BMC Genomics最新文献

{"title":"Deciphering the molecular transcriptomic mechanisms of carbon ion beams and X-ray on rice seedlings.","authors":"Jianing Ding, Chaoli Xu, Yan Du, Xiao Liu, Jingmin Chen, Zhe Li, Jing Long, Yukun Sheng, Wenjie Jin, Dan Xu, Libin Zhou","doi":"10.1186/s12864-025-11488-y","DOIUrl":"https://doi.org/10.1186/s12864-025-11488-y","url":null,"abstract":"<p><strong>Background: </strong>Ionizing radiation (IR) is an abiotic stress factor that can be not only a means to explore plant resistance but also a potent mutagen in agricultural breeding. The diverse physical parameters of different types of IR result in varying effects on plants, which in turn leads to differences in the spectrum of genetic variations in the offspring. Investigating plant response mechanisms to different IR is crucial for enhancing plant resistance and comprehending of the differences in mutation generation from various physical mutagenic sources in mutation breeding. Nevertheless, the mechanism underlying the complex responses of plants to different IR are not yet fully comprehended.</p><p><strong>Results: </strong>we conducted transcriptome sequencing on rice seedlings that exhibited a relative root length of approximately 69% after being exposed to carbon ion beams (CIBs) and X-ray respectively. The results revealed that X-ray induced a greater number of differentially expressed genes (DEGs) than CIBs, with 5681 and 2198 DEGs were identified respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that DNA replication, damage repair, phytohormone signaling, and antioxidant pathways were implicated in the response of rice seedling to IR. These pathways demonstrated diverse response patterns following different IR. Additionally, through two IR with different linear energy transfer (LET), we found some common DEGs that contribute to the radiation response in rice seedlings, such as LOC4331062, LOC4333870.</p><p><strong>Conclusion: </strong>This study offers insights into the molecular transcriptomic mechanisms underlying the impacts of IR on rice seedlings. It provides a new perspective for further exploration of irradiation-induced damage repair factors and understanding the reasons for the differences in mutations created by different mutagenic sources in plants.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"308"},"PeriodicalIF":3.5,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11951728/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143742199","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-locus genome-wide association mapping for major agronomic and yield-related traits in sorghum (Sorghum bicolor (L.) moench) landraces.","authors":"Addisu Getahun, Admas Alemu, Habte Nida, Adugna Abdi Woldesemayat","doi":"10.1186/s12864-025-11458-4","DOIUrl":"https://doi.org/10.1186/s12864-025-11458-4","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Sorghum is a vital cereal crop for over 750 million people, ranking 5th globally. It has multiple purposes, including food, feed, and biofuels, and is essential in Ethiopia, which has a rich genetic diversity of various agroecological zones.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Objective: &lt;/strong&gt;Explore marker-trait associations (MTAs) to identify quantitative trait nucleotides (QTNs) and new candidate genes associated with agronomic and yield contributing traits in Ethiopian sorghum landraces using multi-locus GWAS models to assist the genomic-assisted breeding strategies.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Method: &lt;/strong&gt;This study investigates the genetic basis of agronomic traits in Ethiopian sorghum landraces through multi-locus Genome-Wide Association Studies (ML-GWAS). 216 landraces, improved varieties, and check cultivars were obtained from the Ethiopian Biodiversity Institute and the National Sorghum Improvement Program for this study. The experiment was conducted over two cropping seasons, employing an α-lattice design for phenotyping key traits such as days to flowering, days to maturity, plant height, seed number per plant, grain yield, and thousand seed weight. A mixed linear model (MLM) was used to analyze the phenotypic data and estimate the genetic parameters including variances and the broad sense heritability. GBS with the ApeKI restriction enzyme provided 50,165 high-quality SNP markers. The six ML-GWAS models identified significant QTNs with a LOD score threshold value of ≥ 4.0. The analysis revealed major QTNs associated with traits across multiple chromosomes, supported by a stringent filtering criterion that ensured reliability. Co-localization with known QTLs was explored using the Sorghum QTL Atlas database and candidate genes within significant QTN regions, providing the genetic architecture influencing agronomic performance were identified via the Phytozome platform using the biomaRt package.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Result: &lt;/strong&gt;Pearson correlation analysis revealed significant associations among most traits, with p-values less than 0.0001, except for grain yield per plant which showed lower correlations with other traits. Genetic variability analysis indicated that days to flowering exhibited high heritability (0.7) and genetic advance (19.6%) as percent of mean, suggesting strong genetic control, while grain yield displayed extremely low h&lt;sup&gt;2&lt;/sup&gt; (0.003). A total of 351,692 SNP markers were identified across 10 sorghum chromosomes from 216 Ethiopian sorghum landraces, and we have been refining this to 50,165 filtered SNPs. Manhattan plots indicated significant marker-trait associations (MTAs) across multiple chromosomes, particularly for days to flowering and plant height. Significant QTNs were associated with key traits including flowering time, plant height, and grain yield. ML-GWAS identified 176 QTNs with varying LOD scores and phenotypic effects. Multiple genes linked to these QTNs highlight the complexity of genetic inte","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"304"},"PeriodicalIF":3.5,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11951778/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143742230","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":"Metabolomics and transcriptomics analyses reveal the complex molecular mechanisms by which the hypothalamus regulates sexual development in female goats.","authors":"Qing Li, Tianle Chao, Yanyan Wang, Peipei He, Lu Zhang, Jianmin Wang","doi":"10.1186/s12864-025-11492-2","DOIUrl":"10.1186/s12864-025-11492-2","url":null,"abstract":"<p><strong>Background: </strong>The hypothalamus is a critical organ that regulates sexual development in animals. However, current research on the hypothalamic regulation of sexual maturation in female goats remains limited. In this study, we conducted metabolomic and transcriptomic analyses on the hypothalamic tissues of female Jining grey goats at different stages of sexual development (1 day old (neonatal, D1, n = 5), 2 months old (prepuberty, M2, n = 5), 4 months old (sexual maturity, M4, n = 5), and 6 months old (breeding period, M6, n = 5)).</p><p><strong>Results: </strong>A total of 418 differential metabolites (DAMs) were identified in this study, among which the abundance of metabolites such as anserine, L-histidine, carnosine, taurine, and 4-aminobutyric gradually increased with the progression of sexual development. These metabolites may regulate neuronal development and hormone secretion processes by influencing the metabolism of histidine and phenylalanine. Through combined transcriptomic and metabolomic analyses, we identified that differentially expressed genes such as mitogen-activated protein kinase kinase kinase 9 (MAP3K9), prune homolog 2 with BCH domain (PRUNE2), and potassium voltage-gated channel interacting protein 4(KCNIP4) may jointly regulate the development and energy metabolism of hypothalamic Gonadotropin-releasing hormone neurons in conjunction with DAMs, including LPC22:5, 2-Arachidonyl Glycerol ether, LPE22:5, and Lysops22:5. Additionally, we elucidated the molecular mechanism through which glutathione metabolism regulates sexual maturation in goats.</p><p><strong>Conclusions: </strong>In summary, this study illustrates the dynamic changes in metabolites and mRNA within hypothalamic tissue during postnatal sexual maturation in female Jining grey goats. This research may provide significant scientific insights for future animal breeding.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"303"},"PeriodicalIF":3.5,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11951529/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143728394","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 of the invasive North American Haemaphysalis longicornis tick as a template for bovine anti-tick vaccine discovery.","authors":"Mohamed Abdallah Mohamed Moustafa, Miranda M Barnes, Nicole E Wagner, Deanna Bodine, Kylie Bendele, Pete D Teel, Perot Saelao, Dana C Price","doi":"10.1186/s12864-025-11477-1","DOIUrl":"https://doi.org/10.1186/s12864-025-11477-1","url":null,"abstract":"<p><strong>Background: </strong>The ixodid tick Haemaphysalis longicornis Neumann, commonly referred to as the Asian longhorned tick, has expanded its range outside of East Asia into countries such as Australia, New Zealand, and the United States. Since the first U.S. detection in 2017, H. longicornis has spread to 21 states and the District of Columbia and has been implicated as a vector of various human and animal pathogens including Theileria orientalis Ikeda genotype, a causal agent of bovine theileriosis. Facilitated in part by the parthenogenetic nature of invasive populations, this tick has become a paramount threat to agricultural rangelands and U.S. livestock production. Reliance on traditional acaricides for vector control selects for resistant individuals, reducing the effectiveness of many chemical tools over time. Thus, focus has shifted to alternative control mechanisms including anti-tick vaccine development. To further such research, here we sequence and assemble a high-quality H. longicornis genome and robust gene catalog from invasive North American ticks while also providing an organ-specific transcriptomic expression catalog and in-depth informatic screening of the tick proteome for potential bovine antigenic molecules with potential utility as vaccine candidates.</p><p><strong>Results: </strong>Using a combination of PacBio HiFi single-molecule sequencing and Hi-C chromosome conformation capture data, our genome assembly contains 270 scaffolds and spans a haploid genome size of 3.09 Gbp with an N50 of 213.4 Mbp. Gene prediction identified 21,947 high-confidence gene structures containing 96.2% of the core Arthropoda odb10 orthologs. Our organ-specific transcriptome library comprising salivary glands, midgut, ovaries, foreleg and hindleg additionally highlights potential anti-tick vaccine candidates and metabolic pathways to target for future in vitro trials.</p><p><strong>Conclusions: </strong>Single-molecule sequencing of a triploid, parthenogenetic North American Haemaphysalis longicornis tick allowed for the generation of a highly contiguous genome assembly that, when coupled with extensive transcriptome profiling, resulted in a robust gene catalog containing multiple candidates for further study as anti-tick vaccine antigens.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"307"},"PeriodicalIF":3.5,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11951522/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143742223","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":"Efficient blockLASSO for polygenic scores with applications to all of us and UK Biobank.","authors":"Timothy G Raben, Louis Lello, Erik Widen, Stephen D H Hsu","doi":"10.1186/s12864-025-11505-0","DOIUrl":"10.1186/s12864-025-11505-0","url":null,"abstract":"<p><p>We develop a \"block\" LASSO (blockLASSO) approach for training polygenic scores (PGS) and demonstrate its use in All of Us (AoU) and the UK Biobank (UKB). blockLASSO utilizes the approximate block diagonal structure (due to chromosomal partition of the genome) of linkage disequilibrium (LD). The new implementation can be used for exploratory and methods research where repeated PGS training is necessary and expensive. For 11 different phenotypes, in two different biobanks, and across 5 different ancestry groups (African, American, East Asian, European, and South Asian) - we demonstrate that blockLASSO is generally as effective for training PGS as a (global) LASSO. Previous work has shown penalized regression methods produce competitive PGS to alternative approaches. It has been shown that some phenotypes are more/less polygenic than others. Using sparse algorithms, an accurate PGS can be trained for type 1 diabetes (T1D) using <math><mrow><mo>∼</mo> <mn>100</mn></mrow> </math> single nucleotide variants (SNVs), but a PGS for body mass index (BMI) would need more than 10k SNVs. blockLASSO produces similar PGS for phenotypes while training with just a fraction of the variants per block. Within AoU (using only genetic information) block PGS for T1D reaches an AUC of <math><mrow><mn>0</mn> <mo>.</mo> <msub><mn>63</mn> <mrow><mo>±</mo> <mn>0.02</mn></mrow> </msub> </mrow> </math> and for BMI a correlation of <math><mrow><mn>0</mn> <mo>.</mo> <msub><mn>21</mn> <mrow><mo>±</mo> <mn>0.01</mn></mrow> </msub> </mrow> </math> , whereas a global LASSO approach which finds for T1D an AUC <math><mrow><mn>0</mn> <mo>.</mo> <msub><mn>65</mn> <mrow><mo>±</mo> <mn>0.03</mn></mrow> </msub> </mrow> </math> and BMI a correlation <math><mrow><mn>0</mn> <mo>.</mo> <msub><mn>19</mn> <mrow><mo>±</mo> <mn>0.03</mn></mrow> </msub> </mrow> </math> . This new block approach is more computationally efficient and scalable than naive global machine learning approaches and makes it ideal for exploratory methods investigations based on penalized regression.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"302"},"PeriodicalIF":3.5,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11948729/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143728393","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":"MuPETFlow: multiple ploidy estimation tool from flow cytometry data.","authors":"C Gómez-Muñoz, G Fischer","doi":"10.1186/s12864-025-11470-8","DOIUrl":"10.1186/s12864-025-11470-8","url":null,"abstract":"<p><strong>Background: </strong>Ploidy, representing the number of homologous chromosome sets, can be estimated from flow cytometry data acquired on cells stained with a fluorescent DNA dye. This estimation relies on a combination of tools that often require scripting, individual sample curation, and additional analyses.</p><p><strong>Results: </strong>To automate the ploidy estimation for multiple flow cytometry files, we developed MuPETFlow-a Shiny graphical user interface tool. MuPETFlow allows users to visualize cell fluorescence histograms, detect the peaks corresponding to the different cell cycle phases, perform a linear regression using standards, make ploidy or genome size predictions, and export results as figures and table files. The tool was benchmarked with known ploidy datasets from yeast and plant species, yielding consistent ploidy results. MuPETFlow's peaks detection and performance were also compared to those of other tools.</p><p><strong>Conclusions: </strong>MuPETFlow stands out as the only tool offering in-app ploidy detection, multiple peak detection, multi-sample visualization, and automation capabilities. These features significantly accelerate the analysis, making it especially valuable for projects involving large datasets.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"301"},"PeriodicalIF":3.5,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11948760/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143717561","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 chromatin accessibility and selective signals of meat rabbits reveal key Cis-regulatory elements and variants during postnatal development of skeletal muscles in rabbits.","authors":"Kun Du, Dai-Hua Wang, Shen-Qiang Hu, Yu Xia, Qian Wu, Mao-Qing Gu, Xi-Wen Chen","doi":"10.1186/s12864-025-11496-y","DOIUrl":"10.1186/s12864-025-11496-y","url":null,"abstract":"<p><strong>Background: </strong>The development of skeletal muscles is intricately modulated by multiple genetic factors and significantly impacts the economic value of meat rabbits. However, our knowledge of epigenetics in rabbit skeletal muscles remains largely unknown.</p><p><strong>Results: </strong>In this study, we collected leg skeletal muscles of rabbits and performed assays for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) to detect open chromatin across three developmental stages: birth (D1), weaning (D35), and adulthood (D75). A total of 126,959 accessible chromatin regions (ACRs) were identified across samples, and a broad increase and decrease in chromatin accessibility were found from D1 to D35 and D35 to D75, respectively. Integrative analysis of chromatin accessibility and transcriptome data revealed ACRs that were nearly closed at D1 but highly accessible at D35 and D75 were significantly enriched in skeletal muscle development. Cis-regulation analysis further revealed that genes dominated by enhancers mainly play roles in the neuron development of rabbit skeletal muscles. Moreover, the detection of selection signals of meat rabbits and the footprinting analysis of transcription factor at open chromatin revealed that both base transversion (Chr13:12144967 A-> G) and the dynamics of chromatin accessibility at the PRDM1 binding site might regulate ZSWIM5 during the development of skeletal muscles in rabbits.</p><p><strong>Conclusions: </strong>Our study provided a category of potential cis-regulatory elements for understanding the development of skeletal muscles at the tissue level and might facilitate potential insights into growth regulation in rabbits.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"296"},"PeriodicalIF":3.5,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11934498/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143708382","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 AAT gene family in quinoa and analysis of its expression pattern under abiotic stresses.","authors":"Hanxue Li, Chunhe Jiang, Junna Liu, Ping Zhang, Li Li, Rongbo Li, Liubin Huang, Xuqin Wang, Guofei Jiang, Yutao Bai, Lingyuan Zhang, Peng Qin","doi":"10.1186/s12864-025-11491-3","DOIUrl":"10.1186/s12864-025-11491-3","url":null,"abstract":"<p><strong>Background: </strong>Plant amino acid transporters play an important role in the absorption of soil amino acids by roots, the transport of amino acids between xylem and phloem, plant growth and development, and response to abiotic stress.</p><p><strong>Result: </strong>In this study, we identified 147 AAT genes in the quinoa genome sequence and categorized them into 12 subfamilies on the basis of their similarity and phylogenetic relationships with AAT found in Arabidopsis thaliana. Interestingly, these AAT genes are not evenly distributed on the quinoa chromosomes. Instead, most of these genes are centrally located on the outer edges of the chromosome arms. After performing motif analysis and gene structure analysis, we observed the consistent presence of similar motifs and intron-exon distribution patterns among subfamilies. Tissue expression analysis revealed that CqAAT gene was less expressed in fruits and more expressed in roots, stems, leaves and flowers. Meanwhile, expression analysis under four adversities of high temperature, low temperature, waterlogging, and drought and different treatments of nitrogen, phosphorus, and potash fertilizers found that two genes of the CqGAT subfamily, AUR62031750 and AUR62023955 were up-regulated expressed under abiotic stresses.</p><p><strong>Conclusions: </strong>In summary, there is a significant differentiation in the tissue expression and stress expression of the CqAAT gene, indicating that CqAATs play a role in regulating growth and development under abiotic stress.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"298"},"PeriodicalIF":3.5,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11938623/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143708386","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":"Isolation and characterization of a roseophage representing a novel genus in the N4-like Rhodovirinae subfamily distributed in estuarine waters.","authors":"Xingyu Huang, Chen Yu, Longfei Lu","doi":"10.1186/s12864-025-11463-7","DOIUrl":"10.1186/s12864-025-11463-7","url":null,"abstract":"<p><strong>Background: </strong>Roseobacteraceae, often referred to as the marine roseobacter clade (MRC), are pivotal constituents of bacterial communities in coastal and pelagic marine environments. During the past two decades, 75 roseophages that infect various Roseobacteraceae lineages have been isolated. The N4-like roseophage clade, which encompasses 15 members, represents the largest clade among these roseophages. N4-like phages form a monophyletic group, classified as family Schitoviridae. And all N4-like roseophages form a unique clade within Schitoviridae and has been classified as the Rhodovirinae subfamily.</p><p><strong>Results: </strong>In this study, we isolated a novel roseophage, vB_DshP-R7L, that infects Dinoroseobacter shibae DFL12 from Xiamen Bay in the East China Sea. Conserved genes of Schitoviridae have been identified in the genome of vB_DshP-R7L, and following phylogenetic analysis suggests that the newly isolated phage is a member of the Rhodovirinae subfamily and represents the sole member of a novel genus, Gonggongvirus. The genome of vB_DshP-R7L harbors six auxiliary metabolic genes (AMGs), most of which potentially enhance DNA de novo synthesis. Additionally, a gene encoding ribosomal protein was identified. Comparative genomic analysis of AMG content among Rhodovirinae indicates a distinct evolutionary history characterized by independent ancient horizontal gene transfer events. Read-mapping analysis reveals the prevalence of vB_DshP-R7L and other Rhodovirinae roseophages in estuarine waters.</p><p><strong>Conclusions: </strong>Our work illustrates the genomic features of a novel roseophage clade among the subfamily Rhodovirinae. The AMG content of vB_DshP-R7L is under severe purification selection, which reveals their possible ecological importance. We also demonstrated that vB_DshP-R7L and other Rhodovirinae roseophages are only detected in estuaries. Our isolation and characterization of this novel phage expands the understanding of the phylogeny, gene transfer history, and biogeography of Rhodovirinae infecting marine Roseobacteraceae.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"295"},"PeriodicalIF":3.5,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11934525/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143708393","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":"Transcriptomic characterisation of acute myeloid leukemia cell lines bearing the same t(9;11) driver mutation reveals different molecular signatures.","authors":"Elise Georges, William Ho, Miren Urrutia Iturritza, Lel Eory, Kamila Malysz, Ulduz Sobhiafshar, Alan L Archibald, Daniel J Macqueen, Barbara Shih, David Garrick, Douglas Vernimmen","doi":"10.1186/s12864-025-11415-1","DOIUrl":"10.1186/s12864-025-11415-1","url":null,"abstract":"<p><strong>Background: </strong>Acute myeloid leukemia (AML) is the most common type of acute leukemia, accounting for 20% of cases in children and adolescents. Genome-wide studies have identified genes that are commonly mutated in AML, including many epigenetic regulators involved in either DNA methylation (DNMT3A, TET2, IDH1/2) or histone post-translational modifications (ASXL1, EZH2, MLL1). Several cell lines derived from AML patients are widely used in cancer research. Whether important differences in these cell lines exist remains poorly characterised.</p><p><strong>Results: </strong>Here, we used RNA sequencing (RNA-Seq) to contrast the transcriptome of four commonly used AML-derived cell lines: THP-1, NOMO-1, MOLM-13 bearing the common initiating t(9;11) translocation, and MV4.11 bearing the t(4;11) translocation. Gene set enrichment analyses and comparison of key transcription and epigenetic regulator genes revealed important differences in the transcriptome, distinguishing these AML models. Among these, we found striking differences in the expression of clusters of genes located on chromosome 19 encoding Zinc Finger (ZNF) transcriptional repressors. Low expression of many ZNF genes within these clusters is associated with poor survival in AML patients.</p><p><strong>Conclusion: </strong>The present study offers a valuable resource by providing a detailed comparative characterisation of the transcriptome of cell lines within the same AML subtype used as models for leukemia research.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"300"},"PeriodicalIF":3.5,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11938659/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143708400","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}