Pub Date : 2025-11-01Epub Date: 2025-09-17DOI: 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.
{"title":"Organelle genomes of progeny of Tripidium arundinaceum × Saccharum spontaneum and sugarcane cultivar revealed their inheritance and characterization after hybridization","authors":"Sicheng Li , Shan Zhou , Fengzhen Wu , Yuxin Huang , Yang Zhao , Baoqing Zhang , Gemin Zhang , Weixing Duan , Xiping Yang","doi":"10.1016/j.ygeno.2025.111107","DOIUrl":"10.1016/j.ygeno.2025.111107","url":null,"abstract":"<div><div>Sugarcane (<em>Saccharum</em> spp.) breeding often involves hybridization with distantly related wild species (such as <em>Tripidium arundinaceum</em>) 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 (<em>Tripidium arundinaceum</em> × <em>Saccharum spontaneum</em>), a subsequent hybrid F₁ GXASF<sub>1</sub> 08–2-28, a first-generation backcross GXASBC<sub>1</sub> 12-A6–3, and a second-generation backcross GXASBC<sub>2</sub> 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.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111107"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145091662","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-01Epub Date: 2025-09-12DOI: 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.
{"title":"Comparative transcriptome analysis revealed the molecular response mechanism of sugar beet (Beta vulgaris L.) against Cercospora Leaf Spot disease","authors":"Hongyong Lou , Guangzhou Ding , Fangpu Cai , Chunlei Zhao , Yanli Li","doi":"10.1016/j.ygeno.2025.111109","DOIUrl":"10.1016/j.ygeno.2025.111109","url":null,"abstract":"<div><div><em>Cercospora leaf spot</em> (CLS), caused by the hemibiotrophic fungus <em>Cercospora beticola</em> (<em>C. beticola</em>), critically threatens global sugar beet production through defoliation and chlorosis, reducing root yields by ≤50 % and impairing sucrose crystallization. As fungicide resistance escalates in <em>C. beticola</em> 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.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111109"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145045580","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-01Epub Date: 2025-10-17DOI: 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.
{"title":"Computational methods for the analysis of long-read RNA-seq data","authors":"Kristina Santucci, Yuning Cheng, Si-Mei Xu, Michael Janitz","doi":"10.1016/j.ygeno.2025.111144","DOIUrl":"10.1016/j.ygeno.2025.111144","url":null,"abstract":"<div><div>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.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111144"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145321326","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-01Epub Date: 2025-09-30DOI: 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.
{"title":"Integrated genomic and transcriptomic analysis identifies novel candidate genes affecting carcass backfat thickness in pigs","authors":"Qian Liu , Jianghui Yu , Xinjie Ai , Huiying Xu , Zijian Qiu , Liming Xu , Jinfeng Ma , Jin Zhou , Chenxi Liu , Qingbo Zhao , Pinghua Li , Ruihua Huang","doi":"10.1016/j.ygeno.2025.111117","DOIUrl":"10.1016/j.ygeno.2025.111117","url":null,"abstract":"<div><div>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 <em>Sus scrofa</em> 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, <em>S100A12</em>, <em>XKR4</em> and <em>PENK</em>, 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.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111117"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145212461","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-01Epub Date: 2025-10-27DOI: 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。
{"title":"Genomic and physiological characterization of beer spoiling Megasphaera spp.","authors":"Manuel J. Arnold , Matthias A. Ehrmann , Yohanes N. Kurniawan , Koji Suzuki , Wolfgang Liebl","doi":"10.1016/j.ygeno.2025.111139","DOIUrl":"10.1016/j.ygeno.2025.111139","url":null,"abstract":"<div><div>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 (<em>M. cerevisiae</em>, <em>M. paucivorans</em> and <em>M. sueciensis</em>). 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 % (<em>v</em>/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.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111139"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145400499","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-01Epub Date: 2025-10-08DOI: 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。
{"title":"Strategic intercropping with mulberry (Morus alba L.) predictably modulates rhizosphere microbiome assembly and enriches pathways for secondary metabolite production","authors":"Zhou Hu , Yuheng Lei , Tianrui Li , Tingfu Zhang , Qian Yang , Jun Yang , Gaiqun Huang , Delong Guan , Jian Zou","doi":"10.1016/j.ygeno.2025.111129","DOIUrl":"10.1016/j.ygeno.2025.111129","url":null,"abstract":"<div><div>Intercropping is a key strategy for sustainable agriculture, but its effects on the rhizosphere microbiome remain poorly understood. Here, we investigated how intercropping mulberry (<em>Morus alba L.</em>) with functionally distinct partners—a nitrogen-fixing legume (<em>Pisum sativum</em>), a saprotrophic fungus (<em>Morchella esculenta</em>), and a medicinal plant (<em>Polygonatum sibiricum</em>)—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 <em>Bradyrhizobium</em> 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.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111129"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145274395","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-01Epub Date: 2025-10-08DOI: 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.
{"title":"Geogenomic mapping of drug-resistant Mycobacterium tuberculosis from Ireland and overseas","authors":"Cian Ennis , Gaetan Thilliez , Ronan F. O’Toole","doi":"10.1016/j.ygeno.2025.111132","DOIUrl":"10.1016/j.ygeno.2025.111132","url":null,"abstract":"<div><div>In this study, we performed an in-depth comparison of genome-sequenced <em>Mycobacterium tuberculosis</em> 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 <em>i.e.</em> 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 <em>M. tuberculosis</em> 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 <em>M. tuberculosis</em> 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.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111132"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145274306","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-01Epub Date: 2025-10-06DOI: 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.
{"title":"A bioinformatics pipeline for identifying homoplasmic and heteroplasmic mitochondrial DNA SNVs in single-cell RNA-Seq datasets","authors":"Zhiling Guan , Patrick Lindsey , Rick Kamps , Hubert J.M. Smeets","doi":"10.1016/j.ygeno.2025.111122","DOIUrl":"10.1016/j.ygeno.2025.111122","url":null,"abstract":"<div><div>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.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111122"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145250509","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-01Epub Date: 2025-09-08DOI: 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.
{"title":"A modular pipeline for evidence-integrated genome annotation across species: A case study on Schmidtea mediterranea","authors":"Anastasiia Zaremba, Małgorzata Marszałek-Zeńczak, Annasha Dutta, Anna Samelak-Czajka, Paulina Jackowiak","doi":"10.1016/j.ygeno.2025.111104","DOIUrl":"10.1016/j.ygeno.2025.111104","url":null,"abstract":"<div><div>Despite advancements in genome annotation tools, challenges persist for non-classical model organisms with limited genomic resources, such as <em>Schmidtea mediterranea</em>. 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 <em>de novo</em> 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 <em>S. mediterranea</em> 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 <span><span>https://github.com/Norreanea/SmedAnno</span><svg><path></path></svg></span>.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111104"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145033061","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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.
{"title":"scRNA-seq of Penaeus japonicus hemocytes under environmentally-induced restriction of sand-diving behavior","authors":"Huimin Zhang , Xinyu Zhou , Yang Zhang , Jiahan Yu , Junjie Qi , Jing Xu , Panpan Wang , Fei Yu , Jianxin Zhang , Huan Gao","doi":"10.1016/j.ygeno.2025.111125","DOIUrl":"10.1016/j.ygeno.2025.111125","url":null,"abstract":"<div><div><em>Penaeus japonicus</em> 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 (<em>HSP60</em>) and circadian rhythm genes (<em>period</em>, <em>timeless</em>) at different time points after stress induction, identifying 6 h post-transition as the timepoint with the most significant stress response (<em>p < 0.05</em>). 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 <em>P. japonicus.</em> RNA in situ hybridization localized <em>pxt</em>, <em>IGSF10</em>, and <em>IFI30</em> 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 (<em>p < 0.05</em>), 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 <em>P. japonicus</em> 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 <em>trpa1</em>, <em>trpm</em>, 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 <em>P. japonicus</em> and identifies candidate genes for future functional studies on behavioral regulation.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111125"},"PeriodicalIF":3.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145212372","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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