Genomics最新文献_第10页

High-fat diet promotes kidney lipid droplet deposition contributing to the pathogenesis of obesity-related glomerulopathy in mice through gut microbial metabolism 高脂肪饮食通过肠道微生物代谢促进肾脏脂滴沉积，参与小鼠肥胖相关性肾小球病变的发病机制。

IF 3 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genomics

Pub Date : 2025-11-01 Epub Date: 2025-11-03 DOI: 10.1016/j.ygeno.2025.111151

Kai-Wen Cai , Ying-Ying Xie , Zi-Yan Deng , Zong-Chao Yu , Hong-Wei Wu , Zhuang-Feng Weng , Zhen-Chuan Lin , Bin Xia , Xiao-Hua Wang , Zhi-Hua Zheng , Chun Tang , Ting Zhu , Yong-Ping Lu

Background

Obesity-related glomerulopathy (ORG) is a kidney disorder associated with obesity, where dysbiosis of the gut microbiota and disturbances in lipid metabolism play crucial roles in its development. However, the exact mechanisms by which imbalances in gut microbiota influence lipid metabolism and contribute to the pathogenesis of ORG are still not fully understood.

Methods

A high-fat diet (HFD)-induced ORG model was established using 6-week-old male C57BL/6 J mice to investigate the role of gut microbiota and gut-derived metabolites in ORG progression. 16S rRNA sequencing was employed to profile the gut microbiota, while liquid chromatography-tandem mass spectrometry (LC-MS/MS) was applied for metabolite analysis in fecal, serum, and kidney samples.

Results

Compared to age-matched normal diet (ND) mice, ORG mice exhibited significant increases in triglycerides (TG), cholesterol (CHO), and urinary albumin-to-creatinine ratio (UACR), alongside enhanced lipid droplet accumulation in renal tubules and glomerular hypertrophy. Metabolomic analysis revealed altered metabolic profiles in ORG mice, particularly the reprogramming of glycerophospholipid metabolism. Additionally, 16S rRNA sequencing demonstrated reduced gut microbiota diversity in ORG mice relative to the ND group. Further investigation revealed that the shift in renal glycerophospholipid metabolism and elevated blood lipid levels in ORG mice were closely linked to gut microbiota dysbiosis, specifically increased abundance of Lachnospiraceae and decreased abundance of Muribaculaceae.

Conclusion

The dysbiosis of gut microbiota induced by a HFD leads to glycerophospholipid metabolic reprogramming, promoting lipid droplet deposition in the kidneys and contributing to ORG progression. Our study highlights the contribution of gut microbial metabolism to the development of ORG, offering new perspectives for potential therapeutic strategies targeting the gut in ORG treatment.

背景：肥胖相关性肾小球病（obesity -related glomerullopathy， ORG）是一种与肥胖相关的肾脏疾病，其中肠道菌群失调和脂质代谢紊乱在其发展中起着至关重要的作用。然而，肠道菌群失衡影响脂质代谢并导致ORG发病的确切机制尚不完全清楚。方法：以6周龄雄性C57BL/6 J小鼠为实验对象，建立高脂饮食（HFD）诱导的ORG模型，研究肠道菌群和肠道源性代谢物在ORG进展中的作用。采用16S rRNA测序分析肠道微生物群，采用液相色谱-串联质谱（LC-MS/MS）分析粪便、血清和肾脏样品的代谢物。结果：与年龄匹配的正常饮食（ND）小鼠相比，ORG小鼠表现出甘油三酯（TG）、胆固醇（CHO）和尿白蛋白与肌酐比率（UACR）的显著增加，同时肾小管脂滴积聚增强，肾小球肥大。代谢组学分析显示，ORG小鼠的代谢谱发生了改变，尤其是甘油磷脂代谢的重编程。此外，16S rRNA测序显示，相对于ND组，ORG小鼠的肠道微生物群多样性减少。进一步的研究表明，ORG小鼠肾脏甘油磷脂代谢的改变和血脂水平的升高与肠道菌群失调密切相关，特别是Lachnospiraceae的丰度增加和Muribaculaceae的丰度减少。结论：HFD诱导的肠道菌群失调导致甘油磷脂代谢重编程，促进肾脏脂滴沉积，促进ORG进展。我们的研究强调了肠道微生物代谢对ORG发展的贡献，为ORG治疗中针对肠道的潜在治疗策略提供了新的视角。

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引用次数: 0

Construction of a genome-wide linkage map and QTL mapping for growth and hypoxia tolerance traits in Chinese longsnout catfish (Leiocassis longirostris) 中国长鼻鲶鱼生长和耐缺氧性状全基因组连锁图谱的构建及QTL定位

IF 3 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genomics

Pub Date : 2025-11-01 Epub Date: 2025-11-19 DOI: 10.1016/j.ygeno.2025.111157

Fenfei Liang , Zhiru Yang , Wei Liu , Faling Zhang , Xia Liang , Cheng Zhao , Guosong Zhang

The Chinese longsnout catfish (Leiocassis longirostris) is an important freshwater aquaculture species, and the selective breeding of fast-growth and hypoxia tolerance population will have a positive impact on its industry. In order to promote the breeding process of Chinese longsnout catfish, construction of the genetic linkage map and identification of molecular markers associated with fast-growth and hypoxia tolerance is critical for the marker-assisted selection (MAS) of Chinese longsnout catfish. In the present study, whole-genome resequencing was used to construct a high-density genetic linkage map of the Chinese longsnout catfish. The map containing 2946 bin markers was distributed over 26 linkage groups (LGs) with a total genetic coverage of 1980.76 cM and an average density of 0.67 cM. Based on the genetic map, quantitative trait locus (QTL) mapping results suggested that 17 QTLs associated with growth traits and 1 QTL associated with hypoxia tolerance were identified in eight LGs with the phenotypic variability explained (PVE) ranged from 5.1 % to 9.3 %. Four SNP loci from these QTLs were associated with the phenotypic traits validated by Kompetitive Allele Specific PCR or Sanger sequencing. In addition, the expression of three candidate genes for growth traits and five candidate genes for hypoxia tolerance was examined in different growth speed populations and the process of hypoxia exposure and reoxygenation, respectively. The high-density genetic linkage map and QTLs for growth traits and hypoxia tolerance obtained in the present study could further provide the basis for genetic breeding and molecular marker-assisted breeding of Chinese longsnout catfish.

中国长鼻鲶鱼（Leiocassis longirostris）是一种重要的淡水养殖品种，对其快速生长和耐缺氧种群的选育将对其产业产生积极影响。为了促进中国长鼻鲶鱼的育种进程，构建遗传连锁图谱和鉴定与快速生长和耐缺氧相关的分子标记是中国长鼻鲶鱼标记辅助选择（MAS）的关键。本研究采用全基因组重测序技术构建了中国长鼻鲶鱼高密度遗传连锁图谱。该图谱包含2946个标记，分布在26个连锁群（LGs）上，总遗传盖度为1980.76 cM，平均密度为0.67 cM。基于遗传图谱，数量性状位点（QTL）定位结果表明，8个LGs中鉴定出17个与生长性状相关的QTL和1个与耐缺氧相关的QTL，表型变异解释（PVE）范围为5.1% ~ 9.3%。这些qtl中的4个SNP位点与竞争性等位基因特异性PCR或Sanger测序验证的表型性状相关。此外，还检测了3个生长性状候选基因和5个耐缺氧候选基因在不同生长速度群体以及缺氧暴露和再氧化过程中的表达情况。本研究获得的生长性状和耐缺氧性状的高密度遗传连锁图谱和qtl可进一步为中国长鼻鲶鱼的遗传育种和分子标记辅助育种提供依据。

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引用次数: 0

Organelle genomes of progeny of Tripidium arundinaceum × Saccharum spontaneum and sugarcane cultivar revealed their inheritance and characterization after hybridization 杂交后的三叶草（Tripidium arundinaceum × Saccharum spontanum）与甘蔗品种后代细胞器基因组揭示了它们的遗传和特性。

IF 3 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genomics

Pub Date : 2025-11-01 Epub Date: 2025-09-17 DOI: 10.1016/j.ygeno.2025.111107

Sicheng Li , Shan Zhou , Fengzhen Wu , Yuxin Huang , Yang Zhao , Baoqing Zhang , Gemin Zhang , Weixing Duan , Xiping Yang

Sugarcane (Saccharum spp.) breeding often involves hybridization with distantly related wild species (such as Tripidium arundinaceum) to improve stress resistance, but mitochondrial and chloroplast inheritance across multiple backcross generations remains poorly understood. In this study, we employed PacBio and Illumina sequencing to assemble and compare the mitochondrial genomes (mitogenomes) and chloroplast genome of four genotypes: an distant hybrid F₁ GXAS 07–6-1 (Tripidium arundinaceum × Saccharum spontaneum), a subsequent hybrid F₁ GXASF₁ 08–2-28, a first-generation backcross GXASBC₁ 12-A6–3, and a second-generation backcross GXASBC₂ 15–114. Maternal inheritance preserves key co-linear gene clusters, whereas MTPT content varies, indicating post-hybridization structural adjustments. Our study confirms strict maternal inheritance of mitochondrial and chloroplast genomes across hybrid and backcross generations and validates mitochondrial transmission using organelle-specific markers, providing insights into organellar inheritance and references for sugarcane breeding.

甘蔗（Saccharum spp）的育种通常涉及与远亲野生物种（如Tripidium arundinaceum）杂交以提高抗逆性，但线粒体和叶绿体在多个回交代之间的遗传仍然知之甚少。在本研究中，我们采用PacBio和Illumina测序技术，对远缘杂交品种F₁GXAS 07-6-1 （Tripidium arundinaceum × Saccharum spontanum）、后续杂交品种F₁GXASF1 08-2-28、第一代回交品种GXASBC1 12-A6-3和第二代回交品种GXASBC2 15-114四种基因型的线粒体基因组（有线粒体基因组）和叶绿体基因组进行了组装和比较。母系遗传保留了关键的共线性基因簇，而MTPT含量发生了变化，表明杂交后结构发生了调整。本研究证实了线粒体和叶绿体基因组在杂交代和回交代之间的严格母系遗传，并利用细胞器特异性标记验证了线粒体遗传，为甘蔗细胞器遗传研究提供了新的思路和参考。

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引用次数: 0

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

Genomics

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

Genomics

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。

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

Genomics

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

Genomics

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。

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

Genomics

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

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

Genomics

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

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

Genomics

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