BMC Genomics最新文献

{"title":"A computational HLA allele-typing protocol to de-noise and leverage nanopore amplicon data.","authors":"Jalal Siddiqui, Rohita Sinha, James Grantham, Ronnie LaCombe, Judith R Alonzo, Scott Cowden, Steven Kleiboeker","doi":"10.1186/s12864-025-11547-4","DOIUrl":"https://doi.org/10.1186/s12864-025-11547-4","url":null,"abstract":"<p><strong>Background: </strong>Rapid turnaround time for a third-field resolution deceased donor human leukocyte antigen (HLA) typing is critical to improve organ transplantation outcomes. Third generation DNA sequencing platforms such as Oxford Nanopore (ONT) offer the opportunity to deliver rapid results at single nucleotide level resolution, in particular sequencing data that could be denoised computationally. Here we present a computational pipeline for up-to third-field HLA allele typing following ONT sequencing.</p><p><strong>Results: </strong>From a R10.3 flow cell batch of 31 samples of known HLA allele types, up to 10,000 ONT reads were aligned using BWA aligner to reference allele sequences from the IPD-IMGT/HLA database. For each gene, the top two hits to reference alleles at the third field were selected. Using our pipeline, we obtained the following percent concordance at the 1st, 2nd and 3rd field: HLA-A (98.4%, 98.4%, 98.4%), HLA-B (100%, 96.8%, 96.8%), HLA-C (100%, 98.4%, 98.4%), HLA-DPA1 (100%, 96.8%, 96.8%), HLA-DPB1 (100%, 100%, 98.4%), HLA-DQA1 (100%, 98.4%, 98.4%), HLA-DQB1 (100%, 98.4%, 98.4%), HLA-DRB1 (83.9%, 64.5%, 64.5%), HLA-DRB3 (82.6%, 73.9%, 73.9%), HLA-DRB4 (100%, 100%, 100%) and HLA-DRB5 (100%, 100%, 100%). By running our pipeline on an additional R10.3 flow cell batch of 63 samples, the following percent concordances were obtained:: HLA-A (100%, 96.8%, 88.1%), HLA-B (100%, 90.5.4%, 88.1%), HLA-C (100%, 99.2%, 99.2%), HLA-DPA1 (100%, 98.4%, 97.6%), HLA-DPB1 (98.4%, 97.6%, 92.9%), HLA-DQA1 (100%, 100%, 98.4%), HLA-DQB1 (100%, 97.6%, 96.0%), HLA-DRB1 (88.9%, 68.3%, 68.3%), HLA-DRB3 (81.0%, 61.9%, 61.9%), HLA-DRB4 (100%, 97.4%, 94.7%) and HLA-DRB5 (73.3%, 66.7%, 66.7%). In addition, our pipeline demonstrated significantly improved concordance compared to publicly available pipeline HLA-LA and concordances close to Athlon2 in commercial development.</p><p><strong>Conclusion: </strong>Our algorithm had a > 96% concordance for non-HLA-DRB genes at 3rd field on the first batch and > 88% concordance for non-HLA-DRB genes at 3rd field and > 90% at 2nd field on the second batch tested. In addition, it out-performs HLA-LA and approaches the performance of the Athlon2. This lays groundwork for better utilizing Nanopore sequencing data for HLA typing especially in improving organ transplant outcomes.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"356"},"PeriodicalIF":3.5,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143810266","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}

{"title":"Genetic diversity and population structure in Ethiopian mustard (Brassica carinata A. Braun) revealed by high-density DArTSeq SNP genotyping.","authors":"Yirssaw Demeke Ambaw, Andargachew Gedebo Abitea, Temesgen Magule Olango","doi":"10.1186/s12864-025-11469-1","DOIUrl":"https://doi.org/10.1186/s12864-025-11469-1","url":null,"abstract":"<p><strong>Background: </strong>Ethiopian mustard (Brassica carinata (A) Braun) is a promising oilseed crop with the potential for sustainable biofuel and bio-industrial applications. Despite the presence of diverse germplasms in Ethiopia, their genetic diversity remains largely unexplored. This study evaluated the genetic diversity and population structure of 188 B. carinata genotypes using high-density Single Nucleotide Polymorphism (SNP) markers generated though DArTseq™ Genotyping-by-Sequencing (GBS). Of the 15,515 identified DArTSeq SNPs, 3,793 high-quality markers were retained and used to analyze the genetic diversity and population structure.</p><p><strong>Results: </strong>The results from STRUCTURE, principal coordinate analysis (PCoA), and neighbor-joining tree analyses revealed two slightly distinct subpopulations, with Pop1 predominantly comprising genotypes from the Oromia and Amhara regions (86.17%), whereas Pop2 primarily consisted of released varieties, suggests the influence of targeted selection. Despite the presence of subpopulations, PCoA indicated a relatively limited overall genetic diversity among the genotypes. Analysis of Molecular Variance (AMOVA) revealed higher genetic variation within populations (65.19%) than between populations (34.81%), resulting in low genetic differentiation (PhiPT = 0.02) and high gene flow (Nm = 5.74). Notably, subpopulation formation was not strongly correlated with geographical origin, highlights that factors beyond geography, such as gene flow and selection pressure, may have played a significant role in shaping the observed genetic diversity. Genetic diversity indices revealed a slightly low-to-moderate variation within the B. carinata populations, as evidenced by the slightly low expected heterozygosity (He = 0.21) and moderate polymorphic information content (PIC = 0.36).</p><p><strong>Conclusion: </strong>Overall, this study revealed a moderate level of genetic diversity within the evaluated B. carinata genotypes. The results offer valuable insights into the genetic structure of this species and highlight the need for targeted strategies to enhance genetic diversity in future breeding initiatives and conservation efforts.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"354"},"PeriodicalIF":3.5,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143810268","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}

{"title":"Transcriptomic analysis of Myxococcus xanthus csgA, fruA, and mrpC mutants reveals extensive and diverse roles of key regulators in the multicellular developmental process.","authors":"Mark A Farrugia, Ramya Rajagopalan, Lee Kroos","doi":"10.1186/s12864-025-11417-z","DOIUrl":"https://doi.org/10.1186/s12864-025-11417-z","url":null,"abstract":"<p><strong>Background: </strong>The bacterium Myxococcus xanthus provides an important multicellular model for understanding stress responses. The regulatory proteins CsgA, FruA, and MrpC are essential to survive prolonged starvation by forming fruiting bodies, which are mounds containing hardy round spores formed from vegetative rods, but the genome-wide pathways affected by these proteins remain poorly understood. Only a fruA mutant transcriptome and MrpC ChIP-seq have been reported. We describe RNA-seq transcriptome analysis of csgA, fruA, and mrpC mutants relative to a wild-type laboratory strain midway during the starvation-induced developmental process, when mounds, but not spores, have formed.</p><p><strong>Results: </strong>We show that CsgA, FruA, and MrpC broadly impact developmental gene expression, with over 60% of the genes differentially expressed in one or more mutants. Building upon previous investigations, we found that strongly regulated genes in the mrpC mutant correlate with MrpC DNA-binding sites located ~ 80 bp upstream of transcriptional start sites. We also confirmed that FruA directly or indirectly regulates many genes negatively, as well as many others positively. CsgA regulates indirectly and its strongest effects are positive. MrpC strongly stimulates fruA transcription and FruA accumulation, impacting many genes, but our results reveal that MrpC is also a strong negative or positive regulator of hundreds of genes independently of FruA. Indeed, we observed nearly every possible pattern of coregulation, unique regulation, and counterregulation by comparing the wild-type and mutant transcriptomes, indicating diverse roles of CsgA, FruA, and MrpC in the developmental gene regulatory network. The genes most strongly regulated were coregulated in two or three of the mutants. Each set of genes exhibiting differential expression in one or more mutants was analyzed for enrichment of gene ontology (GO) terms or KEGG pathways, and predicted protein-protein interactions. These analyses highlighted enrichment of pathways involved in cellular signaling, protein synthesis, energetics, and envelope function. In particular, we describe how CsgA, FruA, and MrpC control production of ribosomes, lipid signals, and peptidoglycan intermediates during development.</p><p><strong>Conclusions: </strong>By comparing wild-type and mutant transcriptomes midway in development, this study documents individual and coordinate regulation of crucial pathways by CsgA, FruA, and MrpC, providing a valuable resource for future investigations.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"355"},"PeriodicalIF":3.5,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143810272","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}

{"title":"scAMZI: attention-based deep autoencoder with zero-inflated layer for clustering scRNA-seq data.","authors":"Lin Yuan, Zhijie Xu, Boyuan Meng, Lan Ye","doi":"10.1186/s12864-025-11511-2","DOIUrl":"10.1186/s12864-025-11511-2","url":null,"abstract":"<p><strong>Background: </strong>Clustering scRNA-seq data plays a vital role in scRNA-seq data analysis and downstream analyses. Many computational methods have been proposed and achieved remarkable results. However, there are several limitations of these methods. First, they do not fully exploit cellular features. Second, they are developed based on gene expression information and lack of flexibility in integrating intercellular relationships. Finally, the performance of these methods is affected by dropout event.</p><p><strong>Results: </strong>We propose a novel deep learning (DL) model based on attention autoencoder and zero-inflated (ZI) layer, namely scAMZI, to cluster scRNA-seq data. scAMZI is mainly composed of SimAM (a Simple, parameter-free Attention Module), autoencoder, ZINB (Zero-Inflated Negative Binomial) model and ZI layer. Based on ZINB model, we introduce autoencoder and SimAM to reduce dimensionality of data and learn feature representations of cells and relationships between cells. Meanwhile, ZI layer is used to handle zero values in the data. We compare the performance of scAMZI with nine methods (three shallow learning algorithms and six state-of-the-art DL-based methods) on fourteen benchmark scRNA-seq datasets of various sizes (from hundreds to tens of thousands of cells) with known cell types. Experimental results demonstrate that scAMZI outperforms competing methods.</p><p><strong>Conclusions: </strong>scAMZI outperforms competing methods and can facilitate downstream analyses such as cell annotation, marker gene discovery, and cell trajectory inference. The package of scAMZI is made freely available at https://doi.org/10.5281/zenodo.13131559 .</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"350"},"PeriodicalIF":3.5,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143802331","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}

{"title":"Multi-omics reveals the mechanism of quality discrepancy between Gayal (Bos frontalis) and yellow cattle beef.","authors":"Lin Han, Runqi Fu, Chunjia Jin, Huan Gao, Binlong Fu, Qian Li, Ye Yu, Min Qi, Jiawei Zhang, Shengyong Mao, Jing Leng","doi":"10.1186/s12864-025-11519-8","DOIUrl":"10.1186/s12864-025-11519-8","url":null,"abstract":"<p><strong>Background: </strong>Producing high-quality beef with enhanced muscle composition and reduced fat content is critical for meeting consumer preferences and supporting a balanced diet. Given the substantial variability in beef quality across cattle breeds, this study aimed to identify key determinants of meat quality by examining Gayal (Bos frontalis) and yellow cattle (Bos taurus) through a multi-disciplinary approach.</p><p><strong>Results: </strong>The results demonstrated that Gayal cattle exhibited superior meat quality, characterized by higher levels of protein, flavor-enhancing and essential amino acids, total amino acids, and polyunsaturated fatty acids (PUFAs), alongside reduced fat content, with similar trends observed in serum hormone and amino acid profiles. Distinct differences in gut microbial composition, enzymatic activities, and metabolites were observed between the breeds. Gayal displayed increased abundances of key bacterial taxa such as Akkermansia, Paeniclostridium, Escherichia-Shigella, and Clostridium sensu stricto 1, which were associated with enhanced volatile fatty acids (VFAs), ammoniacal nitrogen, and enzymatic activity in the colon. Transcriptomic analysis of the psoas major (PM) muscle revealed significant changes in genes linked to muscle development, amino acid metabolism, and lipid metabolism. Genes related to intestinal amino acid absorption were upregulated in Gayal, while those connected to short-chain fatty acid absorption were downregulated. Correlation analyses underscored the role of gut microbiota and metabolic profiles in modulating gene expression associated with lipid and amino acid metabolism, ultimately influencing meat flavor and quality.</p><p><strong>Conclusions: </strong>These findings provide actionable insights into the genetic and microbial factors underlying beef quality, offering a foundation for enhancing local cattle resources, optimizing breeding programs, and advancing the production of premium beef to meet both market and dietary needs.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"351"},"PeriodicalIF":3.5,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143802326","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}

{"title":"Genome-wide identification and transcriptome analysis of the cytochrome P450 genes revealed its potential role in the growth of Flammulina filiformis.","authors":"Xun Liu, Xinmin Liang, Jing Han, Yuqin Cui, Mengting Lei, Bo Wang, Dinghong Jia, Weihong Peng, Xiaolan He","doi":"10.1186/s12864-025-11555-4","DOIUrl":"10.1186/s12864-025-11555-4","url":null,"abstract":"<p><strong>Background: </strong>The CYP450 family members have been extensively studied in plants, where they play essential roles in metabolism, responses to biotic and abiotic stresses, and the regulation of growth and development. However, their functions in edible fungi remain largely unexplored. Flammulina filiformis, an economically important mushroom, lacks a comprehensive analysis of its CYP450 genes. Therefore, this study aims to identify and characterize the CYP450 gene family in F. filiformis at the genome-wide level, investigate their expression patterns, and explore their potential biological functions, providing valuable insights into their roles in fungal growth and adaptation.</p><p><strong>Results: </strong>In this study, 59 CYP450 genes, categorizing into 6 distinct clades, were identified within the genome of F. filiformis. Subcellular localization predictions suggested that the majority of these CYP450 genes are located in the endomembrane system. These 59 genes were distributed randomly across 12 chromosomes. Gene duplication analysis revealed the presence of 3 pairs of tandem repeats and 3 pairs of segmental repeat genes. Transcriptomic analysis revealed 861 differentially expressed genes (DEGs) in ML compared with M, and 3208 DEGs in P compared with ML. The 'oxidoreductase activity' category was significantly enriched in the ML vs. M and P vs. ML comparisons, with CYP450 genes being predominantly represented among the DEGs. Transcriptional expression analysis demonstrated that 4 genes exhibited the highest expression levels in the M sample, 6 genes in the ML sample, and 10 genes in the primordium. Furthermore, quantitative real-time PCR (qRT-PCR) analysis revealed that 11 genes, including HNY6_9861, HNY6_4590, HNY6_1561, HNY6_281, HNY6_12367, HNY6_8704, HNY6_9581, HNY6_8517, HNY6_11881, HNY6_9098 and HNY6_5841, exhibited an increasing trend in expression levels across the lower, middle and upper parts of the stipe in both white and yellow strains. This suggests that CYP450 genes may involved in the elongation of the stipe of F. filiformis.</p><p><strong>Conclusions: </strong>These results provide a foundation for further exploration of the molecular evolution mechanism and potential functions of the CYP450 genes of F. filiformis in the regulation of growth and development.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"346"},"PeriodicalIF":3.5,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143802309","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}

{"title":"Identification of the ADH gene family in Trichosporon asahii and the role of TaADH_like in pathogenicity and fluconazole resistance.","authors":"Zhen Liu, Xiaoping Ma, Xiangwen Zeng, Zhiguo Li, Ruiguo Liu, Rongyan Luo, Weichen Wang, Muhammad Salman Tahir, Chengdong Wang, Yu Gu","doi":"10.1186/s12864-025-11546-5","DOIUrl":"10.1186/s12864-025-11546-5","url":null,"abstract":"<p><p>Alcohol dehydrogenase has been studied in regulation of fungal growth and development, stress response and pathogenesis, but its function in T. asahii remains unexplored. In this study, we analyzed the ADH gene family in T. asahii for the first time, identifying six ADH genes and containing conserved ADH_N and ADH_Zinc_N domains. We constructed an overexpression strain of the most significantly differentially expressed gene TaADH_like and compared its phenotypes with those of the wild-type strain, focusing on colony morphology, biofilm biomass, stress response, drug resistance, and pathogenicity. The results showed that TaADH_like overexpression reduced sensitivity to hypoxic conditions, altered the hyphae-to-yeast transition, and led to slower growth, decreased colonization ability, reduced tissue damage, and lower lethality. Increased osmotic stress sensitivity and the involvement of the HOG MAPK pathway in the hyphae-to-yeast conversion contributed to the reduced colonization capacity of T. asahii. Furthermore, the overexpression of TaADH_like promoted biofilm formation and led to a slight enhancement in fluconazole resistance in T. asahii. This study is the first to elucidate the function of the alcohol dehydrogenase gene in T. asahii, providing a foundation for future genetic research on this pathogen.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"352"},"PeriodicalIF":3.5,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143802322","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}

{"title":"Diversity and evolution analysis of RNA viruses in three wheat aphid species.","authors":"Ke-Hui Feng, Yu-Hua Qi, Zhuang-Xin Ye, Ting Li, Gao-Yang Jiao, Chuan-Xi Zhang, Jian-Ping Chen, Gang Lu, Jun-Min Li","doi":"10.1186/s12864-025-11512-1","DOIUrl":"10.1186/s12864-025-11512-1","url":null,"abstract":"<p><strong>Background: </strong>Although advances in metagenomics, viral diversity and non-retroviral endogenous viral elements (EVEs) in wheat aphids remain underexplored. By analyzing 470 publicly available datasets and one laboratory-generated transcriptome, the RNA virome and EVEs in the genomes of Sitobion avenae, Schizaphis graminum, and Rhopalosiphum padi were systematically investigated.</p><p><strong>Results: </strong>We identified 43 RNA viruses, including 12 novel and 31 known RNA viruses. These viruses were widely distributed and abundant in different geographic populations of three wheat aphid species. +ssRNA viruses were the dominant type of aphid viruses. Besides, 90 EVEs were discovered in the genomes of three aphid species. In addition, the EVEs exhibit potential domestication and novel functional roles within aphid genomes.</p><p><strong>Conclusions: </strong>This study expands the understanding of RNA virus diversity in aphids and provides valuable insights into the potential functions of EVEs in virus-host coevolution.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"353"},"PeriodicalIF":3.5,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143802307","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}

{"title":"Identification and expression profile analysis of circRNAs associated with goat uterus with different fecundity during estrous cycle.","authors":"Xiaolong Du, Yufang Liu, Xiaoyun He, Lin Tao, Meiying Fang, Mingxing Chu","doi":"10.1186/s12864-025-11489-x","DOIUrl":"10.1186/s12864-025-11489-x","url":null,"abstract":"<p><strong>Background: </strong>The Yunshang Black Goat, a distinguished meat goat breed native to China, is renowned for its superior reproductive capabilities. Despite this, there is considerable phenotypic variability within the breed. During the reproductive cycle, the uterus plays a pivotal role, with its functions evolving in line with the different stages of the cycle. This study focuses on the uterine tissues, including both the endometrium and myometrium, of Yunshang Black Goats with high fecundity (HF) and low fecundity (LF) during the proliferative (FP) and secretory (LP) phases of the estrous cycle. By examining these tissues, we aim to elucidate the underlying molecular and physiological mechanisms of the observed differences in reproductive success.</p><p><strong>Results: </strong>High-throughput sequencing was conducted, followed by bioinformatics analysis to identify the expression profiles of circRNAs. A total of 7,445 circRNAs were identified through the integration of findings from find_circ and CIRI2 software. Comparative analyses between the FPLF vs. FPHF and LPLF vs. LPHF revealed 149 differentially expressed (DE) circRNAs (94 up-regulated and 55 down-regulated) and 276 DE circRNAs (56 up-regulated and 220 down-regulated), respectively. The enrichment analysis indicated that the primary pathways involved were the Sphingolipid signaling pathway, MAPK signaling pathway, and GnRH signaling pathway, all of which are closely associated with cellular growth and development. Additionally, several key candidate genes were identified, such as FGF2 and MBTPS1. We also predicted a total of 281 miRNA-circRNA binding pairs, encompassing 263 circRNAs and 60 miRNAs, and simultaneously, 14 coding circRNAs were anticipated.</p><p><strong>Conclusion: </strong>Based on the analysis, we have established the expression profiles of circRNAs during the follicular and luteal phases, respectively. Furthermore, using various analytical methods and data from high- and low-yield experimental control groups over different periods, we have identified multiple circRNAs that affect the high reproductive capacity of goats. Through enrichment analysis of the host genes of these circRNAs, we have discovered several key candidate genes. These findings provide fundamental data for the study of the molecular mechanisms underlying the fecundity of goats and pave the way for future genetic improvement strategies.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"349"},"PeriodicalIF":3.5,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143802311","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}

{"title":"RNA-sequencing demonstrates transcriptional differences between human vocal fold fibroblasts and myofibroblasts.","authors":"Michelle Bretl, Lingxin Cheng, Christina Kendziorski, Susan L Thibeault","doi":"10.1186/s12864-025-11533-w","DOIUrl":"10.1186/s12864-025-11533-w","url":null,"abstract":"<p><strong>Background: </strong>Differentiation of fibroblasts into myofibroblasts is necessary for wound healing, but excessive myofibroblast presence and persistence can result in scarring. Treatment for scarring is limited largely due to a lack of comprehensive understanding of how fibroblasts and myofibroblasts differ at the transcript level. The purpose of this study was to characterize transcriptional profiles of injured fibroblasts relative to normal fibroblasts, utilizing fibroblasts from the vocal fold as a model.</p><p><strong>Results: </strong>Utilizing bulk RNA sequencing technology, we identified differentially expressed genes between four cell lines of normal fibroblasts (cVFF), one line of scarred fibroblasts (sVFF), and four lines of fibroblasts treated with transforming growth factor-beta 1 (TGF-β1), representing an induced-scar phenotype (tVFF). Principal component analysis revealed clustering of normal fibroblasts separate from the clustering of fibroblasts treated with TGF-β1; scarred fibroblasts were more similar to normal fibroblasts than fibroblasts treated with TGF-β1. Enrichment analyses revealed pathways related to cell signaling, receptor-ligand activity, and regulation of cell functions in scarred fibroblasts, pathways related to cell adhesion in normal fibroblasts, and pathways related to ECM binding in fibroblasts treated with TGF-β1. Although transcriptomic profiles between scarred fibroblasts and fibroblasts treated with TGF-β1 were relatively dissimilar, the most highly co-expressed genes were enriched in pathways related to actin cytoskeleton binding, which supports the use of fibroblasts treated with TGF-β1 to represent a scarred cell phenotype.</p><p><strong>Conclusions: </strong>Transcriptomics of normal fibroblasts differ from myofibroblasts, including from those retrieved from scar and those treated with TGF-β1. Despite large differences in transcriptomics between tVFF and sVFF, tVFF serve as a useful in vitro model of myofibroblasts and highlight key similarities to myofibroblasts extracted from scar pathology, as well as expected differences related to normal fibroblasts from healthy vocal folds.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"347"},"PeriodicalIF":3.5,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143802328","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}