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Comparative transcriptome analysis revealed the molecular response mechanism of sugar beet (Beta vulgaris L.) against Cercospora Leaf Spot disease 比较转录组分析揭示了甜菜(Beta vulgaris L.)对Cercospora叶斑病的分子响应机制
IF 3 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-11-01 Epub Date: 2025-09-12 DOI: 10.1016/j.ygeno.2025.111109
Hongyong Lou , Guangzhou Ding , Fangpu Cai , Chunlei Zhao , Yanli Li
Cercospora leaf spot (CLS), caused by the hemibiotrophic fungus Cercospora beticola (C. beticola), critically threatens global sugar beet production through defoliation and chlorosis, reducing root yields by ≤50 % and impairing sucrose crystallization. As fungicide resistance escalates in C. beticola populations, developing genetically resistant sugar beet becomes imperative. We dissected CLS resistance mechanisms via comparative transcriptomics of resistant (81GM241) and susceptible (KWS6661) genotypes across four infection stages (0–30 dpi). Resistant plants deployed a triphasic defense strategy: During early infection (10 dpi), rapid activation of phenylpropanoid biosynthesis, fatty acid elongation, and glutathione metabolism established dual barriers of lignin-mediated cell wall fortification and ROS scavenging. By mid-infection (20 dpi), pathogen recognition receptors triggered MAPK-WRKY cascades that amplified jasmonate-mediated defenses while mobilizing flavonoid antimicrobials. In late infection (30 dpi), systemic downregulation of photosynthetic antenna proteins redirected resources to tryptophan-derived phytoalexins, sustaining defense without growth penalties. Crucially, resistant plants proactively anticipated stress through coordinated calcium signaling (CDPK), pectin methylesterase-driven cell wall remodeling, and antioxidant activation before pathogen proliferation. In contrast, susceptible plants exhibited delayed ROS detoxification and impaired signal transduction. This phased defense architecture—initiating with pathogen recognition and transient oxidative bursts, progressing through sustained immune activation, and culminating in metabolic optimization—provides a molecular framework for breeding resistant varieties by stacking phase-specific defense regulators.
由半生物营养真菌甜菜Cercospora beticola (C. beticola)引起的Cercospora叶斑病(CLS)通过落叶和褪绿严重威胁全球甜菜生产,使根产量减少≤50%,并损害蔗糖结晶。随着甜菜种群中杀菌剂抗性的升级,开发具有遗传抗性的甜菜变得势在必行。通过比较四个感染阶段(0-30 dpi)的耐药基因型(81GM241)和易感基因型(KWS6661)的转录组学,我们剖析了CLS的耐药机制。抗性植物采用了三重防御策略:在感染早期(10 dpi),苯丙素生物合成、脂肪酸延伸和谷胱甘肽代谢的快速激活建立了木质素介导的细胞壁强化和ROS清除的双重屏障。在感染中期(20 dpi),病原体识别受体触发MAPK-WRKY级联反应,放大茉莉酸介导的防御,同时动员类黄酮抗毒素。在感染后期(30 dpi),光合天线蛋白的系统性下调将资源重定向到色氨酸衍生的植物抗毒素,在不损害生长的情况下维持防御。关键是,抗性植物通过协调钙信号(CDPK)、果胶甲基酯酶驱动的细胞壁重塑和病原体增殖前的抗氧化激活来主动预测胁迫。相反,易感植物表现出ROS解毒延迟和信号转导受损。这种阶段性防御体系——从病原体识别和短暂的氧化爆发开始,经过持续的免疫激活,最终在代谢优化中达到高潮——通过堆叠阶段性防御调节因子,为培育抗性品种提供了分子框架。
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引用次数: 0
Computational methods for the analysis of long-read RNA-seq data 长读rna序列数据分析的计算方法
IF 3 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-11-01 Epub Date: 2025-10-17 DOI: 10.1016/j.ygeno.2025.111144
Kristina Santucci, Yuning Cheng, Si-Mei Xu, Michael Janitz
Advancements in the accuracy of long-read sequencing technologies and bioinformatic approaches have broadened the applications of RNA sequencing (RNA-seq). This review covers such developments across various aspects of genomics, transcriptomics, and proteomics, focussing on the discovery and characterisation of new genes, transcriptional isoforms, and proteins. This review also explores the different approaches to characterise transcript isoforms that transcribed from both annotated and unannotated novel genes, such as determining protein-coding potential, functional domains, and conserved regions. Finally, the long-read RNA-seq (lrRNA-seq) based approaches for analysing co-transcriptional and post-transcriptional events, such as alternative splicing, polyadenylation, and RNA modifications, are elaborated. Conflicting recommendations, limitations, and priorities for future research for such methods reported by previous studies are also addressed. Overall, this review intends to demonstrate how integrated analyses can be achieved with lrRNA-seq in various areas of molecular biology.
长读测序技术和生物信息学方法的准确性的提高,扩大了RNA测序(RNA-seq)的应用范围。这篇综述涵盖了基因组学、转录组学和蛋白质组学各个方面的发展,重点是新基因、转录异构体和蛋白质的发现和表征。这篇综述还探讨了不同的方法来表征从带注释和未带注释的新基因转录的转录异构体,如确定蛋白质编码电位、功能域和保守区域。最后,详细阐述了基于长读RNA-seq (lrRNA-seq)的方法,用于分析共转录和转录后事件,如选择性剪接、聚腺苷化和RNA修饰。本文还讨论了先前研究报告的这些方法的相互矛盾的建议、局限性和未来研究的优先事项。总之,这篇综述旨在展示如何利用lrna -seq在分子生物学的各个领域实现综合分析。
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引用次数: 0
Integrated genomic and transcriptomic analysis identifies novel candidate genes affecting carcass backfat thickness in pigs 综合基因组学和转录组学分析确定了影响猪胴体背膘厚度的新的候选基因。
IF 3 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-11-01 Epub Date: 2025-09-30 DOI: 10.1016/j.ygeno.2025.111117
Qian Liu , Jianghui Yu , Xinjie Ai , Huiying Xu , Zijian Qiu , Liming Xu , Jinfeng Ma , Jin Zhou , Chenxi Liu , Qingbo Zhao , Pinghua Li , Ruihua Huang
The carcass backfat thickness (BFT) provides a valuable indication of fat deposition and carcass leanness, which are essential for the determination of carcass grading and pricing. Identifying genetic loci and crucial genes related to BFT using integrated multi-omics methods offers significant contributions to the genetic advancement of pig. In the present study, 418 Chinese Suhuai pigs were slaughtered, and carcass BFT were subsequently measure. We conducted a genome-wide association study (GWAS) based on SNP chip data and imputed whole-genome sequencing data (iWGS), respectively. Significant quantitative trait loci (QTL) correlated with carcass BFT were identified on Sus scrofa chromosome (SSC) 2, SSC4, and SSC14, with the most significant single-nucleotide polymorphisms (SNPs) explaining 6.58 %–9.91 % of the phenotypic variance. Bayesian fine mapping validated two previously reported quantitative trait loci (QTLs), narrowing the most refined confidence interval to 3 kb (SSC2, 37.337–37.340 Mb and SSC4, 75.407–77.006 Mb), while identifying two novel QTLs (SSC14, 137.086–138.863 Mb and SSC4, 95.237–96.894 Mb) associated with carcass BFT. Furthermore, transcriptome analysis identified 322 differentially expressed genes (DEGs) and several critical regulatory pathways related to lipid and energy metabolism, including fatty acid and pyruvate metabolism. The integration of genomic and transcriptomic data identified three pivotal candidate genes, S100A12, XKR4 and PENK, which are typically associated with BFT. Transcriptome-wide association study (TWAS) and Phenome-wide association study (PheWAS) provided further evidence that these three genes were significantly associated with BFT and fatty acid composition. This study uncovers novel insights into the important genes and molecular markers related to carcass BFT in pig.
胴体背膘厚度(BFT)是脂肪沉积和胴体瘦度的重要指标,对胴体分级和定价具有重要意义。利用综合多组学方法鉴定与BFT相关的遗传位点和关键基因对猪的遗传进步有重要贡献。本研究屠宰了418头中国苏淮猪,随后测定了胴体肥厚。我们分别基于SNP芯片数据和全基因组测序数据进行了全基因组关联研究(GWAS)。结果表明,与胴体肥力相关的显著数量性状位点(QTL)分布在猪的SSC 2、SSC4和SSC14染色体上,其中最显著的单核苷酸多态性(snp)解释了6.58 % ~ 9.91 %的表型变异。贝叶斯精细定位验证了两个先前报道的数量性状位点(qtl),将最精细的置信区间缩小到3 kb (SSC2, 37.337-37.340 Mb和SSC4, 75.407-77.006 Mb),同时鉴定出两个与胴体BFT相关的新qtl (SSC14, 137.086-138.863 Mb和SSC4, 95.237-96.894 Mb)。此外,转录组分析确定了322个差异表达基因(DEGs)和一些与脂质和能量代谢相关的关键调控途径,包括脂肪酸和丙酮酸代谢。整合基因组和转录组学数据确定了三个关键的候选基因:S100A12、XKR4和PENK,它们通常与BFT相关。转录组全关联研究(TWAS)和表型全关联研究(PheWAS)进一步证明这三个基因与BFT和脂肪酸组成显著相关。本研究对猪胴体肥厚相关的重要基因和分子标记有了新的认识。
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引用次数: 0
Genomic and physiological characterization of beer spoiling Megasphaera spp. 啤酒腐坏Megasphaera的基因组和生理特性。
IF 3 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-11-01 Epub Date: 2025-10-27 DOI: 10.1016/j.ygeno.2025.111139
Manuel J. Arnold , Matthias A. Ehrmann , Yohanes N. Kurniawan , Koji Suzuki , Wolfgang Liebl
Beer spoiling bacteria represent a major concern for the brewing industry. Anaerobic spoilers of the genus Megasphaera are especially dreadful. Until now, the genome analysis of Megasphaera spp. was limited to mammal-associated species, yet beer borne Megasphaera species and their abilities to tolerate the multiple high stress factors in their niche were broadly overlooked. This study is the first to carry out an in silico genome comparison of ten strains from three different beer spoiling Megasphaera species (M. cerevisiae, M. paucivorans and M. sueciensis). We experimentally show a hitherto unseen resilience of beer spoiling Megasphaera strains, which can grow in lager beer with an isoα-acids content of up to 120 IBU, an ethanol concentration of up to 7.0 % (v/v) and at pH 4.0. The genomes revealed genes appearing to aid survival in the harsh brewing environment mainly comprised of hop, ethanol and acid stress.
啤酒腐坏细菌是酿酒行业关注的主要问题。Megasphaera属的厌氧破坏者尤其可怕。到目前为止,人们对巨斑蛛的基因组分析仅限于哺乳动物的亲缘种,而啤酒源的巨斑蛛及其对生态位中多种高应激因素的耐受能力却被广泛忽视。本研究首次对三种不同的啤酒腐坏Megasphaera物种(M. cerevisiae, M. paucivorans和M. sueciensis)的10株菌株进行了计算机基因组比较。我们通过实验显示了迄今为止未见的啤酒变质Megasphaera菌株的恢复能力,它可以在异α-酸含量高达120 IBU、乙醇浓度高达7.0 % (v/v)和pH 4.0的啤酒中生长。基因组揭示了在恶劣的酿造环境中帮助生存的基因,主要包括啤酒花、乙醇和酸胁迫。
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引用次数: 0
Strategic intercropping with mulberry (Morus alba L.) predictably modulates rhizosphere microbiome assembly and enriches pathways for secondary metabolite production 桑树策略间作可预测地调节根际微生物组的组装并丰富次生代谢物的产生途径。
IF 3 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-11-01 Epub Date: 2025-10-08 DOI: 10.1016/j.ygeno.2025.111129
Zhou Hu , Yuheng Lei , Tianrui Li , Tingfu Zhang , Qian Yang , Jun Yang , Gaiqun Huang , Delong Guan , Jian Zou
Intercropping is a key strategy for sustainable agriculture, but its effects on the rhizosphere microbiome remain poorly understood. Here, we investigated how intercropping mulberry (Morus alba L.) with functionally distinct partners—a nitrogen-fixing legume (Pisum sativum), a saprotrophic fungus (Morchella esculenta), and a medicinal plant (Polygonatum sibiricum)—shapes its rhizosphere bacterial community. Compared to monoculture, all intercropping systems significantly increased bacterial diversity and established unique community structures and functional signatures. Legume intercropping specifically enriched nitrogen-cycling bacteria like Bradyrhizobium and enhanced nitrogen metabolism pathways, whereas fungal intercropping fostered anaerobic decomposers. Crucially, all systems enriched pathways for secondary metabolite biosynthesis, suggesting a potential to enhance mulberry's economic value. Our findings establish that strategic partner selection is a powerful microbiome design tool, enabling predictable modulation of rhizosphere function for sustainable mulberry cultivation.
间作是可持续农业的一项关键策略,但其对根际微生物群的影响仍知之甚少。在这里,我们研究了桑树(Morus alba L.)与功能不同的伙伴——固氮豆科植物(Pisum sativum)、腐养真菌(Morchella esculenta)和药用植物(Polygonatum sibiricum)的间作是如何塑造其根际细菌群落的。与单作相比,所有间作制度均显著增加了细菌多样性,并建立了独特的群落结构和功能特征。豆科作物间作特别富集了缓生根瘤菌等氮循环细菌,增强了氮代谢途径,而真菌间作则培养了厌氧分解者。至关重要的是,所有系统都丰富了次生代谢物生物合成的途径,这表明有可能提高桑树的经济价值。我们的研究结果表明,战略合作伙伴选择是一种强大的微生物组设计工具,可以预测根际功能的调节,以实现桑树的可持续种植。
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引用次数: 0
Geogenomic mapping of drug-resistant Mycobacterium tuberculosis from Ireland and overseas 爱尔兰和海外耐药结核分枝杆菌的地理基因组图谱。
IF 3 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-11-01 Epub Date: 2025-10-08 DOI: 10.1016/j.ygeno.2025.111132
Cian Ennis , Gaetan Thilliez , Ronan F. O’Toole
In this study, we performed an in-depth comparison of genome-sequenced Mycobacterium tuberculosis isolates from Ireland with isolates from other countries. The sequenced isolates from Ireland mostly belonged to Lineage 4 (64.15 %) with Lineages 2 (17.27 %), 1 (13.21 %), 3 (5.22 %), and 5 (0.15 %) also represented. Of these, Lineages 2 (47.57 %) and 4 (34.95 %) accounted for the majority of the isolates that were resistant to at least rifampicin. By performing hierarchical clustering of the genomes, we determined that many drug-resistant (DR) strains of Lineage 2 collected in Ireland belonged to larger international clusters of the bacterium that were dominant in countries that included Estonia, Georgia, Ukraine, and Moldova. Lineage 4 DR-TB strains isolated in Ireland were also commonly part of large international clusters but the major countries differed i.e. Eswatini, Germany, United Kingdom, and Mozambique. Based on single nucleotide polymorphism (SNP) analysis, there was no evidence found of widespread onward transmission of DR-TB isolates in Ireland. This indicates that a key source of DR-TB in Ireland is translocation of M. tuberculosis from countries where specific genetic clusters of drug-resistant strains are prevalent. This study has implications for interpreting future trends in TB drug resistance. As an open economy with extensive international travel connections, Ireland is sensitive to the emergence of resistant isolates of M. tuberculosis elsewhere. In addition to caution being applied with respect to TB presenting in individuals from high multi-drug resistant (MDR) TB burden countries, vigilance is also needed for TB in persons from countries where large phylogenetic clusters of DR-TB occur.
在这项研究中,我们对来自爱尔兰和其他国家的结核分枝杆菌分离株进行了深入的基因组测序比较。来自爱尔兰的测序分离株主要属于谱系4(64.15 %),谱系2(17.27 %)、1(13.21 %)、3(5.22 %)和5(0.15 %)也有代表。其中,2号菌株(47.57 %)和4号菌株(34.95 %)至少对利福平耐药。通过对基因组进行分层聚类,我们确定在爱尔兰收集的许多耐药(DR)谱系2菌株属于在爱沙尼亚、格鲁吉亚、乌克兰和摩尔多瓦等国家占主导地位的较大的国际细菌群。在爱尔兰分离的谱系4耐药结核菌株通常也是大型国际聚集性病例的一部分,但主要国家有所不同,即斯瓦蒂尼、德国、英国和莫桑比克。根据单核苷酸多态性(SNP)分析,在爱尔兰没有发现广泛传播耐药结核分离株的证据。这表明,爱尔兰耐药结核病的一个关键来源是结核分枝杆菌从普遍存在特定耐药菌株遗传群的国家的易位。这项研究对解释结核病耐药性的未来趋势具有启示意义。作为一个拥有广泛国际旅行联系的开放经济体,爱尔兰对其他地方出现的耐药结核分枝杆菌分离株非常敏感。除了对来自耐多药结核病高负担国家的个人出现的结核病采取谨慎态度外,还需要对来自发生大量耐多药结核病聚集性病例的国家的个人出现的结核病保持警惕。
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引用次数: 0
A bioinformatics pipeline for identifying homoplasmic and heteroplasmic mitochondrial DNA SNVs in single-cell RNA-Seq datasets 在单细胞RNA-Seq数据集中鉴定同质和异质线粒体DNA snv的生物信息学管道。
IF 3 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-11-01 Epub Date: 2025-10-06 DOI: 10.1016/j.ygeno.2025.111122
Zhiling Guan , Patrick Lindsey , Rick Kamps , Hubert J.M. Smeets
Mitochondrial DNA (mtDNA) single nucleotide variants (SNVs) are associated with various pathologies, predominantly in energy-demanding tissues like muscles and brain. Characterizing these SNVs at the single-cell level is crucial for understanding their mechanism and clinical manifestation. Publicly available single-cell RNA sequencing (scRNA-seq) data could be an invaluable resource, but existing pipelines fall short in reliable detection of mtDNA SNVs from scRNA-seq data. Therefore, we developed a novel bioinformatics pipeline, that includes quality control, alignment to the mitochondrial genome, SNV calling, and annotation, and that filters-out sequencing errors. Coverage-dependent thresholds are customizable for detecting heteroplasmic SNVs. Duplicate reads can be retained as the majority were valid biological duplicates. Strand bias errors, exceeding a 1:3 ratio, RNA modification-induced errors, identified by the presence of multiple alternative alleles at the same position, and overrepresented SNVs were removed. Our data demonstrated that this pipeline effectively detects homoplasmic and heteroplasmic mtDNA SNVs in scRNA-Seq data.
线粒体DNA (mtDNA)单核苷酸变异(snv)与多种病理有关,主要发生在肌肉和大脑等高能量组织中。在单细胞水平上表征这些snv对于了解其机制和临床表现至关重要。公开的单细胞RNA测序(scRNA-seq)数据可能是一种宝贵的资源,但现有的管道在从scRNA-seq数据中可靠地检测mtDNA snv方面存在不足。因此,我们开发了一种新的生物信息学管道,包括质量控制、线粒体基因组比对、SNV调用和注释,并过滤掉测序错误。覆盖率相关的阈值可定制用于检测异质性snv。重复的读取可以保留,因为大多数是有效的生物重复。去除超过1:3比例的链偏置错误、RNA修饰引起的错误(通过在同一位置存在多个替代等位基因来识别)和过度代表的snv。我们的数据表明,该管道可以有效地检测scRNA-Seq数据中的同质和异质mtDNA snv。
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引用次数: 0
A modular pipeline for evidence-integrated genome annotation across species: A case study on Schmidtea mediterranea 跨物种证据整合基因组注释的模块化管道:以地中海Schmidtea mediterranea为例
IF 3 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-11-01 Epub Date: 2025-09-08 DOI: 10.1016/j.ygeno.2025.111104
Anastasiia Zaremba, Małgorzata Marszałek-Zeńczak, Annasha Dutta, Anna Samelak-Czajka, Paulina Jackowiak
Despite advancements in genome annotation tools, challenges persist for non-classical model organisms with limited genomic resources, such as Schmidtea mediterranea. To address these challenges, we developed a flexible and scalable genome annotation pipeline that integrates short-read (Illumina) and long-read (PacBio) sequencing technologies. The pipeline combines reference-based and de novo assembly methods, effectively handling genomic variability and alternative splicing events. To improve splice site detection accuracy, DeepSplice deep learning predictions are used. Functional annotation is conducted to filter out low-confidence transcripts and ensure biological relevance. Applying this pipeline to the asexual strain of S. mediterranea revealed thousands of previously undescribed putative genes and transcripts, and improved the existing gene models, highlighting its utility in annotating complex, underexplored genomes. The modularity and comprehensiveness of our pipeline ensure its adaptability for genome annotation across diverse species, making it a valuable tool for annotating genomes of non-model organisms and supporting broader genomic research. The source code and implementation details are available at https://github.com/Norreanea/SmedAnno.
尽管基因组注释工具取得了进步,但对于基因组资源有限的非经典模式生物(如地中海Schmidtea mediterranea),挑战仍然存在。为了应对这些挑战,我们开发了一个灵活且可扩展的基因组注释管道,该管道集成了短读(Illumina)和长读(PacBio)测序技术。该管道结合了基于参考和从头组装方法,有效地处理基因组变异性和替代剪接事件。为了提高剪接位点检测的准确性,使用了DeepSplice深度学习预测。功能标注过滤低置信度转录本,保证生物学相关性。将该管道应用于地中海稻的无性菌株,揭示了数千个先前未描述的假定基因和转录本,并改进了现有的基因模型,突出了其在注释复杂的、未开发的基因组方面的应用。该管道的模块化和全面性确保了其对不同物种基因组注释的适应性,使其成为非模式生物基因组注释和支持更广泛的基因组研究的有价值的工具。源代码和实现细节可在https://github.com/Norreanea/SmedAnno上获得。
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引用次数: 0
scRNA-seq of Penaeus japonicus hemocytes under environmentally-induced restriction of sand-diving behavior 环境诱导的潜沙行为限制下日本对虾血细胞的scrna序列分析。
IF 3 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-11-01 Epub Date: 2025-09-30 DOI: 10.1016/j.ygeno.2025.111125
Huimin Zhang , Xinyu Zhou , Yang Zhang , Jiahan Yu , Junjie Qi , Jing Xu , Panpan Wang , Fei Yu , Jianxin Zhang , Huan Gao
Penaeus japonicus is an economically important marine shrimp species, but its sand-diving habit affects the further improvement of their culture yield. To investigate the molecular response to the restriction of sand-diving behavior, we designed three culture systems: the sandy group, the sandless group, and the sandless stress group (transfer the individuals to a sandless pond after a week in the sandy group). First, we analyzed the expression differences of stress-related (HSP60) and circadian rhythm genes (period, timeless) at different time points after stress induction, identifying 6 h post-transition as the timepoint with the most significant stress response (p < 0.05). A total of 25,371 highly expressed genes were detected across cell clusters, which were further classified into 13 distinct cell subpopulations. Manual annotation categorized these into granular cells (GCs), semi-granular cells (SGCs), hyaline cells (HCs), prohemocyte-like cells, and functional cells. qRT-PCR analysis confirmed the expression profiles of 13 highly expressed genes in GCs, SGCs, and HCs of P. japonicus. RNA in situ hybridization localized pxt, IGSF10, and IFI30 to GCs, HCs, and SGCs, respectively, validating the accuracy of cell clusters classification based on marker genes. Single-cell transcriptome differential expression analysis revealed significant gene expression differences among the three groups (p < 0.05), with most differentially expressed genes (DEGs) concentrated in cluster 2 (GCs) and cluster 8 (HCs), suggesting their close association with burrowing behavior regulation. qRT-PCR analysis of these DEGs in hemocytes from P. japonicus reared under different substrate conditions yielded results consistent with the scRNA-seq data, confirming the reliability of the transcriptomic findings. Furthermore, comparative analysis between groups identified key candidate DEGs, including trpa1, trpm, and the cut protein family, that may play pivotal roles in the response to environmental change and the restriction of natural behavior, though their specific functions require further validation. This study provides a theoretical foundation for understanding the molecular stress response to substrate deprivation in P. japonicus and identifies candidate genes for future functional studies on behavioral regulation.
日本对虾(Penaeus japonicus)是经济上重要的海虾种,但其潜沙习性影响了其养殖产量的进一步提高。为了研究潜沙行为限制下的分子反应,我们设计了三种培养系统:有沙组、无沙组和无沙应激组(在有沙组一周后将个体转移到无沙池中)。首先,我们分析了应激相关基因(HSP60)和昼夜节律基因(period, timeless)在应激诱导后不同时间点的表达差异,确定6 h后为应激反应最显著的时间点(p
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引用次数: 0
Comparative transcriptomics reveal universal and compound-specific mechanisms of insecticide response in the mulberry looper (Phthonandria atrilineata) 比较转录组学揭示了桑树环虫(Phthonandria atrilineata)对杀虫剂反应的普遍和化合物特异性机制。
IF 3 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-11-01 Epub Date: 2025-09-30 DOI: 10.1016/j.ygeno.2025.111121
Delong Guan , Yingcan Qin , Jing Song , Yue Qin , Shihao Zhang , Lei Xin , Xiaodong Li
Understanding insect molecular responses to different insecticides is essential for sustainable pest management. This study presents a comprehensive transcriptomic analysis of Phthonandria atrilineata exposed to insecticides with distinct modes of action. RNA sequencing was performed on larvae treated with organophosphates (trichlorfon, malathion, and trichlorfon-malathion mixture) and mitochondrial inhibitors (methoxyfenozide and chlorfenapyr). Our analysis revealed both mechanism-specific responses and conserved xenobiotic defense programs. We identified 180 commonly upregulated genes involved in detoxification and sensory perception pathways, and 357 commonly downregulated genes indicating suppression of carbohydrate metabolism and developmental processes under chemical stress. Fuzzy clustering revealed nine distinct expression modules, with organophosphates primarily affecting neuronal functions while mitochondrial inhibitors triggered metabolic reprogramming centered on energy balance and protein homeostasis. Additionally, the trichlorfon-malathion mixture produced synergistic effects on endocrine signaling pathways. These findings illuminate the molecular architecture of insecticide responses, providing valuable insights for pest management strategies and resistance monitoring in agricultural settings.
了解昆虫对不同杀虫剂的分子反应对害虫的可持续管理至关重要。本研究提出了一个全面的转录组学分析的phthonandia atrilineata暴露于杀虫剂与不同的作用模式。对有机磷(敌百虫、马拉硫磷和敌百虫-马拉硫磷混合物)和线粒体抑制剂(甲氧虫酰肼和氯虫腈)处理的幼虫进行RNA测序。我们的分析揭示了机制特异性反应和保守的外源防御程序。我们确定了180个与解毒和感觉知觉通路相关的常见上调基因,以及357个表明化学胁迫下碳水化合物代谢和发育过程受到抑制的常见下调基因。模糊聚类揭示了9个不同的表达模块,其中有机磷酸盐主要影响神经元功能,而线粒体抑制剂则触发以能量平衡和蛋白质稳态为中心的代谢重编程。此外,敌百虫-马拉硫磷混合物对内分泌信号通路产生协同作用。这些发现阐明了杀虫剂反应的分子结构,为害虫管理策略和农业环境中的抗性监测提供了有价值的见解。
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引用次数: 0
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Genomics
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