BMC Genomics最新文献

{"title":"Unraveling key transposable elements in pathogen-induced bovine mastitis through comparative in vivo and in vitro transcriptomic analysis.","authors":"Songyan An, Siyuan Mi, Siqian Chen, Yongjie Tang, Yue Xing, Yi Jing, Ying Yu","doi":"10.1186/s12864-025-11740-5","DOIUrl":"10.1186/s12864-025-11740-5","url":null,"abstract":"<p><strong>Background: </strong>Bovine mastitis poses significant hazards to the yield and quality of dairy products, severely hindering the development of the dairy industry. Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli) are well-established as two of the primary pathogens causing the disease. Transposable elements (TEs), occupying a notable proportion of livestock genomes, primarily function as regulatory elements modulating gene expression. Extensive studies have indicated that TEs contribute to transcriptional changes in the host during pathogen invasion. However, despite their potential significance, the key functional TEs associated with bovine mastitis remain unclear, highlighting the need to explore the critical roles of TEs in the immune processes of this disease.</p><p><strong>Results: </strong>In this study, in vitro and in vivo mastitis models were established using bovine mammary alveolar cells (Mac-T cells) and Chinese Holstein cows, respectively. In vitro findings showed distinct expression profiles of genes and TEs in response to challenges posed by S. aureus and E. coli. Specifically, 1,750 differentially expressed genes (DE Genes) and 3,046 differentially expressed TEs (DE TEs) were identified in the S. aureus challenge, while 2,353 DE Genes and 22,259 DE TEs were identified in the E. coli challenge. TEs were found to regulate the expression of genes primarily within immune-related pathways, including IL-17 and HIF-1 signaling pathways. TE-gene-QTL regulatory networks were established, providing preliminary insights into the molecular genetic mechanisms of TE regulation. By integrating in vitro and in vivo data, we identified and further validated two TE instances from MER53/DNA transposon and MIRc/SINE families as stably activated and repressed transcriptional markers for S. aureus mastitis, respectively.</p><p><strong>Conclusions: </strong>Our research underscores the potential regulatory roles of TEs in the pathogenesis of bovine mastitis and highlights their applicability as molecular markers for early diagnosis and prevention of this economically significant disease. Our study offers novel insights for the breeding and improvement of resistance to pathogen-induced mastitis in dairy cattle.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"611"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12210757/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538425","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":"Circular RNA expression in ALS is progressively deregulated and tissue-dependent.","authors":"Leticia Moreno-García, Laura Moreno-Martínez, Miriam de la Torre, Sofía Macías-Redondo, Alberto García-Redondo, Rosario Osta, Janne Markus Toivonen, Ana Cristina Calvo","doi":"10.1186/s12864-025-11725-4","DOIUrl":"10.1186/s12864-025-11725-4","url":null,"abstract":"<p><strong>Background: </strong>There is increasing evidence on the role of circular RNAs (circRNAs) in neuronal and muscular processes. Accordingly, their dysregulation is associated with neurodegenerative diseases and myopathies. We investigated circRNA expression in the central nervous system (CNS) and skeletal muscle, the two main tissues affected in amyotrophic lateral sclerosis (ALS).</p><p><strong>Results: </strong>Based on circRNA sequencing analysis in spinal cord from ALS mice (SOD1G93A) followed by a literature search, 30 circRNAs potentially involved in ALS were tested. All selected circRNAs were downregulated in the SOD1G93A spinal cord, whereas only half of these were quantifiable and were generally upregulated in quadriceps muscle of SOD1G93A mice. Such tissue-dependent expression pattern was observed in both sexes and circRNA abundance in the spinal cord was higher than in the muscle, both in wild type and in SOD1G93A mice. Finally, we assessed the 18 circRNAs with the largest expression differences and the highest degree of interspecies conservation in brain samples from sporadic ALS (sALS) patients and healthy controls. Similar to the mouse model, circRNA levels tended to decrease in the CNS of sALS patients.</p><p><strong>Conclusions: </strong>Expression of circRNAs may be systematically altered in the two tissues most affected by ALS in a progressive and opposed manner. Although more detailed studies are warranted, circRNAs are potentially related to ALS etiopathogenesis and could possibly serve as future biomarkers, therapeutic targets, or customized therapeutic tools to modulate the pathology.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"576"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12211884/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538274","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":"Comparative analysis of plastome structure in Sphagnum species from China.","authors":"Xian-Lin Guo, Fu-Min Xie, Chao-Jie Wang, Yi-Hang Ding, Wen-Chao Yan, Kai Fang, Huai Chen","doi":"10.1186/s12864-025-11763-y","DOIUrl":"10.1186/s12864-025-11763-y","url":null,"abstract":"<p><strong>Background: </strong>Sphagnum L. (peat mosses) comprises approximately 291 recognized species distributed worldwide except Antarctica. Plastomes are useful for investigating structure evolution and phylogeny due to their conserved structure. However, Sphagnum species endemic to China have been underrepresented in plastome-based studies, hindering a comprehensive understanding of their evolutionary history.</p><p><strong>Results: </strong>Analysis of 13 plastomes of eight Sphagnum species from China, revealed both inter-and intraspecific variations. Plastome sizes ranged from 138,958 bp (S. acutifolioides) to 141,257 bp (S. ovatum), with conserved gene content (86 CDSs, 37 tRNAs, 8 rRNAs). All plastomes exhibited a typical quadripartite structure: LSC (96,896-99,205 bp), SSC (21,187-21,381 bp), and IRs (10,298-10,391 bp). The IR boundaries and adjacent genes were consistent, except in S. squarrosum, where chIL entered IRb and ndhF entered IRa. Premature termination of the petN gene was detected in all species except S. medium and S. palustre (population: GZ and HB). Codons with RSCU > 1.00 favored A/U at the third position, with UUA (Leucine) and GCU (Alanine) being most common. SSRs dominated by mono- and di-repeats, with tri-repeats were highly conserved. Phylogenetic analysis supported the placement of S. ovatum, S. subsecundum, and S. acutifolioides in subgenus Subsecunda; S. medium and S. palustre in subgenus Sphagnum; and S. warnstorfii, S. fuscum, and S. squarrosum in subgenus Acutifolia.</p><p><strong>Conclusion: </strong>Despite overall structural conservation, expanded sampling revealed both inter- and intraspecific plastome variation in Sphagnum, underscoring the utility of plastomes for phylogenetic inference and assessing genetic diversity. These findings enhance our understanding of Chinese Sphagnum species and their evolutionary relationships.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"585"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12211238/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538275","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":"Comprehensive genomic study of Plasmodium falciparum in Sierra leone: genetic variation and resistance patterns.","authors":"Xin-Jie Zhan, Shen-Bo Chen, Tian-Yu Wang, Yi-Wen Duan, Hai-Mo Shen, Jun-Hu Chen, Jing-Jing Xie","doi":"10.1186/s12864-025-11771-y","DOIUrl":"10.1186/s12864-025-11771-y","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"584"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12210811/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538278","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":"Core histone families of mollusca: systematic identification, evolutionary insights, and functional analysis.","authors":"Yalin Guan, Xiaomei Chen, Xuan Zhu, Fuyun Liu, Yuanting Ma, Wentao Han, Rui Yang, Yuli Li, Lisui Bao, Shi Wang, Zhenmin Bao, Jing Wang","doi":"10.1186/s12864-025-11776-7","DOIUrl":"10.1186/s12864-025-11776-7","url":null,"abstract":"<p><strong>Background: </strong>Histones are the basic packaging units of eukaryotic DNA and are essential for the dynamics of chromatin and the regulation of epigenetics. Canonical histones and their variants exhibit important functional differences in biological processes. However, little is known about the role of histone family members in molluscs, which are known for their ecological and morphological diversity.</p><p><strong>Results: </strong>Core histone families of 28 molluscan species (12 bivalves, 8 gastropods, 6 cephalopods, 1 scaphopod and 1 polyplacophora) were systematically identified. The evolutionary conservation and lineage-specific innovations were discovered using phylogenomic and transcriptomic analyses. Cephalopods showed a striking expansion of canonical histone genes with brain-enriched expression patterns. Synteny analyses revealed conserved, collinear histone clusters unique to cephalopods. Histone variants, specially H2A and H3 paralogs, display conserved motifs potentially involved in nucleosome stability and lineage-specific residues involved in functional specialization. Developmental transcriptomics revealed the dynamic expression of histone variants in early embryogenesis and the gonads, suggesting that H2A and H3 variants are involved in chromatin remodeling, pluripotency maintenance and germline regulation. Macro-H2A was highly expressed during larval neurodevelopment and in sensory organs, suggesting important roles in neural plasticity.</p><p><strong>Conclusion: </strong>This study represents the first comprehensive inventory and characterization of core histone genes in molluscs, and will facilitate understanding of the evolutionary patterns and functional properties of core histones in relation to neurogenesis of molluscs. These findings advance our understanding of chromatin evolution and its contribution to phenotypic innovation in non-model taxa.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"594"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12210499/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538281","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":"Assessing the role of key genes involved in the reproductive success of the honey bee parasite Varroa destructor.","authors":"Irina Muntaabski, Ricardo Salvador, Romina M Russo, Juan P Wulff, Lucas Landi, María C Liendo, Silvia B Lanzavecchia, Alejandra C Scannapieco","doi":"10.1186/s12864-025-11805-5","DOIUrl":"10.1186/s12864-025-11805-5","url":null,"abstract":"<p><p>The ectoparasite Varroa destructor is the primary global threat to the western honey bee, Apis mellifera. Growing resistance to acaricide-based treatments has spurred interest in alternative control strategies. In this study, we employed a novel and efficient dsRNA delivery method to explore the potential of RNA interference (RNAi)-based approaches for Varroa control in honey bee colonies. We assessed the effects of silencing six target genes (ptch1, ap-1, larp6, chisal, vg1, and vg6) on mite mortality and reproduction through a semi-field experiment. Gene expression analysis revealed significantly reduced transcript levels in mites treated with dsRNA compared to dsGFP controls, with knockdown efficiencies ranging from 88.6% to 97.2%. Silencing of ptch1, ap-1, and vg1 genes resulted in a significant increase in mite infertility, aligning with their known roles in oocyte maturation and embryogenesis. Additionally, silencing of chisal, previously described as essential for effective Varroa feeding, led to a marked increase in mite mortality. These results highlight promising gene targets for RNAi-based Varroa control strategies. Furthermore, our study provides new insights into the molecular pathways involved in mite reproduction and survival, including Wnt, c-Jun N-terminal kinase, Hedgehog, and apoptosis, paving the way for the development of more effective biotechnological control tools.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"622"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12211768/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538301","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":"Integrated transcriptome and metabolome analyses unraveled critical roles of small intestine during the weaning period of Vespertilio sinensis.","authors":"Zixuan Li, Wei Guo, Yujia Chu, Xiao Tan, Hui Wang, Jiang Feng, Tong Liu","doi":"10.1186/s12864-025-11784-7","DOIUrl":"10.1186/s12864-025-11784-7","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"587"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12211977/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538399","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":"Joint analysis of whole-genome methylation and transcriptome in avian pullorum disease and validation of gene function.","authors":"Jiongwen Wu, Weiming Liang, Aijun Liu, Xiaomeng Wang, Zhexia Fan, Xuerong Ma, Shuya Chen, Cheng Fang, Xiquan Zhang, Qingbin Luo","doi":"10.1186/s12864-025-11821-5","DOIUrl":"10.1186/s12864-025-11821-5","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"617"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12211800/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538400","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":"Mechanisms underlying the estradiol mediated protection of yak oviduct epithelial cells against ER-Ca²⁺ imbalance.","authors":"Xiaolin Ye, Meng Wang, Yangyang Pan, Tianhao Li, Jinglei Wang, Ling Zhao, Rui Zhang, Yan Cui, Sijiu Yu","doi":"10.1186/s12864-025-11804-6","DOIUrl":"10.1186/s12864-025-11804-6","url":null,"abstract":"<p><strong>Background: </strong>Extreme weather events are occurring with increasing frequency worldwide. Oviduct epithelial cells (OECs), which provide nutrients and a microenvironment critical for reproductive processes such as fertilization and early embryonic development, are vulnerable to extreme hyperthermia climate. Mitigating heat induced damage to yak oviduct epithelial cells (YOECs) may thus contribute to improving reproductive health. Studies have shown that hyperthermia reduces SERCA protein levels, leading to ER-Ca²⁺ dyschondrosteosis and subsequent cellular injury; this phenomenon indicates that ER-Ca imbalance is a critical factor in cellular damage. Estradiol (E₂), which not only promotes the YOEC functions essential for fertilization and early embryonic development but also participates in calcium regulation, is hypothesized to alleviate ER-Ca²⁺ imbalance induced YOEC damage. To test this hypothesis, we compared the ER-Ca²⁺ distribution and hyperthermia/ hapsigargin (TG, a SERCA inhibitor)-mediated cellular damage in YOECs under high temperature conditions. Proteomic sequencing was employed to analyze protein level changes in TG treated YOECs with ER-Ca²⁺ imbalance before and after E₂ treatment, elucidating the mechanism whereby E₂ mitigates YOEC injury.</p><p><strong>Results: </strong>E₂ can alleviate the damage in YOECs caused by TG. This effect is associated with perturbations in the restored serine 927 phosphorylation site in type 3 inositol 1,4,5-trisphosphate receptor (IP3R3). Restoration of the serine 927 phosphorylation site in IP3R3 leads to an increase in ER-Ca²⁺ levels, which activates the calmodulin phosphatase/nuclear factor of the activated T cells pathway and promotes cell function, and reduces YOECs apoptosis under ER-Ca²⁺ conditions.</p><p><strong>Conclusion: </strong>Our research results indicate that E₂ protects YOECs under ER-Ca²⁺ imbalance by increasing the protein expression of IP3R3 serine 927, highlighting the close relationship between protein expression and phosphorylation modification during ER-Ca²⁺ imbalance. These findings deepen our understanding of ER-Ca²⁺ imbalance damage and lay the foundation for further research and mitigation of related diseases.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"613"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12210435/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538401","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":"Analysis of NUDIX enzymes across fungi reveals previously unrecognized diversity.","authors":"Zofia Pasterny, Drishtee Barua, Eugenio Mancera, Anna Muszewska","doi":"10.1186/s12864-025-11778-5","DOIUrl":"10.1186/s12864-025-11778-5","url":null,"abstract":"<p><strong>Background: </strong>The NUDIX superfamily encompasses highly diverse enzymes involved in a plethora of biological functions such as mRNA metabolism, DNA repair, and lipid peroxidation. These hydrolases are found in all domains of life and show surprising versatility in terms of the substrates that they process. The knowledge about the diversity of fungal NUDIX proteins is fragmentary, being largely limited to a small number of characterized enzymes from yeasts. To address this knowledge gap systematically, we performed a detailed analysis of the NUDIX hydrolases across 183 fungal proteomes.</p><p><strong>Results: </strong>Members of six of the known NUDIX families were present in fungi being particularly abundant in Glomeromycota. Phylogenetic analysis and sequence clustering grouped fungal NUDIX enzymes in 25 subfamilies, 13 of which did not cluster with previously known enzymes. These 13 newly identified subfamilies all belong to the canonical NUDIX family, and structural comparison revealed a typical NUDIX fold with α-β-α sandwich structure. Molecular docking suggested Ap3A and Ap4A as substrates with the highest binding affinity, but their possible cellular roles remain unclear. We also found evidence of expression of most of the genes that encode these enzymes, suggesting physiological relevance.</p><p><strong>Conclusions: </strong>Our analysis offers a comprehensive perspective on the structural and sequence relationships of the NUDIX superfamily across fungi with potential to guide experimental characterization of their biological functions.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"606"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12210691/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538298","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}