Pub Date : 2025-12-11DOI: 10.1016/j.ygeno.2025.111173
Fei Li , Jinbang Qin , Zhaomin Yao , Yiping Xu , Yabing Zhu , Yan Wang , Lan Huang , Wenxuan Luo , Zhiguo Wang , Fengfeng Zhou
N7-methylguanosine (m7G) is a common RNA modification linked to multiple diseases. Accurate detection of m7G sites is vital for elucidating its biological roles, but conventional methods are often laborious and costly. AI-based approaches offer alternatives, yet most rely on balanced datasets, ignoring real-world imbalances where negative samples vastly outnumber positives. This discrepancy may lead to overestimated model performance. To address this, we reconstructed independent test sets with low positive-to-negative ratios and benchmarked various models. We propose OCm7G, an ensemble of one-class classifiers with hierarchical thresholding. OCm7G achieves performance comparable to state-of-the-art methods on balanced sets and surpasses them in highly imbalanced scenarios, despite using only 52.5 % of the training data. Moreover, OCm7G offers interpretable predictions, aiding researchers in understanding model decisions. The source code and datasets are publicly available at: https://github.com/lidaosheng/OCm7G.
{"title":"OCm7G: An interpretable one-class predictor for m7G methylation sites trained with limit negative samples","authors":"Fei Li , Jinbang Qin , Zhaomin Yao , Yiping Xu , Yabing Zhu , Yan Wang , Lan Huang , Wenxuan Luo , Zhiguo Wang , Fengfeng Zhou","doi":"10.1016/j.ygeno.2025.111173","DOIUrl":"10.1016/j.ygeno.2025.111173","url":null,"abstract":"<div><div>N7-methylguanosine (m7G) is a common RNA modification linked to multiple diseases. Accurate detection of m7G sites is vital for elucidating its biological roles, but conventional methods are often laborious and costly. AI-based approaches offer alternatives, yet most rely on balanced datasets, ignoring real-world imbalances where negative samples vastly outnumber positives. This discrepancy may lead to overestimated model performance. To address this, we reconstructed independent test sets with low positive-to-negative ratios and benchmarked various models. We propose OCm7G, an ensemble of one-class classifiers with hierarchical thresholding. OCm7G achieves performance comparable to state-of-the-art methods on balanced sets and surpasses them in highly imbalanced scenarios, despite using only 52.5 % of the training data. Moreover, OCm7G offers interpretable predictions, aiding researchers in understanding model decisions. The source code and datasets are publicly available at: <span><span>https://github.com/lidaosheng/OCm7G</span><svg><path></path></svg></span>.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111173"},"PeriodicalIF":3.0,"publicationDate":"2025-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145752036","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 : 2025-12-09DOI: 10.1016/j.ygeno.2025.111172
Xueyan Ma , Lujie Wen , Dongpo Xu , Wu Jin , Haibo Wen , Huaishun Shen
Corbicula fluminea exhibits two distinct shell color morphs: yellow and black. This study reveals molecular mechanisms behind shell color variation in the Asian clam C. fluminea (yellow vs. black morphs) through comparative transcriptomics of edge/central mantle tissues. Transcriptome assembly identified 24, 174 annotated genes and 2, 234 novel genes. Comparative analyses revealed 238 common differentially expressed genes (DEGs) shared between the YC vs YE and BC vs BE comparisons, along with 575 DEGs in BC vs YC and 460 DEGs in BE vs YE. Transcriptomic profiling demonstrated that Biomineralization genes (calcium/organic matrix-related) showed region-specific expression, driving shell formation. Melanogenesis pathway enrichment and pigmentation genes (tyrosinase, calmodulin, sulfotransferase) may play an important role in pigmentation in C. fluminea. This study expands our understanding of shell biomineralization and pigment deposition in C. fluminea, providing important insights into the genetic and biochemical regulation of shell diversity in bivalves.
{"title":"Transcriptomic analysis of distinct mantle regions in yellow- and black-shelled Asian clam (Corbicula fluminea): Identification of genes associated with Shell biomineralization and pigment deposition","authors":"Xueyan Ma , Lujie Wen , Dongpo Xu , Wu Jin , Haibo Wen , Huaishun Shen","doi":"10.1016/j.ygeno.2025.111172","DOIUrl":"10.1016/j.ygeno.2025.111172","url":null,"abstract":"<div><div><em>Corbicula fluminea</em> exhibits two distinct shell color morphs: yellow and black. This study reveals molecular mechanisms behind shell color variation in the Asian clam <em>C. fluminea</em> (yellow vs. black morphs) through comparative transcriptomics of edge/central mantle tissues. Transcriptome assembly identified 24, 174 annotated genes and 2, 234 novel genes. Comparative analyses revealed 238 common differentially expressed genes (DEGs) shared between the YC vs YE and BC vs BE comparisons, along with 575 DEGs in BC vs YC and 460 DEGs in BE vs YE. Transcriptomic profiling demonstrated that Biomineralization genes (calcium/organic matrix-related) showed region-specific expression, driving shell formation. Melanogenesis pathway enrichment and pigmentation genes (tyrosinase, calmodulin, sulfotransferase) may play an important role in pigmentation in <em>C. fluminea</em>. This study expands our understanding of shell biomineralization and pigment deposition in <em>C. fluminea</em>, providing important insights into the genetic and biochemical regulation of shell diversity in bivalves.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111172"},"PeriodicalIF":3.0,"publicationDate":"2025-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145742021","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 : 2025-12-07DOI: 10.1016/j.ygeno.2025.111170
Bo Ma , Yang Liu , Xin Zhang , Jiayue Yin , Yanhong Wang , Lvping Zhang , Ting Chen , Yugang Wu , Chaoqun Hu , Peng Luo
Litopenaeus vannamei is a species of significant economic importance. In this study, we applied ATAC-seq and RNA-seq to compare shrimp from super-fast growth (SFG) and slow growth (SG) groups to investigate the mechanisms underlying growth performance. Chromatin accessibility was higher in the SFG group than SG group, and a total of 765 differentially accessible regions (DARs) were identified. Promoter-associated analysis of DARs-related genes revealed their predominant involvement in energy metabolism and cell proliferation. Transcriptome analysis indicated that genes related to molting and light reception may contribute to growth performance. Integrated analysis of ATAC-seq and RNA-seq data suggested that chromatin accessibility likely influences growth performance by modulating gene expression in key metabolic pathways, including amino acid metabolism, lipid metabolism, and immunity function. Additionally, LvNAGase was identified as a candidate gene regulating growth performance in L. vannamei.
{"title":"Differences in chromatin accessibility and gene expression associated with growth performance in Pacific whiteleg shrimp, Litopenaeus vannamei","authors":"Bo Ma , Yang Liu , Xin Zhang , Jiayue Yin , Yanhong Wang , Lvping Zhang , Ting Chen , Yugang Wu , Chaoqun Hu , Peng Luo","doi":"10.1016/j.ygeno.2025.111170","DOIUrl":"10.1016/j.ygeno.2025.111170","url":null,"abstract":"<div><div><em>Litopenaeus vannamei</em> is a species of significant economic importance. In this study, we applied ATAC-seq and RNA-seq to compare shrimp from super-fast growth (SFG) and slow growth (SG) groups to investigate the mechanisms underlying growth performance. Chromatin accessibility was higher in the SFG group than SG group, and a total of 765 differentially accessible regions (DARs) were identified. Promoter-associated analysis of DARs-related genes revealed their predominant involvement in energy metabolism and cell proliferation. Transcriptome analysis indicated that genes related to molting and light reception may contribute to growth performance. Integrated analysis of ATAC-seq and RNA-seq data suggested that chromatin accessibility likely influences growth performance by modulating gene expression in key metabolic pathways, including amino acid metabolism, lipid metabolism, and immunity function. Additionally, <em>LvNAGase</em> was identified as a candidate gene regulating growth performance in <em>L. vannamei.</em></div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111170"},"PeriodicalIF":3.0,"publicationDate":"2025-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145714046","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 : 2025-12-06DOI: 10.1016/j.ygeno.2025.111167
Joana Rolo , Ana Botelho , Diana Espadinha , Peder Worning , Rita Sobral , Henrik Westh , Maria Miragaia
Staphylococcus epidermidis recently emerged as a major cause of medical device-associated infections. However, the role of the nosocomial environment in its evolution remains poorly understood. To investigate the genomic changes underlying S. epidermidis evolutionary history, we compared genomes of 1960s isolates, before its recognition as a human pathogen, to those from the 1990s, when it became prevalent in hospital-acquired infections.
We found that S. epidermidis from the 1960s and 1990s shared similar population structures, with the A/C cluster predominating in both periods. Recombination was frequent, particularly in the A/C cluster, and occurred throughout the chromosome. Alterations in the mobile genetic elements of the 1990s isolates caused a drastic genomic change, characterized by phage loss, and staphylococcal cassette chromosome elements and insertion sequences acquisition. The 1990s isolates gained multiple antibiotic resistance and virulence genes, which are associated with biofilm formation and persistence. Genomic analysis of the orfX/rmlH vicinity revealed differences between the two groups of isolates. The 1960s isolates harbored a complex orfX/rmlH vicinity containing multiple SCC and pseudoSCC, and genes with high homology to SCCmecIV, while the 1990s isolates contained only SCCmec and ACME. Interestingly, one early isolate carried a disrupted mecA, within a pseudoSCCmecIV, suggesting it may represent a precursor to the contemporary SCCmecIV.
Our results showed that prolonged exposure to the hospital environment drove S. epidermidis genomic remodeling, including the accumulation of genes linked to antibiotic resistance, enhanced colonization, biofilm formation, genome plasticity, and the loss of bacteriophages –contributing to its success as a persistent nosocomial pathogen.
{"title":"Remodeling of Staphylococcus epidermidis genome over three decades of nosocomial exposure","authors":"Joana Rolo , Ana Botelho , Diana Espadinha , Peder Worning , Rita Sobral , Henrik Westh , Maria Miragaia","doi":"10.1016/j.ygeno.2025.111167","DOIUrl":"10.1016/j.ygeno.2025.111167","url":null,"abstract":"<div><div><em>Staphylococcus epidermidis</em> recently emerged as a major cause of medical device-associated infections. However, the role of the nosocomial environment in its evolution remains poorly understood. To investigate the genomic changes underlying <em>S. epidermidis</em> evolutionary history, we compared genomes of 1960s isolates, before its recognition as a human pathogen, to those from the 1990s, when it became prevalent in hospital-acquired infections.</div><div>We found that <em>S. epidermidis</em> from the 1960s and 1990s shared similar population structures, with the A/C cluster predominating in both periods. Recombination was frequent, particularly in the A/C cluster, and occurred throughout the chromosome. Alterations in the mobile genetic elements of the 1990s isolates caused a drastic genomic change, characterized by phage loss, and staphylococcal cassette chromosome elements and insertion sequences acquisition. The 1990s isolates gained multiple antibiotic resistance and virulence genes, which are associated with biofilm formation and persistence. Genomic analysis of the <em>orfX/rmlH</em> vicinity revealed differences between the two groups of isolates. The 1960s isolates harbored a complex <em>orfX/rmlH</em> vicinity containing multiple SCC and pseudoSCC, and genes with high homology to SCC<em>mec</em>IV, while the 1990s isolates contained only SCC<em>mec</em> and ACME. Interestingly, one early isolate carried a disrupted <em>mecA</em>, within a pseudoSCC<em>mec</em>IV, suggesting it may represent a precursor to the contemporary SCC<em>mec</em>IV.</div><div>Our results showed that prolonged exposure to the hospital environment drove <em>S. epidermidis</em> genomic remodeling, including the accumulation of genes linked to antibiotic resistance, enhanced colonization, biofilm formation, genome plasticity, and the loss of bacteriophages –contributing to its success as a persistent nosocomial pathogen.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111167"},"PeriodicalIF":3.0,"publicationDate":"2025-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145707477","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 : 2025-12-06DOI: 10.1016/j.ygeno.2025.111169
Dionysios Fanidis , Eirini Moutsouri , Apostolos Malatras , Alan R. Shuldiner , Anna Alkelai , Christiana Polydorou , Gregory Papagregoriou , Constantinos Deltas
Understanding a population's genetic landscape is essential for the effective implementation of precision medicine strategies. Leveraging exome sequencing data from biobank.cy general-population participants, we assessed the prevalence of medically actionable variants based on ACMG recommendations. To minimize classifier-specific bias, we applied three complementary pathogenicity assignment methods shaping a core and an extended set of alleles, identifying actionable variants in ∼4–5 % of Cypriot individuals. Cardiovascular and cancer-related variants accounted for most findings, with genes such as LDLR, PALB2, RYR1 and HNF1A contributing significantly to the mutational burden. Comparative analyses against other cohorts revealed 19 enriched and 4 unique actionable variants in Cyprus. While most findings overlap with broader populations, this study underscores Cyprus's distinct genetic profile shaped by its complex demographic history. Our findings provide actionable insights for healthcare planning, support population-specific genomic screening programs development, and contribute to the global effort to refine precision medicine applications.
{"title":"Medically actionable DNA variants have a prevalence of 5 % in the Cyprus genetic landscape","authors":"Dionysios Fanidis , Eirini Moutsouri , Apostolos Malatras , Alan R. Shuldiner , Anna Alkelai , Christiana Polydorou , Gregory Papagregoriou , Constantinos Deltas","doi":"10.1016/j.ygeno.2025.111169","DOIUrl":"10.1016/j.ygeno.2025.111169","url":null,"abstract":"<div><div>Understanding a population's genetic landscape is essential for the effective implementation of precision medicine strategies. Leveraging exome sequencing data from biobank.cy general-population participants, we assessed the prevalence of medically actionable variants based on ACMG recommendations. To minimize classifier-specific bias, we applied three complementary pathogenicity assignment methods shaping a core and an extended set of alleles, identifying actionable variants in ∼4–5 % of Cypriot individuals. Cardiovascular and cancer-related variants accounted for most findings, with genes such as <em>LDLR, PALB2, RYR1</em> and <em>HNF1A</em> contributing significantly to the mutational burden. Comparative analyses against other cohorts revealed 19 enriched and 4 unique actionable variants in Cyprus. While most findings overlap with broader populations, this study underscores Cyprus's distinct genetic profile shaped by its complex demographic history. Our findings provide actionable insights for healthcare planning, support population-specific genomic screening programs development, and contribute to the global effort to refine precision medicine applications.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111169"},"PeriodicalIF":3.0,"publicationDate":"2025-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145707497","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 : 2025-12-06DOI: 10.1016/j.ygeno.2025.111168
Lucie Šislerová , Michal Petrovič , Michaela Dobrovolná , Jiří Šťastný , Tomaz Rozmaric , Helene Dworak , Libuše Kratochvilová , Lenka Veselá , Barbara Schädl , Florian Gruber , Johannes Grillari , Christian Freystätter , Mikolaj Ogrodnik , Václav Brázda
Sus scrofa is not only a key agricultural species but also a valuable biomedical model due to its physiological and anatomical similarities to humans. We present a comprehensive genome-wide analysis of putative G-quadruplex-forming sequences (PQS) in the pig genome, with a focus on their distribution within regulatory and functionally relevant genomic regions. Our results demonstrate that PQS are non-randomly distributed, showing significant enrichment in promoter regions, untranslated regions, and other regulatory elements. These distribution patterns closely parallel those observed in the human genome, suggesting a conserved role for G-quadruplexes (G4s) across species. Importantly, we provide experimental validation of G4 structures in cells in situ of porcine dorsal skin samples using the G4-specific antibody SG4, confirming their presence at the cellular level. The high degree of similarity in PQS localization between pigs and humans highlights the translational potential of Sus scrofa for studying G4 biology and evaluating G4-targeted therapeutic strategies.
{"title":"G-quadruplex motifs prediction and visualization in Sus scrofa genome","authors":"Lucie Šislerová , Michal Petrovič , Michaela Dobrovolná , Jiří Šťastný , Tomaz Rozmaric , Helene Dworak , Libuše Kratochvilová , Lenka Veselá , Barbara Schädl , Florian Gruber , Johannes Grillari , Christian Freystätter , Mikolaj Ogrodnik , Václav Brázda","doi":"10.1016/j.ygeno.2025.111168","DOIUrl":"10.1016/j.ygeno.2025.111168","url":null,"abstract":"<div><div><em>Sus scrofa</em> is not only a key agricultural species but also a valuable biomedical model due to its physiological and anatomical similarities to humans. We present a comprehensive genome-wide analysis of putative G-quadruplex-forming sequences (PQS) in the pig genome, with a focus on their distribution within regulatory and functionally relevant genomic regions. Our results demonstrate that PQS are non-randomly distributed, showing significant enrichment in promoter regions, untranslated regions, and other regulatory elements. These distribution patterns closely parallel those observed in the human genome, suggesting a conserved role for G-quadruplexes (G4s) across species. Importantly, we provide experimental validation of G4 structures in cells in situ of porcine dorsal skin samples using the G4-specific antibody SG4, confirming their presence at the cellular level. The high degree of similarity in PQS localization between pigs and humans highlights the translational potential of <em>Sus scrofa</em> for studying G4 biology and evaluating G4-targeted therapeutic strategies.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111168"},"PeriodicalIF":3.0,"publicationDate":"2025-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145707305","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 : 2025-12-05DOI: 10.1016/j.ygeno.2025.111166
Peng Yu , Xia Wei , Abdur Rahman Ansari , Xiao Yu Niu , Meng Qi Lu , Tong Wu , Xin Ying Xue , Wei Hua Zou , Ke Li Yang , Hui Song
Porcine Circovirus type 2 (PCV2) is recognized as the smallest animal virus known to cause reproductive failure in sows and can be vertically transmitted through the placenta to infect piglets, leading to Postweaning Multisystemic Wasting Syndrome (PMWS). Long non-coding RNAs (lncRNAs) are involved in numerous physiological and pathological processes, closely related to trophoblast cell invasion, placental development, and fetal growth restriction. To investigate whether PCV2 can infect porcine placental trophoblast cells and to characterize the lncRNA-mRNA expression profiles following infection, this study infected porcine placental trophoblast cells with PCV2 and conducted comparative transcriptome analysis between infected and uninfected cells, followed by qPCR validation of sequencing results. The study confirmed that PCV2 successfully infects porcine placental trophoblast cells, identifying 1714 differentially expressed mRNAs and 254 differentially expressed lncRNAs post-infection. Functional enrichment analysis demonstrated that PCV2 infection modulates the growth and immune responses of porcine placental trophoblast cells. Furthermore, target genes of the differentially expressed lncRNAs were identified through colocalization and coexpression analyses. GO enrichment analysis based on the target genes of the differentially expressed lncRNAs showed abundant transcription in biological processes such as metabolism and regulation of ER-to-Golgi transport, and pathway analysis indicated that PCV2 infection impacts cell cycle, TNF, and IL-17 signaling pathways. This study reveals PCV2's infectivity in porcine placental trophoblast cells, provides the lncRNA-mRNA expression profiles post-infection, and offers critical insights for understanding PCV2's impacts and advancing lncRNA research.
{"title":"PCV2 infects porcine placental trophoblast cells and remodels the lncRNA-mRNA regulatory network","authors":"Peng Yu , Xia Wei , Abdur Rahman Ansari , Xiao Yu Niu , Meng Qi Lu , Tong Wu , Xin Ying Xue , Wei Hua Zou , Ke Li Yang , Hui Song","doi":"10.1016/j.ygeno.2025.111166","DOIUrl":"10.1016/j.ygeno.2025.111166","url":null,"abstract":"<div><div>Porcine Circovirus type 2 (PCV2) is recognized as the smallest animal virus known to cause reproductive failure in sows and can be vertically transmitted through the placenta to infect piglets, leading to Postweaning Multisystemic Wasting Syndrome (PMWS). Long non-coding RNAs (lncRNAs) are involved in numerous physiological and pathological processes, closely related to trophoblast cell invasion, placental development, and fetal growth restriction. To investigate whether PCV2 can infect porcine placental trophoblast cells and to characterize the lncRNA-mRNA expression profiles following infection, this study infected porcine placental trophoblast cells with PCV2 and conducted comparative transcriptome analysis between infected and uninfected cells, followed by qPCR validation of sequencing results. The study confirmed that PCV2 successfully infects porcine placental trophoblast cells, identifying 1714 differentially expressed mRNAs and 254 differentially expressed lncRNAs post-infection. Functional enrichment analysis demonstrated that PCV2 infection modulates the growth and immune responses of porcine placental trophoblast cells. Furthermore, target genes of the differentially expressed lncRNAs were identified through colocalization and coexpression analyses. GO enrichment analysis based on the target genes of the differentially expressed lncRNAs showed abundant transcription in biological processes such as metabolism and regulation of ER-to-Golgi transport, and pathway analysis indicated that PCV2 infection impacts cell cycle, TNF, and IL-17 signaling pathways. This study reveals PCV2's infectivity in porcine placental trophoblast cells, provides the lncRNA-mRNA expression profiles post-infection, and offers critical insights for understanding PCV2's impacts and advancing lncRNA research.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111166"},"PeriodicalIF":3.0,"publicationDate":"2025-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145700484","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 : 2025-11-30DOI: 10.1016/j.ygeno.2025.111165
Mengxian Cai , Wenqing Zhang , Zhengren Chen , Yang Peng , Zenghui Wang , Jing Ou , Tuo Zeng
The Magnoliaceae family represents one of the most ancient angiosperm lineage and provides key insights into early flowering plant evolution. Woonyoungia septentrionalis is an endangered dioecious tree endemic to the karst regions of Southwest China, with small and fragmented populations threatened by habitat loss and low reproductive success. Here, we generated a high-quality chromosome-scale genome assembly of W. septentrionalis with an assembled genome size of 2.62 Gb and 98.9 % completeness based on BUSCO. Repetitive elements occupy 81.23 % of the genome, dominated by long terminal repeat retrotransposons. Ks-based analysis revealed an ancestral whole-genome duplication event around 65 Mya shared with Magnolia species. Phylogenomic analyses indicated that W. septentrionalis represents the earliest diverging lineage within Magnolia sensu lato, reflecting its distinct evolutionary position. Comparative and transcriptomic analyses identified gene family expansions and sex-biased regulatory networks, including hub genes such as MCM2–MCM7, and transcription factors SPL, TCP, and ERF, which may be involved in floral organ differentiation and dioecy formation. This reference genome provides a valuable resource for exploring the molecular basis of reproductive specialization and evolutionary diversification in Magnoliaceae, and supports conservation efforts for this endangered species.
木兰科代表了最古老的被子植物谱系之一，并为早期开花植物的进化提供了关键的见解。乌龙木是中国西南喀斯特地区特有的一种濒危雌雄异株乔木，种群小而分散，生境丧失，繁殖成功率低。在此，我们基于BUSCO构建了高质量的七毛线虫染色体尺度基因组组装，组装的基因组大小为2.62 Gb，完整性为98.9 %。重复元件占基因组的81.23 %，以长末端重复反转录转座子为主。基于ks的分析显示，木兰物种共有约65亿年前的祖先全基因组复制事件。系统基因组学分析表明，白玉兰属属（W. septentrionalis）是厚朴属（Magnolia sensu lato）中最早分化的分支，反映了其独特的进化地位。通过比较和转录组学分析，发现了基因家族扩展和性别偏向调控网络，包括枢纽基因如MCM2-MCM7和转录因子SPL、TCP和ERF，这些基因可能参与花器官分化和雌雄异株形成。该参考基因组为探索木兰科植物生殖专门化和进化多样化的分子基础提供了宝贵的资源，并为木兰科濒危物种的保护工作提供了支持。
{"title":"Chromosome-scale genome of Woonyoungia septentrionalis provides insights into sex differentiation and genomic evolution in Magnoliaceae","authors":"Mengxian Cai , Wenqing Zhang , Zhengren Chen , Yang Peng , Zenghui Wang , Jing Ou , Tuo Zeng","doi":"10.1016/j.ygeno.2025.111165","DOIUrl":"10.1016/j.ygeno.2025.111165","url":null,"abstract":"<div><div>The Magnoliaceae family represents one of the most ancient angiosperm lineage and provides key insights into early flowering plant evolution. <em>Woonyoungia septentrionalis</em> is an endangered dioecious tree endemic to the karst regions of Southwest China, with small and fragmented populations threatened by habitat loss and low reproductive success. Here, we generated a high-quality chromosome-scale genome assembly of <em>W. septentrionalis</em> with an assembled genome size of 2.62 Gb and 98.9 % completeness based on BUSCO. Repetitive elements occupy 81.23 % of the genome, dominated by long terminal repeat retrotransposons. Ks-based analysis revealed an ancestral whole-genome duplication event around 65 Mya shared with <em>Magnolia</em> species. Phylogenomic analyses indicated that <em>W. septentrionalis</em> represents the earliest diverging lineage within <em>Magnolia</em> sensu lato, reflecting its distinct evolutionary position. Comparative and transcriptomic analyses identified gene family expansions and sex-biased regulatory networks, including hub genes such as MCM2–MCM7, and transcription factors SPL, TCP, and ERF, which may be involved in floral organ differentiation and dioecy formation. This reference genome provides a valuable resource for exploring the molecular basis of reproductive specialization and evolutionary diversification in <em>Magnoliaceae</em>, and supports conservation efforts for this endangered species.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111165"},"PeriodicalIF":3.0,"publicationDate":"2025-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145660880","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 : 2025-11-29DOI: 10.1016/j.ygeno.2025.111159
Yi Wu , Lina Zhu , Xuejiao An , Yaojing Yue
Spermatogenesis is a highly regulated biological process involving various cell types, making the accurate identification and classification of different cell populations challenging. Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for resolving cellular heterogeneity at high resolution. In this study, 10× Genomics Chromium™ scRNA-seq was employed to analyze 15,826 testicular cells from three 6-month-old sexually mature Hu sheep, and a high-resolution single-cell transcriptomic atlas was generated. Specifically, six somatic cell subtypes and five germ cell subtypes were identified, which revealed the differentiation trajectory of spermatogenesis. Notably, pseudo-time analysis suggested that Leydig cells and peritubular myoid cells may originate from a common progenitor lineage in sheep. Highly expressed genes were enriched in pathways such as cAMP signaling, PI3K-Akt, and ECM–receptor interaction. Furthermore, immunohistochemical analysis validated specific marker proteins for certain cell types. Collectively, these findings provide novel insights into spermatogenesis and serve as a valuable reference for the in vitro culture of male germ cells.
{"title":"Single-cell RNA sequencing reveals a cellular atlas of the sheep testis","authors":"Yi Wu , Lina Zhu , Xuejiao An , Yaojing Yue","doi":"10.1016/j.ygeno.2025.111159","DOIUrl":"10.1016/j.ygeno.2025.111159","url":null,"abstract":"<div><div>Spermatogenesis is a highly regulated biological process involving various cell types, making the accurate identification and classification of different cell populations challenging. Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for resolving cellular heterogeneity at high resolution. In this study, 10× Genomics Chromium™ scRNA-seq was employed to analyze 15,826 testicular cells from three 6-month-old sexually mature Hu sheep, and a high-resolution single-cell transcriptomic atlas was generated. Specifically, six somatic cell subtypes and five germ cell subtypes were identified, which revealed the differentiation trajectory of spermatogenesis. Notably, pseudo-time analysis suggested that Leydig cells and peritubular myoid cells may originate from a common progenitor lineage in sheep. Highly expressed genes were enriched in pathways such as cAMP signaling, PI3K-Akt, and ECM–receptor interaction. Furthermore, immunohistochemical analysis validated specific marker proteins for certain cell types. Collectively, these findings provide novel insights into spermatogenesis and serve as a valuable reference for the in vitro culture of male germ cells.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111159"},"PeriodicalIF":3.0,"publicationDate":"2025-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145653889","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 : 2025-11-28DOI: 10.1016/j.ygeno.2025.111161
Weijuan Cai , Kunying Chong , Bo Zhou , Yanni Zhao , Binchang Lao , Liang Yin
Aging is an important pathological basis of age-related diseases. However, the similarities and differences among different types of senescent cells of different species and their role in normal homeostasis are poorly understood. Herein, in order to comprehensively map age-related transcriptome changes in multiple tissues of vertebrates during the ageing process, we analyzed 581 samples from 54 aging transcriptome datasets spanning 4 species including Homo sapiens, Mus musculus, Rattus norvegicus and Danio rerio, and identified the novel age-related differentially expressed genes, and obtained specific enriched expression of age-related pathways. Protein-protein interactions of differentially expressed genes in different species with the PTPRC or CD45 as the core were predicted. Through this study, we screened the key biomarkers and signaling pathways that regulate the aging process of tissues and organs in multiple species, which is of great significance for improving age-related tissues and organs by identifying senescent cells.
{"title":"Comprehensive analysis of multiple species identifies novel molecular signatures and pathways involved in aging","authors":"Weijuan Cai , Kunying Chong , Bo Zhou , Yanni Zhao , Binchang Lao , Liang Yin","doi":"10.1016/j.ygeno.2025.111161","DOIUrl":"10.1016/j.ygeno.2025.111161","url":null,"abstract":"<div><div>Aging is an important pathological basis of age-related diseases. However, the similarities and differences among different types of senescent cells of different species and their role in normal homeostasis are poorly understood. Herein, in order to comprehensively map age-related transcriptome changes in multiple tissues of vertebrates during the ageing process, we analyzed 581 samples from 54 aging transcriptome datasets spanning 4 species including Homo sapiens, Mus musculus, Rattus norvegicus and Danio rerio, and identified the novel age-related differentially expressed genes, and obtained specific enriched expression of age-related pathways. Protein-protein interactions of differentially expressed genes in different species with the PTPRC or CD45 as the core were predicted. Through this study, we screened the key biomarkers and signaling pathways that regulate the aging process of tissues and organs in multiple species, which is of great significance for improving age-related tissues and organs by identifying senescent cells.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111161"},"PeriodicalIF":3.0,"publicationDate":"2025-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145648190","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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