BMC Genomics最新文献

{"title":"Phylogenetic analysis, gene rearrangement and divergence time estimation of Patellogastropoda (Mollusca, Gastropoda) based on complete mitochondrial genomes.","authors":"Wanting Liu, Alexei V Chernyshev, Jiji Li, Yingying Ye, Xiangli Dong","doi":"10.1186/s12864-025-11681-z","DOIUrl":"10.1186/s12864-025-11681-z","url":null,"abstract":"<p><strong>Background: </strong>Patellogastropoda, or true limpets, is a major taxonomic group within the Gastropoda, Mollusca. The complete mitochondrial genomes have been widely used to study the phylogenetic relationships of Patellogastropoda. To further enhance the understanding of the phylogenetic relationships among families within this subclass, we obtained the complete mitochondrial genome sequences of five species using third-generation sequencing technology: Limalepeta lima, Lepeta kuragiensis, Lottia versicolor, Lottia instabilis, and Lottia tenuisculpta. We examined mitochondrial genome structure, nucleotide composition and skew, as well as amino acid content and codon usage. Additionally, we assessed selective pressures on protein-coding genes in Lepetidae and Lottiidae species, constructed a phylogenetic tree for Patellogastropoda, analyzed gene arrangement, and estimated the divergence times within Patellogastropoda.</p><p><strong>Results: </strong>The mitochondrial genomes of these five species all encoded 38 genes. They exhibited a higher AT base content, and the protein-coding genes were under purifying selection. The Patellogastropoda was divided into two clades: Clade 1 included a part of the Lottioidea superfamily and the Patelloidea superfamily, whereas the Lottiidae family within the Lottioidea superfamily formed a separate clade (Clade 2). The mitochondrial genomes of the Patellogastropoda exhibited extensive gene rearrangements, particularly those in Lottiidae, which were the most complex. The Patellogastropoda lineage was estimated to have originated in the Paleozoic Permian era, with active differentiation occurring in the Mesozoic Cretaceous and the Cenozoic era.</p><p><strong>Conclusions: </strong>Our research results contribute to a better understanding of the phylogenetic relationships within the Patellogastropoda, and reveal the extensive gene rearrangements, providing further insights into the evolution and genetics of gastropods.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"612"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12210525/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538406","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":"Physiological and broadly targeted metabolomic analyses of barley (Hordeum vulgare L.) in response to low-temperature stress.","authors":"Mingzhai Yu, Zhaxi Luobu, Deqing Zhuoga, Xiaohong Wei, Yawei Tang","doi":"10.1186/s12864-025-11516-x","DOIUrl":"10.1186/s12864-025-11516-x","url":null,"abstract":"<p><p>Barley, as an important grain crop, often suffers from low-temperature stress during growth and development, which constitutes a significant impact on the yield and quality of barley. Therefore, an in-depth study of the metabolic response of barley under low-temperature stress is of great significance to improve the cold tolerance of barley. In this study, metabolites in barley leaves under different times of low-temperature stress were analyzed by ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS), together with physiological data analysis. Result: Low-temperature stress decreased Pn, Gs, Tr, and SPAD in barley leaves, leading to an increase in ROS content, and a total of 800 metabolites were identified by metabolome analysis, belonging to amino acids and their derivatives, phenolic acids, nucleotides, and their derivatives, flavonoids, coumarins, alkaloids, organic acids, and free fatty acids. A total of 92, 91, 40, and 101 significantly different metabolites were identified at 0 h-vs-12 h, 0 h-vs-48 h, 12 h-vs-48 h, and 0 h-vs-Re24h, which were mainly involved in metabolic pathways, biosynthesis of secondary metabolites, ABCs and other metabolites. These differential metabolites were mainly involved in Metabolic pathways, Biosynthesis of secondary metabolites, ABC transporters, Biosynthesis of amino acids, Phenylpropanoid biosynthesis, Tryptophan metabolism, Flavonoid biosynthesis, Glycine, serine and threonine metabolism, Histidine metabolism, and Linoleic acid metabolism. Among them, the main up-regulated metabolites under low-temperature stress were 4-Hydroxyacetophenone, O-Acetylserine, Sinapoylagmatine, and Sinapoylputrescine, and the main down-regulated metabolites were Catechin gallate, D-Melezitose and Epigallocatechin-3-gallate, and the pathways with the highest enrichment of differential metabolites were Glycine, serine and threonine metabolism and Linoleic acid metabolism. Conclusion: Through the comprehensive analysis of physiological and metabolomic data, we initially revealed the metabolic network of barley under low-temperature stress and identified the key metabolites and metabolic pathways related to cold resistance. This study not only provides a new perspective on the molecular mechanism of cold resistance in barley but also provides an important theoretical basis for breeding barley for cold resistance. In the future, we will continue to study the regulatory mechanisms of these key metabolites and metabolic pathways, to produce new barley varieties with stronger cold resistance through genetic engineering and molecular breeding.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"618"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12210896/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538407","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":"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}