Pub Date : 2026-01-01Epub Date: 2025-12-29DOI: 10.1016/j.ygeno.2025.111188
Monika Stefaniuk-Szmukier , Tomasz Szmatoła , Anna Steg , Grzegorz Smołucha , Katarzyna Ropka-Molik
The avian cerebellum is pivotal for multisensory integration and motor control during flight, yet its molecular adaptation to prolonged exertion remains incompletely defined. We profiled cerebellar transcriptomes of ten racing pigeons before and after a 300-km homing flight using whole-transcriptome RNA sequencing. Differential expression analysis revealed robust remodeling of metabolic and proteostatic pathways, including upregulation of SLC35D2, consistent with enhanced UDP-GlcNAc flux through the hexosamine biosynthetic pathway aligned with birds' naturally high glycaemia. Increased VLDLR expression links lipid handling to the reelin signalling cascade, suggesting contributions to navigation and synaptic plasticity, whereas downregulation of HTR1F indicates region-specific serotonergic modulation with exercise. Co-expression network analysis (WGCNA) identified modules enriched for endoplasmic reticulum protein processing and stress responses (PLAA, RAD23, ERN1), alongside intensified ribosome and RNA biogenesis, reflecting an elevated demand for protein synthesis and quality control. Functional enrichment (WebGestalt,) highlighted among others ribosome biogenesis, core metabolic pathways, RNA transport. These insights contribute to understanding the genetic and molecular mechanisms underpinning avian navigation and performance, providing a foundation for further research into flight-related neurophysiology.
{"title":"RNA-Seq reveals flight-induced changes in cerebellar transcriptomic profiles of racing pigeons","authors":"Monika Stefaniuk-Szmukier , Tomasz Szmatoła , Anna Steg , Grzegorz Smołucha , Katarzyna Ropka-Molik","doi":"10.1016/j.ygeno.2025.111188","DOIUrl":"10.1016/j.ygeno.2025.111188","url":null,"abstract":"<div><div>The avian cerebellum is pivotal for multisensory integration and motor control during flight, yet its molecular adaptation to prolonged exertion remains incompletely defined. We profiled cerebellar transcriptomes of ten racing pigeons before and after a 300-km homing flight using whole-transcriptome RNA sequencing. Differential expression analysis revealed robust remodeling of metabolic and proteostatic pathways, including upregulation of <em>SLC35D2</em>, consistent with enhanced UDP-GlcNAc flux through the hexosamine biosynthetic pathway aligned with birds' naturally high glycaemia. Increased <em>VLDLR</em> expression links lipid handling to the reelin signalling cascade, suggesting contributions to navigation and synaptic plasticity, whereas downregulation of <em>HTR1F</em> indicates region-specific serotonergic modulation with exercise. Co-expression network analysis (WGCNA) identified modules enriched for endoplasmic reticulum protein processing and stress responses (<em>PLAA</em>, <em>RAD23</em>, <em>ERN1</em>), alongside intensified ribosome and RNA biogenesis, reflecting an elevated demand for protein synthesis and quality control. Functional enrichment (WebGestalt,) highlighted among others ribosome biogenesis, core metabolic pathways, RNA transport. These insights contribute to understanding the genetic and molecular mechanisms underpinning avian navigation and performance, providing a foundation for further research into flight-related neurophysiology.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111188"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145878055","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 : 2026-01-01Epub 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":"2026-01-01","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}
Molecular analysis of human post-mortem brain tissue holds the promise to identify disease associated mechanisms. Single nuclei RNA-sequencing (snRNA-seq) is a powerful tool for molecular-level investigations of human brain tissue with cell type resolution. In the fast-developing field of post-mortem snRNA-seq, the samples sizes of case/control studies have drastically increased over the last years. Still, to overcome genetic variability across individuals and to investigate the many relevant brain regions that have not yet been sampled, even larger cohorts are necessary. It is thus important to benchmark snRNA-seq methods against each other on relevant tissue. We compared five such methods, 10× Genomics v3.1, 10× Genomics Flex Gene Expression, Parse Biosciences Evercode v2, PIPseq v5.0 from Fluent Biosciences (now acquired by Illumina) and Smart-seq3xpress, using fresh frozen post-mortem human forebrain tissue samples. Using tissue samples from the same three donors for all methods, our investigation revealed comparable overall technical performance among the five methods but suggests that biological variability was better captured with Smart-seq3xpress. We could not model the effect of sample quality, which limits the generalizability of our results. Thus, our study suggests that the selection of snRNA-seq method should mainly be informed by the need of specific data and practical experimental considerations such as hardware requirements, ability to multiplex, tissue quantity input requirements, and transportation of samples/tissues.
{"title":"Benchmarking of single nuclei RNA-seq methods on human post-mortem brain tissue","authors":"Kasra Nikouei , Elin Gruyters , Fatima Memic , Craig A. Stockmeier , Jens Hjerling-Leffler","doi":"10.1016/j.ygeno.2025.111184","DOIUrl":"10.1016/j.ygeno.2025.111184","url":null,"abstract":"<div><div>Molecular analysis of human post-mortem brain tissue holds the promise to identify disease associated mechanisms. Single nuclei RNA-sequencing (snRNA-seq) is a powerful tool for molecular-level investigations of human brain tissue with cell type resolution. In the fast-developing field of post-mortem snRNA-seq, the samples sizes of case/control studies have drastically increased over the last years. Still, to overcome genetic variability across individuals and to investigate the many relevant brain regions that have not yet been sampled, even larger cohorts are necessary. It is thus important to benchmark snRNA-seq methods against each other on relevant tissue. We compared five such methods, 10× Genomics v3.1, 10× Genomics Flex Gene Expression, Parse Biosciences Evercode v2, PIPseq v5.0 from Fluent Biosciences (now acquired by Illumina) and Smart-seq3xpress, using fresh frozen post-mortem human forebrain tissue samples. Using tissue samples from the same three donors for all methods, our investigation revealed comparable overall technical performance among the five methods but suggests that biological variability was better captured with Smart-seq3xpress. We could not model the effect of sample quality, which limits the generalizability of our results. Thus, our study suggests that the selection of snRNA-seq method should mainly be informed by the need of specific data and practical experimental considerations such as hardware requirements, ability to multiplex, tissue quantity input requirements, and transportation of samples/tissues.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111184"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145843579","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}
Integrating Traditional Chinese Medicines (TCMs) into Pelodiscus sinensis aquaculture offers a promising alternative to conventional treatments. Through whole-transcriptome analysis, this study investigated the effects of TCMs on growth and immune regulation, uncovering a complex interplay between coding and non-coding RNAs. We identified three key subsets of differentially expressed genes (DEGs): SpTG1 (low-dose-specific DEGs), SpTG2 (high-dose-specific DEGs), and TG1_TG2 (DEGs common to both low and high doses). These DEG subsets were significantly enriched in pathways pivotal for growth, metabolism, and immunity, such as the PI3K-Akt, TNF, and AMPK signaling pathways. Our findings clarify roles of miRNAs, circRNAs, and lncRNAs in mediating TCM responses, with their potential interactions in competing endogenous RNA (ceRNA) networks suggesting novel regulatory targets. These results position TCMs as sustainable and eco-friendly feed additives. Further research into the specific mechanisms identified here could enable the development of targeted strategies to boost P. sinensis fitness and yield.
{"title":"Whole-transcriptome analysis of TCM effects on growth and immune regulation in Pelodiscus sinensis via coding and non-coding RNAs","authors":"Xin Zhang , Xiuhong Cai , Shirui Yue , Zhangxuan Chen , Mingsong Xiao","doi":"10.1016/j.ygeno.2025.111171","DOIUrl":"10.1016/j.ygeno.2025.111171","url":null,"abstract":"<div><div>Integrating Traditional Chinese Medicines (TCMs) into <em>Pelodiscus sinensis</em> aquaculture offers a promising alternative to conventional treatments. Through whole-transcriptome analysis, this study investigated the effects of TCMs on growth and immune regulation, uncovering a complex interplay between coding and non-coding RNAs. We identified three key subsets of differentially expressed genes (DEGs): SpTG1 (low-dose-specific DEGs), SpTG2 (high-dose-specific DEGs), and TG1_TG2 (DEGs common to both low and high doses). These DEG subsets were significantly enriched in pathways pivotal for growth, metabolism, and immunity, such as the PI3K-Akt, TNF, and AMPK signaling pathways. Our findings clarify roles of miRNAs, circRNAs, and lncRNAs in mediating TCM responses, with their potential interactions in competing endogenous RNA (ceRNA) networks suggesting novel regulatory targets. These results position TCMs as sustainable and eco-friendly feed additives. Further research into the specific mechanisms identified here could enable the development of targeted strategies to boost <em>P. sinensis</em> fitness and yield.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111171"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145774344","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 : 2026-01-01Epub Date: 2025-11-26DOI: 10.1016/j.ygeno.2025.111160
Endashaw Jebessa , Yanhua He , Hao Qu , Lin Chuxiao , Zhifeng Zhao , Haile Berihulay , Peng Chen , Xian Zou , Jian Ji , Dingming Shu , Chenglong Luo
Despite the integrative function of miRNAs and genes in chicken embryonic gonadal sex differentiation, their roles remain poorly understood. Here, we used RNA-seq to analyze 12 gonadal samples from embryonic days 5 (E5) and 9 (E9). Our analysis of miRNA and mRNA expression during this key developmental stage revealed five DEmiRNAs and 235 DEmRNAs consistently associated with left-right asymmetry in female gonads in both F5L vs F5R and F9L vs F9R comparisons. The interaction between DEmiRNAs and target DEmRNAs in the left-right asymmetry of embryonic gonadal development at E5 and E9 in chickens, along with the KEGG pathway enrichment analysis, revealed the involvement of several significant pathways. These include the complement and coagulation cascades, tight junctions, and synthesis and secretion of aldosterone. Differentially expressed miRNAs and target genes at embryonic days 5 and 9 reveal key molecular mechanisms driving gonadal sex differentiation in chickens.
{"title":"Transcriptome profile analysis of miRNA and mRNA in chicken embryo gonad sex differentiation","authors":"Endashaw Jebessa , Yanhua He , Hao Qu , Lin Chuxiao , Zhifeng Zhao , Haile Berihulay , Peng Chen , Xian Zou , Jian Ji , Dingming Shu , Chenglong Luo","doi":"10.1016/j.ygeno.2025.111160","DOIUrl":"10.1016/j.ygeno.2025.111160","url":null,"abstract":"<div><div>Despite the integrative function of miRNAs and genes in chicken embryonic gonadal sex differentiation, their roles remain poorly understood. Here, we used RNA-seq to analyze 12 gonadal samples from embryonic days 5 (E5) and 9 (E9). Our analysis of miRNA and mRNA expression during this key developmental stage revealed five DEmiRNAs and 235 DEmRNAs consistently associated with left-right asymmetry in female gonads in both F5L vs F5R and F9L vs F9R comparisons. The interaction between DEmiRNAs and target DEmRNAs in the left-right asymmetry of embryonic gonadal development at E5 and E9 in chickens, along with the KEGG pathway enrichment analysis, revealed the involvement of several significant pathways. These include the complement and coagulation cascades, tight junctions, and synthesis and secretion of aldosterone. Differentially expressed miRNAs and target genes at embryonic days 5 and 9 reveal key molecular mechanisms driving gonadal sex differentiation in chickens.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111160"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145631388","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 : 2026-01-01Epub 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":"2026-01-01","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 : 2026-01-01Epub Date: 2025-12-26DOI: 10.1016/j.ygeno.2025.111178
Sui Liufu , Wu Wen , Jun Ouyang , Bohe Chen , Kaiming Wang , Lanlin Xiao , Wenwu Chen , Qiuchun Deng , Haiming Ma
Weaning is a critical phase determining post-weaning growth and economic efficiency in pig production. To unravel gut segment-specific mechanisms underlying weaning weight variation, we performed integrated transcriptomic and metabolomic analyses of the mid-jejunum, ileum, and colon in high- (HWW) and low-weaning-weight (LWW) piglets. HWW piglets showed upregulated expression of amino acid transport genes (NOS2, ASS1, GPT2), alongside elevated levels of metabolites including glycochenodeoxycholic acid (GUDCA), deoxycholic acid (GDCA), methionine, and isoleucine. In the ileum, HWW piglets exhibited enrichment in ABC transporter and thyroid hormone pathways, with upregulated metabolites including betaine, cytidine, epigallocatechin, oxidized glutathione, cholylserine, and glutathione linked to enhanced immune homeostasis. In the colon, FUT2 and LYZ were key regulatory genes, and indole-3-carboxylic acid and enterolactone played critical roles in modulating colonic homeostasis. Taken together, our findings identify precise gene–metabolite networks driving intestinal functionality during weaning, offering targeted nutritional and genetic strategies to mitigate growth retardation in piglets.
{"title":"Multi-omics integration uncovers gut segment-specific gene-metabolite networks underlying growth retardation in piglets","authors":"Sui Liufu , Wu Wen , Jun Ouyang , Bohe Chen , Kaiming Wang , Lanlin Xiao , Wenwu Chen , Qiuchun Deng , Haiming Ma","doi":"10.1016/j.ygeno.2025.111178","DOIUrl":"10.1016/j.ygeno.2025.111178","url":null,"abstract":"<div><div>Weaning is a critical phase determining post-weaning growth and economic efficiency in pig production. To unravel gut segment-specific mechanisms underlying weaning weight variation, we performed integrated transcriptomic and metabolomic analyses of the mid-jejunum, ileum, and colon in high- (HWW) and low-weaning-weight (LWW) piglets. HWW piglets showed upregulated expression of amino acid transport genes (<em>NOS2</em>, <em>ASS1</em>, <em>GPT2</em>), alongside elevated levels of metabolites including glycochenodeoxycholic acid (GUDCA), deoxycholic acid (GDCA), methionine, and isoleucine. In the ileum, HWW piglets exhibited enrichment in ABC transporter and thyroid hormone pathways, with upregulated metabolites including betaine, cytidine, epigallocatechin, oxidized glutathione, cholylserine, and glutathione linked to enhanced immune homeostasis. In the colon, <em>FUT2</em> and <em>LYZ</em> were key regulatory genes, and indole-3-carboxylic acid and enterolactone played critical roles in modulating colonic homeostasis. Taken together, our findings identify precise gene–metabolite networks driving intestinal functionality during weaning, offering targeted nutritional and genetic strategies to mitigate growth retardation in piglets.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111178"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145849482","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 : 2026-01-01Epub Date: 2025-12-24DOI: 10.1016/j.ygeno.2025.111182
Xiaoyu Fu , Liming Zhao , Huibin Tian , Deyin Zhang , Yukun Zhang , Yuan Zhao , Jiangbo Cheng , Xiaolong Li , Quanzhong Xu , Dan Xu , Xiaobin Yang , Zongwu Ma , Weiwei Wu , Fadi Li , Weimin Wang , Xiaoxue Zhang
Perirenal fat deposition significantly impacts sheep carcass quality and economic efficiency. To elucidate the underlying genetic regulation, we performed a genome-wide association study (GWAS) on 556 Hu sheep and a comparative transcriptome analysis on 24 Hu sheep (12 with high- and 12 with low-perirenal fat deposition), all with accurate phenotypic records. Furthermore, hub genes and tissue-specific genes (TSGs) were discerned through weighted gene co-expression network analysis (WGCNA) and by leveraging RNA-Seq data from 12 tissues, respectively. qRT-PCR is used to validate the accuracy of RNA-Seq data. GWAS identified significant SNPs near genes including SETD4, TIMP2, SOCS3, and DNAH17. Comparative transcriptome analysis of HPF and LPF groups identified 2072 differentially expressed genes (DEGs), which were significantly associated with lipid storage (LPL), fatty acid homeostasis (APOE, GOT1), and biosynthesis (ACACA). A total of 2333 differential alternative splicing events were identified in 1169 genes, with skipped exons (SE, 30.65 %) being the most common. GO analysis of these SEs showed links to RNA splicing and lipid metabolism, with genes like BSCL2, DGAT1, PLIN5, and PNPLA2 involved in lipid droplet organization and triglyceride storage. WGCNA revealed key modules that were positively and negatively correlated with perirenal fat deposition, emphasizing hub genes (SAR1B, THRSP, ACSS2, KIF5B) associated with lipid droplet organization and metabolism. The integrated analysis of GWAS and RNA-seq identified TIMP2, SOCS3, and DNAH17 as potential key genes involved in regulating perirenal fat deposition in sheep. An association analysis of 372 Hu sheep populations identified significant links (P < 0.05) between perirenal fat deposition traits and mutations in the TIMP2 (g.9759169 G > A) and DNAH17 (g.9494469C > T) genes. Crucially, tissue-specific gene analysis across 12 tissues identified 448 perirenal fat TSGs, of which 75 were also differentially expressed genes (e.g., LPL, THRSP, LEP, ADRB3). In conclusion, our multi-omics study identified key genes influencing perirenal fat deposition in sheep. Notably, mutations in TIMP2 and DNAH17 could serve as candidate markers for enhancing carcass quality through marker-assisted selection.
{"title":"Genome-wide association and transcriptome studies identify candidate genes regulating perirenal fat deposition in sheep","authors":"Xiaoyu Fu , Liming Zhao , Huibin Tian , Deyin Zhang , Yukun Zhang , Yuan Zhao , Jiangbo Cheng , Xiaolong Li , Quanzhong Xu , Dan Xu , Xiaobin Yang , Zongwu Ma , Weiwei Wu , Fadi Li , Weimin Wang , Xiaoxue Zhang","doi":"10.1016/j.ygeno.2025.111182","DOIUrl":"10.1016/j.ygeno.2025.111182","url":null,"abstract":"<div><div>Perirenal fat deposition significantly impacts sheep carcass quality and economic efficiency. To elucidate the underlying genetic regulation, we performed a genome-wide association study (GWAS) on 556 Hu sheep and a comparative transcriptome analysis on 24 Hu sheep (12 with high- and 12 with low-perirenal fat deposition), all with accurate phenotypic records. Furthermore, hub genes and tissue-specific genes (TSGs) were discerned through weighted gene co-expression network analysis (WGCNA) and by leveraging RNA-Seq data from 12 tissues, respectively. qRT-PCR is used to validate the accuracy of RNA-Seq data. GWAS identified significant SNPs near genes including <em>SETD4</em>, <em>TIMP2</em>, <em>SOCS3</em>, and <em>DNAH17</em>. Comparative transcriptome analysis of HPF and LPF groups identified 2072 differentially expressed genes (DEGs), which were significantly associated with lipid storage (<em>LPL</em>), fatty acid homeostasis (<em>APOE</em>, <em>GOT1</em>), and biosynthesis (<em>ACACA</em>). A total of 2333 differential alternative splicing events were identified in 1169 genes, with skipped exons (SE, 30.65 %) being the most common. GO analysis of these SEs showed links to RNA splicing and lipid metabolism, with genes like <em>BSCL2</em>, <em>DGAT1</em>, <em>PLIN5</em>, and <em>PNPLA2</em> involved in lipid droplet organization and triglyceride storage. WGCNA revealed key modules that were positively and negatively correlated with perirenal fat deposition, emphasizing hub genes (<em>SAR1B</em>, <em>THRSP</em>, <em>ACSS2</em>, <em>KIF5B</em>) associated with lipid droplet organization and metabolism. The integrated analysis of GWAS and RNA-seq identified <em>TIMP2</em>, <em>SOCS3</em>, and <em>DNAH17</em> as potential key genes involved in regulating perirenal fat deposition in sheep. An association analysis of 372 Hu sheep populations identified significant links (<em>P</em> < 0.05) between perirenal fat deposition traits and mutations in the <em>TIMP2</em> (g.9759169 G > A) and <em>DNAH17</em> (g.9494469C > T) genes. Crucially, tissue-specific gene analysis across 12 tissues identified 448 perirenal fat TSGs, of which 75 were also differentially expressed genes (e.g., <em>LPL</em>, <em>THRSP</em>, <em>LEP</em>, <em>ADRB3</em>). In conclusion, our multi-omics study identified key genes influencing perirenal fat deposition in sheep. Notably, mutations in <em>TIMP2</em> and <em>DNAH17</em> could serve as candidate markers for enhancing carcass quality through marker-assisted selection.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111182"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145843592","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 : 2026-01-01Epub Date: 2025-11-25DOI: 10.1016/j.ygeno.2025.111158
Fanny Mollandin , Hervé Acloque , Maria Ballester , Marco Bink , Mario Calus , Daniel Crespo-Piazuelo , Pascal Croiseau , Sarah Djebali , Sylvain Foissac , Hélène Gilbert , Elisabetta Giuffra , Cervin Guyomar , Ole Madsen , Marie-José Mercat , Bruno da Costa Perez , Jani de Vos , Andrea Rau
Gene expression is a dynamic phenotype influenced by tissue-specific regulatory mechanisms, which can modulate expression directly or indirectly through cis or trans factors. Identifying genetic variants in these regulatory regions can improve both expression quantitative trait locus (eQTL) mapping and gene expression prediction. Whole genome sequences offer the possibility for enhanced eQTL mapping accuracy, but detecting causal variants remains challenging. Here, we evaluate the potential added-value of integrating tissue-specific epigenetic annotations, such as chromatin accessibility and methylation status, into within-breed genomic predictions of expression for three pig breeds. Functional annotations from early developmental stages improved eQTL mapping interpretability as shown by the enrichment of trait-relevant QTLs. However, despite the use of functional annotations, predictions across breeds remain challenging due to differences in genetic architectures. Our work contributes to the understanding of gene expression regulation in livestock and highlights the value of functional annotations, despite continued challenges for predictions across breeds.
{"title":"Guiding eQTL mapping and genomic prediction of gene expression in three pig breeds with tissue-specific epigenetic annotations from early development","authors":"Fanny Mollandin , Hervé Acloque , Maria Ballester , Marco Bink , Mario Calus , Daniel Crespo-Piazuelo , Pascal Croiseau , Sarah Djebali , Sylvain Foissac , Hélène Gilbert , Elisabetta Giuffra , Cervin Guyomar , Ole Madsen , Marie-José Mercat , Bruno da Costa Perez , Jani de Vos , Andrea Rau","doi":"10.1016/j.ygeno.2025.111158","DOIUrl":"10.1016/j.ygeno.2025.111158","url":null,"abstract":"<div><div>Gene expression is a dynamic phenotype influenced by tissue-specific regulatory mechanisms, which can modulate expression directly or indirectly through <em>cis</em> or <em>trans</em> factors. Identifying genetic variants in these regulatory regions can improve both expression quantitative trait locus (eQTL) mapping and gene expression prediction. Whole genome sequences offer the possibility for enhanced eQTL mapping accuracy, but detecting causal variants remains challenging. Here, we evaluate the potential added-value of integrating tissue-specific epigenetic annotations, such as chromatin accessibility and methylation status, into within-breed genomic predictions of expression for three pig breeds. Functional annotations from early developmental stages improved eQTL mapping interpretability as shown by the enrichment of trait-relevant QTLs. However, despite the use of functional annotations, predictions across breeds remain challenging due to differences in genetic architectures. Our work contributes to the understanding of gene expression regulation in livestock and highlights the value of functional annotations, despite continued challenges for predictions across breeds.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111158"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145617608","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 : 2026-01-01Epub 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":"2026-01-01","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}
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