selection group, achieving editing rates of 11.1-14.3% compared with 4.2-8.3% in the antibiotic selection group. In the T<sub>0</sub> generation, 22.2-38.1% of albino plants from the non-selection group were identified as transgene-free, whereas only 0-5.9% from the selection group were transgene-free. Therefore, our strategy efficiently produced transgene-free genome-edited plants without the need for self-crossing or outcrossing, demonstrating the feasibility of achieving transgene-free genome-edited sorghum plants within a single generation. These findings pave the way for commercializing transgene-free genome-edited lines, particularly for vegetatively propagated crops like pineapple, sugarcane, and banana.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42994-025-00204-9.</p>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 2","pages":"202-214"},"PeriodicalIF":4.6,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12238444/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144610293","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
OsbHLH062 regulates iron homeostasis by inhibiting iron deficiency responses in rice. OsbHLH062通过抑制水稻缺铁反应调节铁稳态。
IF 4.6 4区 农林科学
aBIOTECH Pub Date : 2025-03-03 eCollection Date: 2025-06-01 DOI: 10.1007/s42994-025-00203-w
Wujian Wang, Fengyu He, Hui Zhang, Yue Yang, Xiaojuan Wang, Yue Fu, Huixia Shou, Luqing Zheng
{"title":"OsbHLH062 regulates iron homeostasis by inhibiting iron deficiency responses in rice.","authors":"Wujian Wang, Fengyu He, Hui Zhang, Yue Yang, Xiaojuan Wang, Yue Fu, Huixia Shou, Luqing Zheng","doi":"10.1007/s42994-025-00203-w","DOIUrl":"10.1007/s42994-025-00203-w","url":null,"abstract":"<p><p>Iron (Fe) homeostasis in plant cells is crucial for crop productivity and quality. An intricate transcriptional network involving numerous basic Helix-Loop-Helix (bHLH) transcription factors has been proposed to control Fe homeostasis. In the present study, we characterized rice (<i>Oryza sativa</i>) OsbHLH062, a member of the IVb subgroup of the bHLH family, demonstrating that it negatively regulates Fe-deficiency responses. OsbHLH062 represses transcription by recruiting TOPLESS/TOPLESS-RELATED co-repressors (TPL/TPRs) through its ethylene-responsive element binding factor-associated amphiphilic repression (EAR) motif. Under Fe deficiency, the expression of <i>OsbHLH062</i> is upregulated in roots and downregulated in shoots. Overexpression of <i>OsbHLH062</i> leads to decreased Fe accumulation in the shoot. Furthermore, OsbHLH062 interacts with POSITIVE REGULATOR OF IRON HOMEOSTASIS 1 (OsPRI1) and inhibits its transactivation activity, thereby negatively regulating the expression of many Fe homeostasis-related genes. These results indicate an important role for OsbHLH062 in regulating Fe homeostasis by negatively regulating Fe deficiency responses in rice. This knowledge will aid in the design of Fe-biofortified rice plants that can help to address the global issue of Fe deficiency.</p>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 2","pages":"215-231"},"PeriodicalIF":4.6,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12238704/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144610303","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Manipulating brassinosteroid signaling pathway to genetically improve horticultural plants. 操纵油菜素内酯信号通路以遗传改良园艺植物。
IF 4.6 4区 农林科学
aBIOTECH Pub Date : 2025-02-22 eCollection Date: 2025-06-01 DOI: 10.1007/s42994-025-00201-y
Xiaopeng Li, Jiaxuan Li, Hossain M Zabed, Junjie Li, Min Xiong, Hongyong Shi, Jia Li
{"title":"Manipulating brassinosteroid signaling pathway to genetically improve horticultural plants.","authors":"Xiaopeng Li, Jiaxuan Li, Hossain M Zabed, Junjie Li, Min Xiong, Hongyong Shi, Jia Li","doi":"10.1007/s42994-025-00201-y","DOIUrl":"10.1007/s42994-025-00201-y","url":null,"abstract":"<p><p>Brassinosteroids (BRs), a class of plant-specific steroidal hormones, play crucial roles in regulating various plant physiological functions, such as growth, development, and adaptability to the environment. Despite this broader role of BRs, previously published reviews mainly focused on the molecular mechanisms of BR-mediated regulation of vegetative and reproductive growth of model plants like <i>Arabidopsis</i> and some food crops, such as rice, maize, and wheat. While horticultural plants hold significant economic importance in modern agriculture, less attention has been paid to understanding the role of BRs in regulating the physiological functions of these plants. Given the lack of relevant reviews, this article aims to discuss the major roles of BRs in horticultural plants, particularly fruit and leaf development, whole plant architecture, and adaptive stress response. We also highlight key challenges and provide some future research directions for genetically improving horticultural plants by altering the BR signaling pathway.</p>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 2","pages":"328-345"},"PeriodicalIF":4.6,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12238443/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144610300","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
PhytoCluster: a generative deep learning model for clustering plant single-cell RNA-seq data. PhytoCluster:一个用于植物单细胞RNA-seq数据聚类的生成式深度学习模型。
IF 4.6 4区 农林科学
aBIOTECH Pub Date : 2025-02-20 eCollection Date: 2025-06-01 DOI: 10.1007/s42994-025-00196-6
Hao Wang, Xiangzheng Fu, Lijia Liu, Yi Wang, Jingpeng Hong, Bintao Pan, Yaning Cao, Yanqing Chen, Yongsheng Cao, Xiaoding Ma, Wei Fang, Shen Yan
{"title":"PhytoCluster: a generative deep learning model for clustering plant single-cell RNA-seq data.","authors":"Hao Wang, Xiangzheng Fu, Lijia Liu, Yi Wang, Jingpeng Hong, Bintao Pan, Yaning Cao, Yanqing Chen, Yongsheng Cao, Xiaoding Ma, Wei Fang, Shen Yan","doi":"10.1007/s42994-025-00196-6","DOIUrl":"10.1007/s42994-025-00196-6","url":null,"abstract":"<p><p>Single-cell RNA sequencing (scRNA-seq) technology enables a deep understanding of cellular differentiation during plant development and reveals heterogeneity among the cells of a given tissue. However, the computational characterization of such cellular heterogeneity is complicated by the high dimensionality, sparsity, and biological noise inherent to the raw data. Here, we introduce PhytoCluster, an unsupervised deep learning algorithm, to cluster scRNA-seq data by extracting latent features. We benchmarked PhytoCluster against four simulated datasets and five real scRNA-seq datasets with varying protocols and data quality levels. A comprehensive evaluation indicated that PhytoCluster outperforms other methods in clustering accuracy, noise removal, and signal retention. Additionally, we evaluated the performance of the latent features extracted by PhytoCluster across four machine learning models. The computational results highlight the ability of PhytoCluster to extract meaningful information from plant scRNA-seq data, with machine learning models achieving accuracy comparable to that of raw features. We believe that PhytoCluster will be a valuable tool for disentangling complex cellular heterogeneity based on scRNA-seq data.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42994-025-00196-6.</p>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 2","pages":"189-201"},"PeriodicalIF":4.6,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12237842/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144610304","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Bacillus atrophaeus DX-9 biocontrol against potato common scab involves significant changes in the soil microbiome and metabolome 萎缩性芽孢杆菌DX-9防治马铃薯普通痂病涉及土壤微生物组和代谢组的显著变化
IF 4.6 4区 农林科学
aBIOTECH Pub Date : 2025-02-18 DOI: 10.1007/s42994-025-00199-3
Jingjing Cao, Yue Ma, Jing Fu, Zhiqin Wang, Yonglong Zhao, Naiqin Zhong, Pan Zhao
{"title":"Bacillus atrophaeus DX-9 biocontrol against potato common scab involves significant changes in the soil microbiome and metabolome","authors":"Jingjing Cao,&nbsp;Yue Ma,&nbsp;Jing Fu,&nbsp;Zhiqin Wang,&nbsp;Yonglong Zhao,&nbsp;Naiqin Zhong,&nbsp;Pan Zhao","doi":"10.1007/s42994-025-00199-3","DOIUrl":"10.1007/s42994-025-00199-3","url":null,"abstract":"<div><p>Potato common scab (CS) is a worldwide disease, caused by <i>Streptomyces</i> spp., and its presence reduces the market value of potatoes. A nontoxic and potentially effective approach in many control strategies is the use of antagonistic microbes as biocontrol agents. In this study, <i>Bacillus atrophaeus</i> DX­9 was isolated and assessed for its ability to protect against CS. Through integrated metagenomic and metabolomic analyses, changes in the soil microbial community structure and soil properties were analyzed to understand the effects of <i>Bacillus atrophaeus</i> DX­9 on CS. These studies revealed that DX­9 inoculation could significantly decrease CS disease rate, disease index, and the number of CS pathogens, along with an increase in soil N and P content. Our metagenomic assays identified 102 phyla and 1154 genera, and DX­9 inoculation increased the relative abundances of the phyla Pseudomonadota, Chloroflexota and Gemmatimonadota. Additionally, an increase in the relative abundance of genera, such as <i>Bradyrhizobium</i>, <i>Agrobacterium</i>, and <i>Nitrobacter</i>, were significantly and positively correlated with soil N and P. Metabolomic analysis revealed that DX­9 inoculation significantly increased the soil levels of phytolaccoside A, 7,8­dihydropteroic acid, novobiocin, and azafrin. These compounds were enriched in microbe pathway metabolites, including xenobiotic biodegradation and metabolism, biosynthesis of other secondary metabolites, and metabolism of cofactors and vitamins. In summary, the use of <i>Bacillus atrophaeus</i> DX­9 against potato CS offers an alternative biocontrol method that can improve both soil microbial community and properties. This study provides insight into the potential mechanisms by which microbial inoculants can control CS disease.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 1","pages":"33 - 49"},"PeriodicalIF":4.6,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-025-00199-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143564438","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Convenient, high-efficiency multiplex genome editing in autotetraploid alfalfa using endogenous U6 promoters and visual reporters 利用内源U6启动子和视觉报告子对同源四倍体苜蓿进行便捷、高效的多重基因组编辑
IF 4.6 4区 农林科学
aBIOTECH Pub Date : 2025-02-10 DOI: 10.1007/s42994-025-00200-z
Xiuzhi Xia, Shihao Li, Na Wang, Panxu Cheng, Butuo Zhu, Pengcheng Zhang, Dahai Yang, Hao Lin, Lifang Niu
{"title":"Convenient, high-efficiency multiplex genome editing in autotetraploid alfalfa using endogenous U6 promoters and visual reporters","authors":"Xiuzhi Xia,&nbsp;Shihao Li,&nbsp;Na Wang,&nbsp;Panxu Cheng,&nbsp;Butuo Zhu,&nbsp;Pengcheng Zhang,&nbsp;Dahai Yang,&nbsp;Hao Lin,&nbsp;Lifang Niu","doi":"10.1007/s42994-025-00200-z","DOIUrl":"10.1007/s42994-025-00200-z","url":null,"abstract":"<div><p>CRISPR/Cas is a simple, robust, versatile tool for plant biology studies and precision plant breeding. However, establishing a high-efficiency gene editing system for multiplex editing of the autotetraploid crop alfalfa (<i>Medicago sativa</i> L.), the most important forage legume worldwide, remains a formidable challenge. Here, we systematically identified endogenous <i>U6</i> promoters in alfalfa through transient expression via <i>Agrobacterium</i>-mediated infiltration of alfalfa leaves. We further demonstrated the efficacy of the three most active promoters for genome editing using an optimized alfalfa hairy root system. Subsequently, we established an improved CRISPR/Cas9 multiplex system containing three or four tandemly arrayed <i>MsU6</i>-promoter-driven polycistronic tRNA-sgRNA (PTG) expression cassettes, each consisting of three tRNA-sgRNA units, to simultaneously edit three or four alfalfa genes, coupled with the visual reporter <i>RH1</i> or <i>RUBY</i>. This toolkit showed efficient multiplex editing in the hairy root system with visual selection. We successfully obtained regenerated, red-colored shoots resulting from the stable transformation of alfalfa. These results highlight the potential application of the visual reporter system for the stable transformation of alfalfa. Our improved CRISPR/Cas9 multiplex system enables convenient, high-efficiency multiplex genome editing in alfalfa, providing a versatile toolset to facilitate functional studies of multiple genes and gene families for basic research and the genetic improvement of alfalfa.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 1","pages":"81 - 90"},"PeriodicalIF":4.6,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-025-00200-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143564378","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Atypical RXLR effectors are involved in Phytophthora cactorum pathogenesis 非典型 RXLR 效应器参与了根瘤蚜的致病过程
IF 4.6 4区 农林科学
aBIOTECH Pub Date : 2025-01-27 DOI: 10.1007/s42994-025-00198-4
Zeyang Zheng, Juanjuan Liu, Wenzhong You, Jun Sun, Kehan Wang, Xuemei Zhang, Xinyu Yan, Zhenpan Liu
{"title":"Atypical RXLR effectors are involved in Phytophthora cactorum pathogenesis","authors":"Zeyang Zheng,&nbsp;Juanjuan Liu,&nbsp;Wenzhong You,&nbsp;Jun Sun,&nbsp;Kehan Wang,&nbsp;Xuemei Zhang,&nbsp;Xinyu Yan,&nbsp;Zhenpan Liu","doi":"10.1007/s42994-025-00198-4","DOIUrl":"10.1007/s42994-025-00198-4","url":null,"abstract":"<div><p>RXLR effectors are pathogenic factors secreted from oomycetes to manipulate the immunity of the host. Typical RXLR effectors contain an RXLR-dEER motif at the N-terminus, whereas atypical RXLRs show variations on this motif. The oomycete <i>Phytophthora cactorum</i> is known to infect over 200 plant species, resulting in significant agricultural economic losses. Although genome-wide identification and functional analyses of typical RXLRs from <i>P. cactorum</i> have been performed, little is known of atypical PcaRXLRs. Here, we identified RXLRs, both typical and atypical, in <i>P. cactorum</i> and compared them with those of other oomycete pathogens. Fewer RXLRs were identified in <i>P. cactorum</i> compared with other <i>Phytophthora</i> species, possibly due to fewer duplication events of RXLRs. In contrast, the percentage of atypical RXLRs was higher in <i>P. cactorum</i> than in other species, suggesting significant roles in <i>P. cactorum</i> pathogenesis. Analysis of RXLR gene expression showed that most were transcribed, suggesting their functionality. Transient expression of two atypical RXLRs in <i>Nicotiana benthamiana</i> showed that they induced necrosis dependent on host SGT1 and HSP90. Furthermore, two additional atypical RXLRs suppressed the defense response in <i>N. benthamiana</i> and promoted <i>P. cactorum</i> infection. These results demonstrate the vital role of atypical RXLRs in <i>P. cactorum</i> and provide valuable information on their evolutionary patterns and interactions with host plants.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 1","pages":"50 - 62"},"PeriodicalIF":4.6,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-025-00198-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143564484","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Emerging strategies to improve heat stress tolerance in crops 提高作物抗热胁迫能力的新策略
IF 4.6 4区 农林科学
aBIOTECH Pub Date : 2025-01-24 DOI: 10.1007/s42994-024-00195-z
Jiawei Xiong, Hao Wang, Zhaohui Zhong, Shigui Li, Peng Qin
{"title":"Emerging strategies to improve heat stress tolerance in crops","authors":"Jiawei Xiong,&nbsp;Hao Wang,&nbsp;Zhaohui Zhong,&nbsp;Shigui Li,&nbsp;Peng Qin","doi":"10.1007/s42994-024-00195-z","DOIUrl":"10.1007/s42994-024-00195-z","url":null,"abstract":"<div><p>The heat stress (HS) response in plants involves complex processes at the molecular, cellular, and whole-organism levels. Sensitivity to HS differs based on the species and developmental stage of the plant, making it challenging to define HS and its impacts. Efforts to enhance HS tolerance by traditional breeding are constrained by limited genetic resources, but understanding the mechanisms that regulate HS responses can enable efforts to improve heat tolerance by precision breeding and gene editing. Here, we review recent research on the effects of HS on major cereal crops at different developmental stages and identify key genes potentially involved in the HS response, offering insight for precision molecular breeding. Additionally, we discuss the use of favorable natural variants and gene editing to improve crop tolerance to HS, emphasizing the value of alleles involved in thermomemory, combined stress tolerance, and the stress response–growth balance. This review aims to summarize recent advancements in understanding HS responses in crops, highlighting potential avenues for generating heat-tolerant crops.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 1","pages":"97 - 115"},"PeriodicalIF":4.6,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-024-00195-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143564476","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","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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