Pub Date : 2026-03-01Epub Date: 2026-02-23DOI: 10.1016/j.ygeno.2026.111222
Oliver Brown , Andressa Oliveira de Lima , Yvonne Drechsler , R. David Hawkins
INFO GRAB is an interactive Shiny application designed for efficient exploration and visualization of gene expression data from chicken tissues and cell types. It integrates differential expression, tissue-specific expression, and allele-specific expression functionalities, supported by advanced plotting features, such as volcano plots, heatmaps, PCA, and correlation, as well as an embedded genome viewer. By leveraging DESeq2, Tau-based metrics, and curated multi-omic data, INFO GRAB provides a streamlined, user-friendly approach to large-scale transcriptomic analyses. This tool empowers researchers to investigate regulatory mechanisms and complex genetic traits, advancing poultry genomics and related biological research.
INFO GRAB是一个交互式的Shiny应用程序，旨在有效地探索和可视化鸡组织和细胞类型的基因表达数据。它集成了差异表达、组织特异性表达和等位基因特异性表达功能，由高级绘图功能支持，如火山图、热图、PCA和相关性，以及嵌入式基因组查看器。通过利用DESeq2、基于tau的指标和精心策划的多组学数据，INFO GRAB为大规模转录组学分析提供了一种简化、用户友好的方法。该工具使研究人员能够调查调节机制和复杂的遗传性状，推进家禽基因组学和相关生物学研究。
{"title":"INFO GRAB: An interactive shiny application for gene expression analysis and visualization","authors":"Oliver Brown , Andressa Oliveira de Lima , Yvonne Drechsler , R. David Hawkins","doi":"10.1016/j.ygeno.2026.111222","DOIUrl":"10.1016/j.ygeno.2026.111222","url":null,"abstract":"<div><div>INFO GRAB is an interactive Shiny application designed for efficient exploration and visualization of gene expression data from chicken tissues and cell types. It integrates differential expression, tissue-specific expression, and allele-specific expression functionalities, supported by advanced plotting features, such as volcano plots, heatmaps, PCA, and correlation, as well as an embedded genome viewer. By leveraging DESeq2, Tau-based metrics, and curated multi-omic data, INFO GRAB provides a streamlined, user-friendly approach to large-scale transcriptomic analyses. This tool empowers researchers to investigate regulatory mechanisms and complex genetic traits, advancing poultry genomics and related biological research.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111222"},"PeriodicalIF":3.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147304365","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 : 2026-03-01Epub Date: 2026-02-09DOI: 10.1016/j.ygeno.2026.111213
Sijia Ma , Hui Bai , Lidong Han , Yijing Zhu , Anping Xie , Ruilin Fang , Xvhui Hu , Liguo Zhang , Chao Bian , Xiaohu Su
The Small-Tailed Han (STH) sheep milk has significantly higher fat and protein than DairyMeade (DM) sheep milk. Further study found that the expression of whey protein secretoglobin family 2 A member 2 (SCGB2A2) in STH sheep milk was significantly higher than in DM sheep milk. Thus we surmise that the SCGB2A2 may be involved in the regulation of the mammary biological function. Here, the expression of SCGB2A2 at different lactation periods was detected first. Then the cell proliferation and milk component synthesis effects on ovine mammary epithelial cells (OMECs) were analyzed. And the CUT&Tag analysis was used to identify SCGB2A2 target binding sites at the genome. The transcriptome of SCGB2A2 overexpression and knockdown OMECs was analyzed. Two co-analyses were conducted to further screen out SCGB2A2 potential target genes. Finally, the potential interacting protein was verified by CO-IP and UHLP-MS analysis. Results showed that the SCGB2A2 was expressed highest at the colostrum stage and lowest at the dry milk stage. Immunohistochemical analysis showed that it was mainly expressed in mammary epithelial cells. CCK8 and cell cycle analysis showed that SCGB2A2 promotes the OMECs proliferation. Milk components synthesis detection found that the SCGB2A2 was positively correlated with the CSN2, lactose, and triglyceride (TG). CUT&Tag and transcriptome co-analyses found that 20 genes were consistently detected, including FBP2, IFIT3 and so on. CO-IP analysis demonstrated that mTOR interacted with SCGB2A2. Taken together, we demonstrated that SCGB2A2 plays a positive role in OMECs proliferation and biosynthesis of milk components. Some SCGB2A2 direct regulated genes are involved in the cell proliferation. The regulation of SCGB2A2 for milk components biosynthesis mainly interacts with mTOR. However, the specific regulatory mechanism is needed to further study.
{"title":"Effects study of SCGB2A2 on cell proliferation and milk components biosynthesis in ovine mammary epithelial cells","authors":"Sijia Ma , Hui Bai , Lidong Han , Yijing Zhu , Anping Xie , Ruilin Fang , Xvhui Hu , Liguo Zhang , Chao Bian , Xiaohu Su","doi":"10.1016/j.ygeno.2026.111213","DOIUrl":"10.1016/j.ygeno.2026.111213","url":null,"abstract":"<div><div>The Small-Tailed Han (STH) sheep milk has significantly higher fat and protein than DairyMeade (DM) sheep milk. Further study found that the expression of whey protein secretoglobin family 2 A member 2 (SCGB2A2) in STH sheep milk was significantly higher than in DM sheep milk. Thus we surmise that the SCGB2A2 may be involved in the regulation of the mammary biological function. Here, the expression of SCGB2A2 at different lactation periods was detected first. Then the cell proliferation and milk component synthesis effects on ovine mammary epithelial cells (OMECs) were analyzed. And the CUT&Tag analysis was used to identify SCGB2A2 target binding sites at the genome. The transcriptome of <em>SCGB2A2</em> overexpression and knockdown OMECs was analyzed. Two co-analyses were conducted to further screen out SCGB2A2 potential target genes. Finally, the potential interacting protein was verified by CO-IP and UHLP-MS analysis. Results showed that the SCGB2A2 was expressed highest at the colostrum stage and lowest at the dry milk stage. Immunohistochemical analysis showed that it was mainly expressed in mammary epithelial cells. CCK8 and cell cycle analysis showed that SCGB2A2 promotes the OMECs proliferation. Milk components synthesis detection found that the SCGB2A2 was positively correlated with the CSN2, lactose, and triglyceride (TG). CUT&Tag and transcriptome co-analyses found that 20 genes were consistently detected, including <em>FBP2</em>, <em>IFIT3</em> and so on. CO-IP analysis demonstrated that mTOR interacted with SCGB2A2. Taken together, we demonstrated that SCGB2A2 plays a positive role in OMECs proliferation and biosynthesis of milk components. Some SCGB2A2 direct regulated genes are involved in the cell proliferation. The regulation of SCGB2A2 for milk components biosynthesis mainly interacts with mTOR. However, the specific regulatory mechanism is needed to further study.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111213"},"PeriodicalIF":3.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146165026","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 : 2026-03-01Epub Date: 2026-02-08DOI: 10.1016/j.ygeno.2026.111212
Mayra N. Mendoza Cerna , Sam Stroupe , Ellie Kolb , Matthew Jevit , Shumin Li , Terje Raudsepp , Brian W. Davis
The alpaca (Vicugna pacos) genome poses assembly challenges due to pervasive complex repetitive sequences accounting for approximately 16% of the genome resulting in assembly errors, gaps, and collapsed sequences that have impacted both the quality and completeness of previous alpaca genomes. Here we used PacBio HiFi long reads, Hi-C chromatin conformation capture, optical genome mapping, and manual curation to construct VicPac4, a 2.6Gb alpaca genome of which 2.1Gb is assembled into 36 alpaca autosomes and the X chromosome, each represented by a single scaffold. While all chromosomes improved in size and contiguity, the X chromosome showed the greatest improvement and allowed demarcation of the 6.2 Mb pseudoautosomal region. VicPac4 incorporates several previously unresolved repetitive regions, such as telomeres in 30 chromosomes, nucleolus organizer regions (NORs) in two chromosomes, and 15 tentative centromeres. Notably, we identified a novel tandemly repeated satellite (SAT) exclusive to South American camelids (SAC). The SAC-SAT, with a 267 bp repeat motif, constitutes 2.42% of the alpaca genome and colocalizes with NORs in all SAC species. As most NORs remained unassigned, their numbers and chromosomal locations in camelids were studied by FISH and Oligo-FISH, revealing extensive dynamism across chromosomes, individuals and species. Resolution of NOR positional variation is essential to the understanding of rDNA-associated disease such as minute chromosome syndrome, which induces infertility in female alpacas. Until the development of telomere-to-telomere resources, VicPac4 stands as the most complete and accurate reference among South American camelids, offering a powerful resource to capture genetic variation in the species and advance genomics of alpaca biology and populations.
{"title":"Alpaca chromosome-level reference genome VicPac4 reveals a novel NOR-associated satellite specific to south American camelids","authors":"Mayra N. Mendoza Cerna , Sam Stroupe , Ellie Kolb , Matthew Jevit , Shumin Li , Terje Raudsepp , Brian W. Davis","doi":"10.1016/j.ygeno.2026.111212","DOIUrl":"10.1016/j.ygeno.2026.111212","url":null,"abstract":"<div><div>The alpaca (<em>Vicugna pacos</em>) genome poses assembly challenges due to pervasive complex repetitive sequences accounting for approximately 16% of the genome resulting in assembly errors, gaps, and collapsed sequences that have impacted both the quality and completeness of previous alpaca genomes. Here we used PacBio HiFi long reads, Hi-C chromatin conformation capture, optical genome mapping, and manual curation to construct VicPac4, a 2.6Gb alpaca genome of which 2.1Gb is assembled into 36 alpaca autosomes and the X chromosome, each represented by a single scaffold. While all chromosomes improved in size and contiguity, the X chromosome showed the greatest improvement and allowed demarcation of the 6.2 Mb pseudoautosomal region. VicPac4 incorporates several previously unresolved repetitive regions, such as telomeres in 30 chromosomes, nucleolus organizer regions (NORs) in two chromosomes, and 15 tentative centromeres. Notably, we identified a novel tandemly repeated satellite (SAT) exclusive to South American camelids (SAC). The SAC-SAT, with a 267 bp repeat motif, constitutes 2.42% of the alpaca genome and colocalizes with NORs in all SAC species. As most NORs remained unassigned, their numbers and chromosomal locations in camelids were studied by FISH and Oligo-FISH, revealing extensive dynamism across chromosomes, individuals and species. Resolution of NOR positional variation is essential to the understanding of rDNA-associated disease such as minute chromosome syndrome, which induces infertility in female alpacas. Until the development of telomere-to-telomere resources, VicPac4 stands as the most complete and accurate reference among South American camelids, offering a powerful resource to capture genetic variation in the species and advance genomics of alpaca biology and populations.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111212"},"PeriodicalIF":3.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146156700","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 : 2026-03-01Epub Date: 2026-02-09DOI: 10.1016/j.ygeno.2026.111218
Yiting Wang , Cheng Liu , Zhen Wang , Zhe Zhang , Qishan Wang , Zitao Chen , Yuchun Pan
The Jinhua (JH) pig is a renowned Chinese indigenous breed distinguished by their two-end black phenotype, serve as the exclusive genetic resource for producing Jinhua ham. However, there is currently limited knowledge about the genetic structure and characteristics of JH pigs. This study employed whole-genome sequencing of 1238 individuals representing 67 breeds/lines to elucidate the genetic architecture of JH pigs. Population structure analysis revealed five distinct geographic clusters within Chinese indigenous pigs (North China/CCN, Central China/CCN, East China/ECN, South China/SCN, Southwest China/SWCN), with JH forming an early-diverging lineage in the ECN group exhibiting unique ancestry patterns. Genome-wide scans identified 7995 signatures of positive selection (iSAFE; FDR < 0.05). These signals were enriched in pathways related to immunity, neurodevelopment, and lipid metabolism. Key candidate genes (CLEC7A, D2HGDH, NOVA1) demonstrated breed-specific expression. Balancing selection analysis detected 4630 signals converging on PLA2G2A, a metabolic hub gene influencing intramuscular fat deposition. Two haplotypes (Hap1:41%; Hap2:59%) exhibited antagonistic pleiotropy: Hap1 was associated with enhanced growth performance, whereas Hap2 correlated with superior carcass quality. Our integrative analysis demonstrates that germplasm traits of JH pigs, including tender marbling, disease resilience, and roughage utilization efficiency, result from synergistic effects of directional selection on metabolic/immune genes and balancing selection maintaining fitness trade-offs. This study establishes a framework for delineating adaptive mechanisms in indigenous livestock, providing critical insights for genomic conservation and precision breeding.
{"title":"From genomes to phenomes: Multi-omics dissection of positive and balancing selection in Jinhua pig","authors":"Yiting Wang , Cheng Liu , Zhen Wang , Zhe Zhang , Qishan Wang , Zitao Chen , Yuchun Pan","doi":"10.1016/j.ygeno.2026.111218","DOIUrl":"10.1016/j.ygeno.2026.111218","url":null,"abstract":"<div><div>The Jinhua (JH) pig is a renowned Chinese indigenous breed distinguished by their two-end black phenotype, serve as the exclusive genetic resource for producing Jinhua ham. However, there is currently limited knowledge about the genetic structure and characteristics of JH pigs. This study employed whole-genome sequencing of 1238 individuals representing 67 breeds/lines to elucidate the genetic architecture of JH pigs. Population structure analysis revealed five distinct geographic clusters within Chinese indigenous pigs (North China/CCN, Central China/CCN, East China/ECN, South China/SCN, Southwest China/SWCN), with JH forming an early-diverging lineage in the ECN group exhibiting unique ancestry patterns. Genome-wide scans identified 7995 signatures of positive selection (iSAFE; FDR < 0.05). These signals were enriched in pathways related to immunity, neurodevelopment, and lipid metabolism. Key candidate genes (<em>CLEC7A</em>, <em>D2HGDH</em>, <em>NOVA1</em>) demonstrated breed-specific expression. Balancing selection analysis detected 4630 signals converging on <em>PLA2G2A</em>, a metabolic hub gene influencing intramuscular fat deposition. Two haplotypes (Hap1:41%; Hap2:59%) exhibited antagonistic pleiotropy: Hap1 was associated with enhanced growth performance, whereas Hap2 correlated with superior carcass quality. Our integrative analysis demonstrates that germplasm traits of JH pigs, including tender marbling, disease resilience, and roughage utilization efficiency, result from synergistic effects of directional selection on metabolic/immune genes and balancing selection maintaining fitness trade-offs. This study establishes a framework for delineating adaptive mechanisms in indigenous livestock, providing critical insights for genomic conservation and precision breeding.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111218"},"PeriodicalIF":3.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146164983","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 : 2026-03-01Epub Date: 2026-01-08DOI: 10.1016/j.ygeno.2026.111196
Qi Guo , Yue Zhang , Xin Gui , Lijuan Zhong , Rong Zhong , Yan Jiang , Hongbo Qi
Background
Copy number variations (CNVs) are significant contributors to genetic disorders, making their accurate detection crucial for prenatal diagnosis. While clinical whole exome sequencing (cWES) is increasingly used to identify sequence variants in prenatal samples, the feasibility of using the same cWES data to detect CNVs remains underexplored, particularly in amniotic fluid samples.
Methods
We systematically evaluated seven CNV detection tools (CANOES, CODEX2, CLAMMS, ExomeDepth, XHMM, CNVkit, and GATK/gCNV) across various experimental conditions. Using 132 amniotic fluid (AF) samples, we assessed the impact of control sample type (AF and PB), CNV characteristics (including exon coverage and length), and tool integration strategies on detection accuracy. Performance was evaluated against CNV-seq results as the gold standard, with special focus on detecting pathogenic CNVs.
Results
The choice of control sample substantially influenced detection performance, with PB generally yielding better results than AF. CNV characteristics, particularly exon coverage, clearly affected detection rates, with multi-exon CNVs being more reliably detected than single-exon variants. Individual tools demonstrated varying capabilities, with CANOES achieving the highest recall rate for pathogenic CNVs (70.3%) but all tools showing limited precision (highest 3.4%). Integration of multiple tools appeared to improve overall detection capability for pathogenic variations. This study suggests that effective optimization of WES-based CNV detection should consider control-sample selection, CNV characteristics, and multi-tool integration. While the current precision limitations indicate that WES-based CNV detection cannot yet replace dedicated CNV-seq testing, the findings may inform strategies to streamline prenatal diagnostic workflows by using WES data as an initial CNV screening step, potentially helping to reduce unnecessary additional testing in selected cases.
Conclusion
These findings contribute to developing more effective and efficient genetic testing strategies in prenatal clinical settings, offering a foundation for future improvements in WES-based CNV detection methods.
{"title":"Evaluation of CNV detection tools for prenatal diagnosis using amniotic fluid clinical whole-exome sequencing data","authors":"Qi Guo , Yue Zhang , Xin Gui , Lijuan Zhong , Rong Zhong , Yan Jiang , Hongbo Qi","doi":"10.1016/j.ygeno.2026.111196","DOIUrl":"10.1016/j.ygeno.2026.111196","url":null,"abstract":"<div><h3>Background</h3><div>Copy number variations (CNVs) are significant contributors to genetic disorders, making their accurate detection crucial for prenatal diagnosis. While clinical whole exome sequencing (cWES) is increasingly used to identify sequence variants in prenatal samples, the feasibility of using the same cWES data to detect CNVs remains underexplored, particularly in amniotic fluid samples.</div></div><div><h3>Methods</h3><div>We systematically evaluated seven CNV detection tools (CANOES, CODEX2, CLAMMS, ExomeDepth, XHMM, CNVkit, and GATK/gCNV) across various experimental conditions. Using 132 amniotic fluid (AF) samples, we assessed the impact of control sample type (AF and PB), CNV characteristics (including exon coverage and length), and tool integration strategies on detection accuracy. Performance was evaluated against CNV-seq results as the gold standard, with special focus on detecting pathogenic CNVs.</div></div><div><h3>Results</h3><div>The choice of control sample substantially influenced detection performance, with PB generally yielding better results than AF. CNV characteristics, particularly exon coverage, clearly affected detection rates, with multi-exon CNVs being more reliably detected than single-exon variants. Individual tools demonstrated varying capabilities, with CANOES achieving the highest recall rate for pathogenic CNVs (70.3%) but all tools showing limited precision (highest 3.4%). Integration of multiple tools appeared to improve overall detection capability for pathogenic variations. This study suggests that effective optimization of WES-based CNV detection should consider control-sample selection, CNV characteristics, and multi-tool integration. While the current precision limitations indicate that WES-based CNV detection cannot yet replace dedicated CNV-seq testing, the findings may inform strategies to streamline prenatal diagnostic workflows by using WES data as an initial CNV screening step, potentially helping to reduce unnecessary additional testing in selected cases.</div></div><div><h3>Conclusion</h3><div>These findings contribute to developing more effective and efficient genetic testing strategies in prenatal clinical settings, offering a foundation for future improvements in WES-based CNV detection methods.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111196"},"PeriodicalIF":3.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145948731","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 : 2026-03-01Epub Date: 2026-01-08DOI: 10.1016/j.ygeno.2026.111200
Siqi Jin , Xinxing Dong , Chunlu Zhou , Jinyu Chu , Xinpeng Li , Wangjiao Li , Wenjun Dong , Yunlong Ma , Dawei Yan
In Diqing Prefecture, we identified two Tibetan pig groups that exhibit a significant difference in body size at six months of age, with the large-bodied pigs weighing 55.00 kg and the small-bodied pigs weighing 28.00 kg. To elucidate the genetic distance and relatedness between these two groups, we employed whole-genome resequencing and constructed a genomic dataset containing 247 pigs, including 60 newly sequenced individuals and 187 publicly available samples. We first assessed their phylogenetic relationships through population genetic differentiation analyses, and further explored their genome-wide differences using methods such as nucleotide diversity (θπ), integrated haplotype score (iHS), allele frequency difference (ΔAF), and genome-wide association analysis (GWAS). The results showed that both groups belong to the Diqing Tibetan pig population, and they can be classified as large-bodied and small-bodied Diqing Tibetan pigs, respectively. Combined analyses of selective sweep signals and GWAS revealed that the genomic regions with significant divergence between the two groups mainly contain genes involved in skeletal development, muscle growth, energy metabolism, and endocrine regulation. This study is the first to demonstrate, at the genomic level, that the Diqing Tibetan pig population contains distinct large- and small-bodied types. Although both belong to the same breed, their marked difference in body size leads to substantial variation in meat production capacity. Future studies may employ multi-omics approaches—including transcriptomics, proteomics, and metabolomics—using the two types as comparative models under the same genetic background to systematically identify key genes, proteins, and metabolites that influence meat production performance. The findings of this study not only provide valuable material for further elucidating the mechanisms underlying skeletal and muscle development, but also establish a foundation for breeding Diqing Tibetan pigs with improved meat production traits.
{"title":"Genetic insights into large and small body size variation in Diqing Tibetan pigs: A comparative genomic analysis","authors":"Siqi Jin , Xinxing Dong , Chunlu Zhou , Jinyu Chu , Xinpeng Li , Wangjiao Li , Wenjun Dong , Yunlong Ma , Dawei Yan","doi":"10.1016/j.ygeno.2026.111200","DOIUrl":"10.1016/j.ygeno.2026.111200","url":null,"abstract":"<div><div>In Diqing Prefecture, we identified two Tibetan pig groups that exhibit a significant difference in body size at six months of age, with the large-bodied pigs weighing 55.00 kg and the small-bodied pigs weighing 28.00 kg. To elucidate the genetic distance and relatedness between these two groups, we employed whole-genome resequencing and constructed a genomic dataset containing 247 pigs, including 60 newly sequenced individuals and 187 publicly available samples. We first assessed their phylogenetic relationships through population genetic differentiation analyses, and further explored their genome-wide differences using methods such as nucleotide diversity (θπ), integrated haplotype score (iHS), allele frequency difference (ΔAF), and genome-wide association analysis (GWAS). The results showed that both groups belong to the Diqing Tibetan pig population, and they can be classified as large-bodied and small-bodied Diqing Tibetan pigs, respectively. Combined analyses of selective sweep signals and GWAS revealed that the genomic regions with significant divergence between the two groups mainly contain genes involved in skeletal development, muscle growth, energy metabolism, and endocrine regulation. This study is the first to demonstrate, at the genomic level, that the Diqing Tibetan pig population contains distinct large- and small-bodied types. Although both belong to the same breed, their marked difference in body size leads to substantial variation in meat production capacity. Future studies may employ multi-omics approaches—including transcriptomics, proteomics, and metabolomics—using the two types as comparative models under the same genetic background to systematically identify key genes, proteins, and metabolites that influence meat production performance. The findings of this study not only provide valuable material for further elucidating the mechanisms underlying skeletal and muscle development, but also establish a foundation for breeding Diqing Tibetan pigs with improved meat production traits.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111200"},"PeriodicalIF":3.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145948751","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 : 2026-03-01Epub Date: 2026-01-07DOI: 10.1016/j.ygeno.2026.111197
Yihan Li , Jiangwei Liu , Qian Wang , Yin Li , Xianzhong Wang , Jiaojiao Zhang
Adenosine triphosphate (ATP) is essential for sperm motility. We previously found that optimized non-thermal dielectric barrier discharge (DBD) plasma treatment enhanced boar sperm quality by increasing ATP levels. However, the molecular mechanisms underlying this process, particularly the role of competing endogenous RNA (ceRNA) networks, remain unclear. In this study, a total of 266 mRNAs, 163 miRNAs, and 37 circRNAs were identified as differentially expressed in boar spermatozoa treated with optimized DBD plasma. Functional enrichment analysis revealed that ATP-related pathways, including AMPK, mTOR, and cAMP signaling, were significantly enriched. A circRNA–miRNA–mRNA regulatory network was constructed, and two key ceRNA axes, circRNA7761–miR-7-3p–TECRL/CYP24A1/LOC100515741 and circRNA7508–miR-202-5p–CYP2A19/HHIP/WNT2, were identified in the network. These axes are predicted to enhance ATP production by regulating mitochondrial function and energy homeostasis, thereby improving sperm quality. This study provides novel mechanistic insights into the modulation of sperm energy metabolism by DBD plasma through ceRNA networks, thereby offering new theoretical foundations and potential molecular targets for improving male fertility and treating male infertility.
三磷酸腺苷（ATP）对精子的活力至关重要。我们之前发现，优化的非热介质阻挡放电（DBD）等离子体处理通过提高ATP水平来提高猪精子质量。然而，这一过程的分子机制，特别是内源性RNA （ceRNA）网络的竞争作用仍不清楚。在本研究中，共鉴定出266个mrna、163个mirna和37个circrna在经过优化的DBD血浆处理的猪精子中差异表达。功能富集分析显示，包括AMPK、mTOR和cAMP信号在内的atp相关通路显著富集。构建了一个circRNA-miRNA-mRNA调控网络，并在该网络中鉴定出两个关键的ceRNA轴circrna7761 - mir -7- 3d - tecrl /CYP24A1/LOC100515741和circRNA7508-miR-202-5p-CYP2A19/ hip /WNT2。预计这些轴通过调节线粒体功能和能量稳态来提高ATP的产生，从而提高精子质量。本研究为DBD血浆通过ceRNA网络调控精子能量代谢提供了新的机制见解，从而为提高男性生育能力和治疗男性不育症提供了新的理论基础和潜在的分子靶点。
{"title":"Identification and functional prediction of ceRNA networks regulating ATP levels in boar spermatozoa treated with non-thermal plasma","authors":"Yihan Li , Jiangwei Liu , Qian Wang , Yin Li , Xianzhong Wang , Jiaojiao Zhang","doi":"10.1016/j.ygeno.2026.111197","DOIUrl":"10.1016/j.ygeno.2026.111197","url":null,"abstract":"<div><div>Adenosine triphosphate (ATP) is essential for sperm motility. We previously found that optimized non-thermal dielectric barrier discharge (DBD) plasma treatment enhanced boar sperm quality by increasing ATP levels. However, the molecular mechanisms underlying this process, particularly the role of competing endogenous RNA (ceRNA) networks, remain unclear. In this study, a total of 266 mRNAs, 163 miRNAs, and 37 circRNAs were identified as differentially expressed in boar spermatozoa treated with optimized DBD plasma. Functional enrichment analysis revealed that ATP-related pathways, including AMPK, mTOR, and cAMP signaling, were significantly enriched. A circRNA–miRNA–mRNA regulatory network was constructed, and two key ceRNA axes, circRNA7761–miR-7-3p–TECRL/CYP24A1/LOC100515741 and circRNA7508–miR-202-5p–CYP2A19/HHIP/WNT2, were identified in the network. These axes are predicted to enhance ATP production by regulating mitochondrial function and energy homeostasis, thereby improving sperm quality. This study provides novel mechanistic insights into the modulation of sperm energy metabolism by DBD plasma through ceRNA networks, thereby offering new theoretical foundations and potential molecular targets for improving male fertility and treating male infertility.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111197"},"PeriodicalIF":3.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145943202","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 : 2026-03-01Epub Date: 2026-01-09DOI: 10.1016/j.ygeno.2026.111199
Dan Xiong , Chao Zhang , Jian Xia
A growing body of research suggests that circular RNAs (circRNAs) and 5-methylcytosine (m5C) play crucial roles in the onset and progression of stroke. This includes their potential regulation of neuronal damage and repair under cerebral ischemic conditions. However, the specific features of m5C modification in circRNAs associated with stroke remain unclear. In this study, we established a mouse model of cerebral ischemia (MCAO) and utilized methylated RNA immunoprecipitation sequencing (MeRIP-Seq) to identify m5C peaks. In comparison to the control group, MCAO exhibited significant changes in 1982 m5C peaks, with 1096 peaks upregulated and 886 peaks downregulated. Differentially expressed genes in m5C were identified to have significant involvement in the MAPK signaling pathway, GABAergic synapse, and foxO signaling pathway. Additionally, through integrated analysis of MeRIP-Seq and RNA-Seq data, we identified 24 circRNAs that underwent significant changes in both methylation and expression. This suggests a potential association between stroke and circRNA m5C modification, providing insights into the prognosis of stroke patients and the identification of novel intervention targets.
{"title":"Comprehensive epigenetic analysis on 5-methylcytosine modification of circRNAs in the mouse cerebral ischemia model","authors":"Dan Xiong , Chao Zhang , Jian Xia","doi":"10.1016/j.ygeno.2026.111199","DOIUrl":"10.1016/j.ygeno.2026.111199","url":null,"abstract":"<div><div>A growing body of research suggests that circular RNAs (circRNAs) and 5-methylcytosine (m<sup>5</sup>C) play crucial roles in the onset and progression of stroke. This includes their potential regulation of neuronal damage and repair under cerebral ischemic conditions. However, the specific features of m<sup>5</sup>C modification in circRNAs associated with stroke remain unclear. In this study, we established a mouse model of cerebral ischemia (MCAO) and utilized methylated RNA immunoprecipitation sequencing (MeRIP-Seq) to identify m<sup>5</sup>C peaks. In comparison to the control group, MCAO exhibited significant changes in 1982 m5C peaks, with 1096 peaks upregulated and 886 peaks downregulated. Differentially expressed genes in m5C were identified to have significant involvement in the MAPK signaling pathway, GABAergic synapse, and foxO signaling pathway. Additionally, through integrated analysis of MeRIP-Seq and RNA-Seq data, we identified 24 circRNAs that underwent significant changes in both methylation and expression. This suggests a potential association between stroke and circRNA m<sup>5</sup>C modification, providing insights into the prognosis of stroke patients and the identification of novel intervention targets.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111199"},"PeriodicalIF":3.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145951219","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 : 2026-03-01Epub Date: 2026-02-08DOI: 10.1016/j.ygeno.2026.111217
Lucas M. Carvalho , Jhulia Caroline N.L. da Mota , Amanda A. Ribeiro , Leticia L. Souza , Rafael B. Sposeto , Marcela A.S. Pinhel , Carla B. Nonino , Nicolas Costa-Fraga , Ana Belen Crujeiras , Andrea Gonzales Izquierdo , Angel Diaz-Lagares , Bidossessi W. Hounkpe , Eduardo F. Borba , Bruno Gualano , Carolina F. Nicoletti
Background & aims
The interaction between systemic lupus erythematosus (SLE), excess body weight, and epigenetic variation remains poorly understood. This study investigated the association between excess body weight and genome-wide DNA methylation profiles in subcutaneous adipose tissue (SAT) from patients with SLE.
Methods
In this cross-sectional study, 36 premenopausal women with SLE were classified as normal weight (NW,n = 16) or excess body weight (EBW, n = 20). Anthropometric, metabolic, dietary, and physical activity data were collected. Genome-wide DNA methylation in SAT was assessed using the Infinium HumanMethylationEPIC BeadChip.
Results
A total of 3783 differentially methylated CpG sites (DMCpGs) were identified between groups, with 1165 hypermethylated and 2618 hypomethylated sites in EBW patients. DMCpGs were enriched in promoter and open sea regions and annotated to immune, inflammatory, and metabolic pathways. DNMT1 expression was higher in EBW patients.
Conclusions
Excess body weight is associated with distinct DNA methylation patterns in SAT from patients with SLE.
ClinicalTrials.gov Identifier: NCT05097365
背景与目的：系统性红斑狼疮（SLE）、体重过重和表观遗传变异之间的相互作用尚不清楚。本研究调查了SLE患者体重过重与皮下脂肪组织（SAT）全基因组DNA甲基化谱之间的关系。方法：在本横断面研究中，36例绝经前SLE女性被分为正常体重（NW,n = 16）和超重体重（EBW, n = 20）。收集了人体测量、代谢、饮食和身体活动数据。使用Infinium HumanMethylationEPIC珠芯片评估SAT全基因组DNA甲基化。结果：两组间共鉴定出3783个差异甲基化的CpG位点（dmcpg）， EBW患者中有1165个高甲基化位点和2618个低甲基化位点。dmcpg在启动子区和开放海区富集，并注释到免疫、炎症和代谢途径。DNMT1在EBW患者中表达较高。结论：体重过重与SLE患者SAT中不同的DNA甲基化模式相关。临床试验：gov标识符：NCT05097365。
{"title":"Epigenetic and metabolic signatures in systemic lupus erythematous: The impact of excess body weight on adipose tissue DNA methylation profile","authors":"Lucas M. Carvalho , Jhulia Caroline N.L. da Mota , Amanda A. Ribeiro , Leticia L. Souza , Rafael B. Sposeto , Marcela A.S. Pinhel , Carla B. Nonino , Nicolas Costa-Fraga , Ana Belen Crujeiras , Andrea Gonzales Izquierdo , Angel Diaz-Lagares , Bidossessi W. Hounkpe , Eduardo F. Borba , Bruno Gualano , Carolina F. Nicoletti","doi":"10.1016/j.ygeno.2026.111217","DOIUrl":"10.1016/j.ygeno.2026.111217","url":null,"abstract":"<div><h3>Background & aims</h3><div>The interaction between systemic lupus erythematosus (SLE), excess body weight, and epigenetic variation remains poorly understood. This study investigated the association between excess body weight and genome-wide DNA methylation profiles in subcutaneous adipose tissue (SAT) from patients with SLE.</div></div><div><h3>Methods</h3><div>In this cross-sectional study, 36 premenopausal women with SLE were classified as normal weight (NW,<em>n</em> = 16) or excess body weight (EBW, <em>n</em> = 20). Anthropometric, metabolic, dietary, and physical activity data were collected. Genome-wide DNA methylation in SAT was assessed using the Infinium HumanMethylationEPIC BeadChip.</div></div><div><h3>Results</h3><div>A total of 3783 differentially methylated CpG sites (DMCpGs) were identified between groups, with 1165 hypermethylated and 2618 hypomethylated sites in EBW patients. DMCpGs were enriched in promoter and open sea regions and annotated to immune, inflammatory, and metabolic pathways. DNMT1 expression was higher in EBW patients.</div></div><div><h3>Conclusions</h3><div>Excess body weight is associated with distinct DNA methylation patterns in SAT from patients with SLE.</div><div><span><span>ClinicalTrials.gov</span><svg><path></path></svg></span> Identifier: <span><span>NCT05097365</span><svg><path></path></svg></span></div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111217"},"PeriodicalIF":3.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146156727","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 : 2026-03-01Epub Date: 2026-01-20DOI: 10.1016/j.ygeno.2026.111206
Peter Muchina , Johnson Kinyua , Fathiya Khamis , Chrysantus M. Tanga , Maria Altaf Satti , Grum Gebreyesus , Goutam Sahana , Zexi Cai
Low-coverage whole genome sequencing (lcWGS) combined with genotype imputation provides a cost-efficient alternative to high-coverage sequencing for large-scale genotyping. Although widely implemented in human and livestock genomics, this strategy has not yet been systematically optimized for insects of industrial importance. The black soldier fly (BSF, Hermetia illucens) is increasingly used in global waste bioconversion and sustainable protein production, but genomic resources remain limited. Here, we develop the first BSF haplotype reference panel, containing ∼29.8 million high-quality SNPs from 168 high-coverage genomes, and benchmark imputation performance using a validation experiment in which 33 high-coverage individuals were down-sampled to low coverage and imputed against a reference panel of 135 individuals. We evaluated the performance of three imputation tools, QUILT v1.0.5, GLIMPSE2, and STITCH v1.7.2, across multiple sequencing depths (0.5 × −3×) and allele frequency bins. Based on this validation, QUILT v1.0.5 achieved the highest accuracy overall, particularly for rare variants (MAF < 0.05), whereas GLIMPSE2 delivered comparable accuracy for common variants with approximately twofold faster runtimes. STITCH enabled reference-free imputation but exhibited reduced accuracy relative to reference-based approaches. We then applied the optimized framework to 180 low-coverage (∼1×) BSF genomes, demonstrating the practical utility of the reference panel for large-scale genotyping when true genotypes are unavailable. Together, the reference panel, benchmarking results, and accompanying lcWGS pipeline establish a validated framework for cost-effective BSF genotyping, enabling downstream applications in population monitoring, diversity assessment, and selective breeding.
{"title":"A haplotype reference panel and genotype imputation framework for the black soldier fly (Hermetia illucens)","authors":"Peter Muchina , Johnson Kinyua , Fathiya Khamis , Chrysantus M. Tanga , Maria Altaf Satti , Grum Gebreyesus , Goutam Sahana , Zexi Cai","doi":"10.1016/j.ygeno.2026.111206","DOIUrl":"10.1016/j.ygeno.2026.111206","url":null,"abstract":"<div><div>Low-coverage whole genome sequencing (lcWGS) combined with genotype imputation provides a cost-efficient alternative to high-coverage sequencing for large-scale genotyping. Although widely implemented in human and livestock genomics, this strategy has not yet been systematically optimized for insects of industrial importance. The black soldier fly (BSF, <em>Hermetia illucens</em>) is increasingly used in global waste bioconversion and sustainable protein production, but genomic resources remain limited. Here, we develop the first BSF haplotype reference panel, containing ∼29.8 million high-quality SNPs from 168 high-coverage genomes, and benchmark imputation performance using a validation experiment in which 33 high-coverage individuals were down-sampled to low coverage and imputed against a reference panel of 135 individuals. We evaluated the performance of three imputation tools, QUILT v1.0.5, GLIMPSE2, and STITCH v1.7.2, across multiple sequencing depths (0.5 × −3×) and allele frequency bins. Based on this validation, QUILT v1.0.5 achieved the highest accuracy overall, particularly for rare variants (MAF < 0.05), whereas GLIMPSE2 delivered comparable accuracy for common variants with approximately twofold faster runtimes. STITCH enabled reference-free imputation but exhibited reduced accuracy relative to reference-based approaches. We then applied the optimized framework to 180 low-coverage (∼1×) BSF genomes, demonstrating the practical utility of the reference panel for large-scale genotyping when true genotypes are unavailable. Together, the reference panel, benchmarking results, and accompanying lcWGS pipeline establish a validated framework for cost-effective BSF genotyping, enabling downstream applications in population monitoring, diversity assessment, and selective breeding.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111206"},"PeriodicalIF":3.0,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146018040","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}
扫码关注我们
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号