BMC Genomics最新文献

{"title":"Genome-wide identification and analysis of GH1-containing H1 histones among poplar species.","authors":"Ping Li, Jing Wang, Qimin Zhang, Anmin Yu, Rui Sun, Aizhong Liu","doi":"10.1186/s12864-025-11456-6","DOIUrl":"10.1186/s12864-025-11456-6","url":null,"abstract":"<p><p>Histone H1s are basic nuclear proteins, which played key role in the binding of DNA and nucleosome, eventually the stability of eukaryotic chromatin. In most species, H1s possess an evolutionarily conserved nucleosome-DNA binding globular domain (GH1), which is conserved between species, especially in mammals. However, there is limited information on the phylogeny, structure and function of H1s in poplar. In the present research, 21 GH1-containing proteins found in Populus trichocarpa were classified into three subgroups (H1s, Myb (SANK) GH1 and AT-hook GH1) based on their domains. The Populus H1 proteins contained lysine-rich N-, C-terminal tails and a conserved GH1 domain, particularly the characteristic amino acids in the helix and strand structures of the five H1 subtypes. The phylogenetic and structure diversity analysis of GH1 proteins across different Populus species and model plants revealed three conserved subgroups with characteristic amino acids. The variation in the number of members across the five subtypes was consistent with the evolutionary relationships among Populus species. The conserved characteristic amino acids among same Populus subtype can be served as markers for subtype identification. Furthermore, the abundance analysis of H1s in Populus indicated their unique functions in young tissues and stages, which may be related to DNA methylation. The consistent expression pattern of H1 across Populus species was in accordance with collinearity pairs. Present analyses provided valuable information on the diversity and evolution of H1s in Populus, advocating further research of H1s in plants.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"287"},"PeriodicalIF":3.5,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11931866/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699479","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide identification of the NAC family genes of adzuki bean and their roles in rust resistance through jasmonic acid signaling.","authors":"Liu Shengmiao, Ding Xin, Li Yue, Yin Lihua, Ke Xiwang, Zuo Yuhu","doi":"10.1186/s12864-025-11478-0","DOIUrl":"10.1186/s12864-025-11478-0","url":null,"abstract":"<p><strong>Background: </strong>Adzuki bean (Vigna angularis) rust, caused by the fungus Uromyces vignae, is an important disease affecting adzuki bean yield and quality. Previously, several NAC transcription factors (TFs) were induced by rust infection in a resistant adzuki bean variety, suggesting that NAC TF members may play important roles in rust resistance.</p><p><strong>Results: </strong>To further explore the functions of NAC TFs in rust resistance and to provide a reference for resistant varietal breeding, 101 NAC TFs were identified from the adzuki bean genome. The synteny analysis revealed 25 pairs of VaNACs in the genome, which exhibited whole-genome/segmental duplication. Based on the phylogenetic relationships and conserved motif characteristics, the NAC TFs of V. angularis can be divided into 16 subfamilies. Previous transcriptome data showed that nine VaNACs are significantly induced by rust infection. Here, a cis-acting element analysis of these nine genes revealed that most contain hormone responsive elements, such as abscisic acid and methyl jasmonate (MeJA). The expression levels of these nine VaNACs were dynamically regulated in response to exogenous MeJA treatment, as revealed by quantitative real-time PCR analysis. Among them, seven VaNACs exhibited significantly upregulated expression, peaking at 12 h post treatment (hpt) and remaining significantly higher than that of the untreated control group for 48 hpt. These results suggest that these VaNACs are responsive to MeJA signaling and may play roles in the early and sustained transcriptional regulation of stress-related pathways. The exogenous MeJA decreased rust severity on adzuki bean leaves by 45.68%. Additionally, the expression levels of these nine genes in adzuki bean leaves in response to rust infection after pretreatment with MeJA were investigated. The expression of VaNAC002 rapidly peaked at 24 h post inoculation (hpi) and remained significantly higher than the control from 120 to 192 hpi. Subsequently, transient overexpression of VaNAC002 significantly enhanced the resistance of tobacco to Botrytis cinerea, indicating that VaNAC002 positively regulates plant disease resistance.</p><p><strong>Conclusion: </strong>These findings suggest that adzuki bean NAC family members may play important roles in disease resistance through JA signaling, with VaNAC002 having a positive regulatory role in plant immunity.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"283"},"PeriodicalIF":3.5,"publicationDate":"2025-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11929360/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143690991","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-tool copy number detection highlights common body size-associated variants in miniature pig breeds from different geographical regions.","authors":"Jan Berghöfer, Nadia Khaveh, Stefan Mundlos, Julia Metzger","doi":"10.1186/s12864-025-11446-8","DOIUrl":"10.1186/s12864-025-11446-8","url":null,"abstract":"<p><strong>Background: </strong>Copy number variations (CNVs) represent a common and highly specific type of variation in the genome, potentially influencing genetic diversity and mammalian phenotypic development. Structural variants, such as deletions, duplications, and insertions, have frequently been highlighted as key factors influencing traits in high-production pigs. However, comprehensive CNV analyses in miniature pig breeds are limited despite their value in biomedical research.</p><p><strong>Results: </strong>This study performed whole-genome sequencing in 36 miniature pigs from nine breeds from America, Asia and Oceania, and Europe. By employing a multi-tool approach (CNVpytor, Delly, GATK gCNV, Smoove), the accuracy of CNV identification was improved. In total, 34 homozygous CNVs overlapped with exonic regions in all samples, suggesting a role in expressing specific phenotypes such as uniform growth patterns, fertility, or metabolic function. In addition, 386 copy number variation regions (CNVRs) shared by all breeds were detected, covering 33.6 Mb (1.48% of the autosomal genome). Further, 132 exclusive CNVRs were identified for American breeds, 47 for Asian and Oceanian breeds, and 114 for European breeds. Functional enrichment analysis revealed genes within the common CNVRs involved in body height determination and other growth-related parameters. Exclusive CNVRs were located in the region of genes enriched for lipid metabolism in American minipigs, reproductive traits in Asian and Oceanian breeds, and cardiovascular features and body height in European breeds. In the selected groups, quantitative trait loci associated with body size, meat quality, reproduction, and disease susceptibility were highlighted.</p><p><strong>Conclusion: </strong>This investigation of the CNV landscape of minipigs underlines the impact of selective breeding on structural variants and its role in the development of specific breed phenotypes across geographical areas. The multi-tool approach provides a valuable resource for future studies on the effects of artificial selection on livestock genomes.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"285"},"PeriodicalIF":3.5,"publicationDate":"2025-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11929999/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143691015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Large-scale integration of meta-QTL and genome-wide association study identifies genomic regions and candidate genes for photosynthetic efficiency traits in bread wheat.","authors":"Ming Chen, Tao Chen, Letong Yun, Zhuo Che, Jingfu Ma, Binxue Kong, Jiangying Long, Chunhua Cheng, Kaiqi Guo, Peipei Zhang, Lijian Guo, Delong Yang","doi":"10.1186/s12864-025-11472-6","DOIUrl":"10.1186/s12864-025-11472-6","url":null,"abstract":"<p><strong>Background: </strong>Improving photosynthetic efficiency is an essential strategy for advancing wheat breeding progress. Integrating wheat genetic resources provides an opportunity to discover pivotal genomic regions and candidate genes (CGs) for photosynthetic efficiency traits in wheat.</p><p><strong>Results: </strong>A large-scale meta-QTL (MQTL) analysis was performed with 1363 initial quantitative trait loci (QTLs) for photosynthetic efficiency traits extracted from 66 independent QTL mapping studies over the past decades. Consequently, 718 initial QTLs were refined into 74 MQTLs, which were distributed on all wheat chromosomes except 1D, 3 A, 4B, and 5B. Compared with the confidence interval (CI) of the initial QTL, the CI of the identified MQTL was 0.03 to 10.97 cM, with an average of 1.46 cM, which was 20.46 times narrower than that of the original QTL. The maximum explained phenotypic variance (PVE) of the MQTL ranged from 7.43 to 20.42, with an average of 11.97, which was 1.07 times higher than that of the original QTL. Of these, 54 MQTLs were validated using genome-wide association study (GWAS) data from different natural populations in previous research. A total of 3,102 CGs were identified within the MQTL intervals, where 342 CGs share homology with rice, and 1,043 CGs are highly expressed in leaves, spikes, and stems. These CGs were mainly involved in porphyrin metabolism, glyoxylate, dicarboxylate metabolism, carbon metabolism and photosynthesis antenna proteins metabolism pathways by the in silico transcriptome assessment. For the key CG TaGGR-6A (TraesCS6A02G307700) involved in the porphyrin metabolism pathway, a functional kompetitive allele-specific PCR (KASP) marker was developed at 2464 bp (A/G) position within the 3' untranslated region, successfully distinguishing two haplotypes: TaGGR-6A-Hap I (type AA) and TaGGR-6A-Hap II (type GG). Varieties with the TaGGR-6A-Hap II allele exhibited approximately 13.42% and 11.45% higher flag leaf chlorophyll content than those carrying the TaGGR-6A-Hap I allele. The elite haplotype TaGGR-6A-Hap II was positively selected during wheat breeding, as evidenced by the geographical and annual frequency distributions of the two TaGGR-6A haplotypes.</p><p><strong>Conclusion: </strong>The findings will give further insights into the genetic determinants of photosynthetic efficiency traits and provide some reliable MQTLs and putative CGs for the genetic improvement of photosynthetic efficiency in wheat.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"284"},"PeriodicalIF":3.5,"publicationDate":"2025-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11929995/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143691013","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Altered structural and transporter-related gene expression patterns in the placenta play a role in fetal demise during Porcine reproductive and respiratory syndrome virus infection.","authors":"Angelica Van Goor, Alex Pasternak, Kristen E Walker, Shannon Chick, John C S Harding, Joan K Lunney","doi":"10.1186/s12864-025-11397-0","DOIUrl":"10.1186/s12864-025-11397-0","url":null,"abstract":"<p><strong>Background: </strong>Porcine reproductive and respiratory syndrome virus (PRRSV) can be transmitted across the maternal-fetal-interface from an infected gilt to her fetuses. Although fetal infection status and disease outcomes vary, the mechanisms are not completely understood. The objective was to assess targeted placental structural and transporter-related gene expression patterns. At day 85 of gestation pregnant pigs were challenged with PRRSV, and at 12 days post maternal infection sows and fetuses were sacrificed, and the placental tissue was collected. Grouping of fetuses was by preservation status and PRRS viral load (VL): control (CTRL, n = 14), viable and low VL fetus (VIA_LVF, n = 15), viable and high VL fetus (VIA_HVF, n = 21), meconium mild and low VL fetus (MECm_LVF, n = 14), meconium mild and high VL fetus (MECm_HVF, n = 14), and meconium severe and high VL fetus (MECs_HVF, n = 13). NanoString was used to evaluate the expression of 86 genes: actin cytoskeleton signaling, arachidonic acid pathway, integrin signaling, intercellular junctions, transporters, and VEGF signaling. Statistical analyses were performed using Limma with P ≤ 0.05 considered significant.</p><p><strong>Results: </strong>We identified 1, 7, 0, 29, and 39 differentially expressed genes in VIA_LVF, VIA_HVF, MECm_LVF, MECm_HVF, and MECs_HVF, respectively, contrasted to CTRL. Placental transporter genes were significantly impacted (i.e., downregulation of SLC1A3, SLC1A5, SLC2A1, SLC2A3, SLC2A5, SLC2A10, SLC2A12, SLC7A4, SLC16A5, SLC16A10, and SLC27A6; and upregulation of SLC2A2, SLC16A3, and SLC27A4), compared to CTRL. Actin cytoskeleton signaling (ARHGEF6 and ARHGEF7), arachidonic acid (PTGES3 and PTGIS), integrin signaling (FN1 and ITGB6), intercellular junctions (CDH3 and CDH11), and VEGF signaling (MAPK3 and HPSE) gene groupings were significantly impacted, compared to CTRL.</p><p><strong>Conclusion: </strong>Data reported here indicate that fetal PRRSV infection levels rather than fetal demise is necessary for transcriptional dysregulation of the fetal placenta, with a tendency towards more downregulation in the target gene sets among susceptible fetuses. These results generally support that in susceptible fetuses there is altered solute transportation, placental structural integrity, and reduced angiogenesis. The data described here is associated with fetal PRRS resistance/resilience and susceptibility.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"279"},"PeriodicalIF":3.5,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11927291/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143676634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide association study identifies elite alleles of FLA2 and FLA9 controlling flag leaf angle in rice.","authors":"Tianhu Li, Zhen Yang, Yang Ang, Yingying Zhao, Yanan Zhang, Zhengbo Liu, Hao Sun, Yinping Chang, Mingyu Du, Xianping Cheng, Jinghan Sun, Erbao Liu","doi":"10.1186/s12864-025-11487-z","DOIUrl":"10.1186/s12864-025-11487-z","url":null,"abstract":"<p><strong>Background: </strong>In hybrid rice seed production, rice varieties with a small flag leaf angle (FLA) experience obstacles to cross-pollination at the early heading stage, and farmers usually need to remove flag leaves to achieve artificial pollination. Therefore, the cultivation of rice varieties with large FLAs can not only save a substantial amount of labour in the leaf-cutting process during artificial pollination but also accelerate the mechanization of hybrid rice seed production.</p><p><strong>Results: </strong>In this study, 431 rice accessions were included in a genome-wide association study (GWAS) to identify quantitative trait loci (QTLs) and the superior haplotypes for rice FLA in 2022 and 2023. The aim of the study was to identify new QTLs and provide germplasm resources for the genetic improvement of rice FLA. The population exhibited rich phenotypic variation in FLA in both years. The FLA GWAS was performed with more than 3 million single-nucleotide polymorphisms (SNPs), and eight QTLs associated with FLA were detected; of these, six QTLs located on rice chromosomes 1, 2, 8 and 9 were novel and detected in both years. In addition, these QTLs were analysed by haplotype analysis and functional annotation, and FLA2 and FLA9, which encode xyloglucan fucosyltransferase and cytokinin-O-glucosyltransferase 2, respectively, were identified as candidate genes for FLA regulation in rice. Quantitative real-time polymerase chain reaction (qRT‒PCR) results validated FLA2 and FLA9 as candidate genes. The results of this study showed that the elite alleles of FLA2 and FLA9 can increase FLA in rice. Excellent parents for FLA improvement were predicted through pyramiding breeding.</p><p><strong>Conclusions: </strong>A total of six new QTLs and two candidate genes (FLA2 and FLA9) were identified by a GWAS of 431 rice accessions over two years. The elite alleles and excellent parents predicted in our study can provide important information for the functional analysis of rice FLA-related genes and improvement through pyramiding breeding.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"280"},"PeriodicalIF":3.5,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11927237/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143676642","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Seminal plasma proteomics of asymptomatic COVID-19 patients reveals disruption of male reproductive function.","authors":"Jialyu Huang, Yufang Su, Jiawei Wang, Zheng Fang, Yiwei Zhang, Hong Chen, Xinxia Wan, Yuanhuan Xiong, Ning Song, Houyang Chen, Xingwu Wu","doi":"10.1186/s12864-025-11473-5","DOIUrl":"10.1186/s12864-025-11473-5","url":null,"abstract":"<p><strong>Background: </strong>A considerable proportion of males suffer from asymptomatic SARS-CoV-2 infection, while the effect on reproductive function and underlying pathomechanisms remain unclear.</p><p><strong>Results: </strong>The total sperm count decreased evidently after asymptomatic infection, yet all semen samples were tested to be SARS-CoV-2 RNA negative. Through label‑free quantitative proteomic profiling, a total of 733 proteins were further identified in seminal plasma from 11 COVID-19 patients and seven uninfected controls. Of the 37 differentially expressed proteins, 23 were upregulated and 14 were downregulated in the COVID-19 group compared with control. Functional annotations in Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Reactome showed that these proteins were highly enriched in infection, inflammation, and immunity-related pathways as well as spermatogenesis-associated biological process. Four proteins were significantly correlated with one or more semen parameters in Spearman's coefficient analysis, and seven were filtered as potential hub proteins from the interaction network by MCODE and Cytohubba algorithms. Furthermore, we verified the proteomic results by Western blot analysis of three representative proteins (ITLN1, GSTM2, and PSAP) in the validation cohort.</p><p><strong>Conclusions: </strong>In summary, our study showed that acute asymptomatic COVID-19 could alter the seminal plasma protein profile without direct testicular infection and consequently lead to impaired semen quality. These novel findings should enlighten the physicians about the adverse effects of SARS-CoV-2 infection on male fertility, and provide valuable resources for reproductive biologists to further decipher the molecular functions.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"281"},"PeriodicalIF":3.5,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11927139/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143676566","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The rumen microbiome and its metabolome together with the host metabolome regulate the growth performance of crossbred cattle.","authors":"Wei Zhao, Lina Ma, Lin Xue, Qiufei Jiang, Yuan Feng, Suwan Wang, Jinli Tian, Xiaohua Tian, Yaling Gu, Juan Zhang","doi":"10.1186/s12864-025-11465-5","DOIUrl":"10.1186/s12864-025-11465-5","url":null,"abstract":"<p><strong>Background: </strong>Although it has been demonstrated that gastrointestinal microorganisms greatly influence livestock performance, the effect of gastrointestinal microorganisms on the growth performance of crossbred cattle remains unclear. Due to their superior production characteristics, understanding the impact of gastrointestinal microorganisms on the growth performance of crossbred beef cattle is of significant importance for improving farming efficiency.</p><p><strong>Result: </strong>In this study, healthy Simmental with similar birth date and weight were selected as dams, Simmental (Combination I), Belgian Blue (Combination II) and Red Angus (Combination III) were used as parents for crossbreeding. The progeny of the three combination crosses were measured for growth performance under identical conditions from birth rearing to 18 months of age (n = 30). Rumen fluid and plasma were collected for macro-genomic and non-targeted metabolomic analysis (n = 8). The results showed that Combination II was superior to Combination I and Combination III in body weight (BW) and body height (BH) (P < 0.05). Mycoplasma, Succinivibrio, Anaerostipes, Methanosphaera, Aspergillus, and Acidomyces were significantly increased in the rumen of Combination II (P < 0.05), whereas differentially expressed metabolites (DEMs) 9,10,13-Trihome (11), 9,12,13-Trihome and 9(10)-Epome, and 9(S)-Hpode were reduced in abundance. In addition, plasma DEM PC (14:0/P-18:1(11Z)), PC (16:0/0:0), and PC (17:0/0:0) were down-regulated in combination II. Correlation analysis revealed that Anaerostipes, Methanosphaera, and Succinivibrio were associated with PC (14:0/P-18:1(11Z)), 9(10)-Epome, 9,10,13-Trihome (11), 9(S)-Hpode, 9,10,13-Trihome, PC (17:0/0:0), and PC (16:0/0:0). Growth traits were significantly positively correlated with the three dominant genera, Anaerostipes, Methanosphaera, and Succinivibrio, while significantly negatively correlated with key rumen metabolites and plasma metabolites (P < 0.05).</p><p><strong>Conclusions: </strong>Our study reveals the role of rumen microorganisms and its metabolites with host metabolism in the regulation of growth performance of crossbred cattle, which will contribute to the development of modern cattle breeding.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"278"},"PeriodicalIF":3.5,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11927116/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143676605","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole-genome bisulfite sequencing of X and Y sperm in Holstein bulls reveals differences in autosomal methylation status.","authors":"Aishao Shangguan, Fengling Ding, Rui Ding, Wei Sun, Xihe Li, Xiangnan Bao, Tiezhu Zhang, Huihui Chi, Qi Xiong, Mingxin Chen, Yang Zhou, Shujun Zhang","doi":"10.1186/s12864-025-11402-6","DOIUrl":"10.1186/s12864-025-11402-6","url":null,"abstract":"<p><p>A comprehensive understanding of the molecular differences between X and Y sperm in Holstein bull semen is crucial for advancing sex control technologies. While previous studies have primarily focused on proteomic and transcriptomic differences, the genome-wide DNA methylation differences between these sperm types remains largely unexplored. In this study, we employed whole-genome bisulfite sequencing to systematically compare the autosomal methylation profiles of X and Y sperm. Although global methylation patterns showed remarkable consistency between the two sperm types, our localized comparative analysis revealed 12,175 differentially methylated regions mapping to 2,041 genes (differentially methylated genes, DMGs). Functional enrichment analysis of these DMGs revealed their involvement in essential biological processes, particularly in energy metabolism and membrane voltage regulation. Notably, SPA17 and CHCHD3, identified as hypermethylated genes in X sperm in this study, have also been reported to show lower protein expression levels in X sperm compared to Y sperm. Furthermore, we identified 28 DMGs functionally associated with spermatogenesis and 5 DMGs related to fertilization. Our findings lay the foundation for thorough understanding of molecular differences between X and Y sperm in bull, providing essential insights for the development of more advanced sex control technologies in the future.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"282"},"PeriodicalIF":3.5,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11927118/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143676688","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"JSNMFuP: a unsupervised method for the integrative analysis of single-cell multi-omics data based on non-negative matrix factorization.","authors":"Bai Zhang, Mengdi Nan, Liugen Wang, Hanwen Wu, Xiang Chen, Yongle Shi, Yibing Ma, Jie Gao","doi":"10.1186/s12864-025-11462-8","DOIUrl":"10.1186/s12864-025-11462-8","url":null,"abstract":"<p><p>With the rapid advancement of sequencing technology, the increasing availability of single-cell multi-omics data from the same cells has provided us with unprecedented opportunities to understand the cellular phenotypes. Integrating multi-omics data has the potential to enhance the ability to reveal cellular heterogeneity. However, data integration analysis is extremely challenging due to the different characteristics and noise levels of different molecular modalities in single-cell data. In this paper, an unsupervised integration method (JSNMFuP) based on non-negative matrix factorization is proposed. This method integrates the information extracted from the latent variables of each omic through a consensus graph. High-dimensional geometrical structure is captured in the original data and biologically-related feature links across modalities are incorporated into the model using regularization terms. JSNMFuP can be utilized for data visualization and clustering, facilitating marker characterization and gene ontology enrichment analysis, providing rich biological insights for downstream analysis. The application on real datasets shows that JSNMFuP has superior performance in cell clustering. The factors are interpretable, making it an effective method for analyzing cell heterogeneity using single-cell multi-omics data.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"274"},"PeriodicalIF":3.5,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11924690/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143668884","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}