BMC Genomics最新文献

{"title":"Accurate prediction of virulence factors using pre-train protein language model and ensemble learning.","authors":"Guanghui Li, Jian Zhou, Jiawei Luo, Cheng Liang","doi":"10.1186/s12864-025-11694-8","DOIUrl":"10.1186/s12864-025-11694-8","url":null,"abstract":"<p><strong>Background: </strong>As bacterial pathogens develop increasing resistance to antibiotics, strategies targeting virulence factors (VFs) have emerged as a promising and effective approach for treating bacterial infections. Existing methods mainly relied on sequence similarity, and remote homology relationships cannot be discovered by sequence analysis alone.</p><p><strong>Results: </strong>To address this limitation, we developed a protein language model and ensemble learning approach for VF identification (PLMVF). Specifically, we extracted features from protein sequences using ESM-2 and their three-dimensional (3D) structures using ESMFold. We calculated the true TM-score of the proteins based on their 3D structures and trained a TM-predictor model to predict structural similarity, thereby capturing hidden remote homology information within the sequences. Subsequently, we concatenated the sequence-level features extracted by ESM-2 with the predicted TM-score features to form a comprehensive feature set for prediction. Extensive experimental validation demonstrated that PLMVF achieved an accuracy (ACC) of 86.1%, significantly outperforming existing models across multiple evaluation metrics. This study provided an ideal tool for identifying novel targets in the development of anti-virulence therapies, offering promise for the effective prevention and control of pathogenic bacterial infections.</p><p><strong>Conclusions: </strong>The proposed PLMVF model offers an efficient computational approach for VF identification.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"517"},"PeriodicalIF":3.5,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12093764/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144118717","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, characterization, and expression analysis of the MADS-box gene family in grass pea (Lathyrus sativus) under salt stress conditions.","authors":"Mohamed Abdelsattar, Ahmed E Nassar, Khaled H Mousa, Ahmed Hussein, Manal M S El-Baghdady, Khaled H Radwan, Manar S Ibrahim, Achraf El Allali, Aladdin Hamwieh, Alsamman M Alsamman, Zakaria Kehel","doi":"10.1186/s12864-025-11661-3","DOIUrl":"10.1186/s12864-025-11661-3","url":null,"abstract":"<p><strong>Background: </strong>The MADS-box gene family possesses significant potential to improve crop production under harsh conditions by regulating growth, development, and the expression of floral organs. The grass pea (Lathyrus sativus), a crop grown predominantly in arid and semi-arid regions, could benefit greatly from the functions of MADS-box genes, which are not yet well characterized in this promising plant.</p><p><strong>Results: </strong>In this study, a comprehensive analysis of all MADS-box genes in grass pea was performed at both the genomic and transcriptomic levels. A total of 46 genes were identified and classified based on their MADS-box domains. A comparative phylogenetic analysis with apple, Arabidopsis, and rice categorized the grass pea genes into 31 type I genes (M <math><mi>α</mi></math> , M <math><mi>β</mi></math> , M <math><mi>γ</mi></math> ) and 15 type II genes (MIKCc, MIKC*). Annotation analysis revealed variations in the intron-exon structures of the genes, with most type I genes being intronless. Ten distinct conserved motifs were identified across the genes. Structural analysis revealed the presence of MEF2-like and SRF-TF domains in the grass pea proteins. Protein-protein interaction analysis revealed extensive interactions among type II MADS-box genes, while enrichment analysis showed their involvement in various aspects of plant life, particularly floral organ development. Examination of the cis-elements in the promoter regions of the genes revealed up to 76 potential cis-elements, which were categorized into four groups based on their putative role in transcriptional regulation. RNA-seq was used to profile gene expression under different conditions to gain insights into their potential functional significance. Quantitative PCR (qPCR) analysis validated the expression levels of eight selected genes (LSMADS_D1, LSMADS_R5, LSMADS_R7, LSMADS_R9, LSMADS_D11, LSMADS_D13, LSMADS_R13, and LSMADS_D29) under salt stress conditions and confirmed their involvement in stress responses.</p><p><strong>Conclusion: </strong>This study represents the first genome-wide exploration of the MADS-box gene family in grass pea. Our results provide valuable insights that could improve our understanding of the plant's genomics, contribute to strengthening its resilience to challenging conditions, and help position it as an important crop in arid regions.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"519"},"PeriodicalIF":3.5,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12096561/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144118721","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":"Chromatin accessibility and transcriptomic profiles of sheep pituitary function associated with fecundity.","authors":"Shanglai Li, Bingru Zhao, Peiyong Chen, Yu Cai, Hui Xu, Chenbo Yan, Feng Wang, Yanli Zhang","doi":"10.1186/s12864-025-11621-x","DOIUrl":"10.1186/s12864-025-11621-x","url":null,"abstract":"<p><strong>Background: </strong>The pituitary gland, a central regulator of the hypothalamic-pituitary-gonadal (HPG) axis, plays a pivotal role in reproductive efficiency by precisely controlling the secretion of gonadotropins, including follicle-stimulating hormone (FSH) and luteinizing hormone (LH). Chromatin accessibility enables physical interactions between promoters and chromatin-binding factors to drive the gene expression. Despite this mechanistic insight, the chromatin accessibility landscape of the sheep pituitary and its functional implications for reproductive traits remain largely unexplored. To address this knowledge gap, we performed an integrated multi-omics analysis of ATAC-seq and RNA-seq profiling of pituitary from sheep with divergent fecundity phenotypes.</p><p><strong>Results: </strong>We identified 1,567 differential accessibility regions (DARs) and 768 differentially expressed genes (DEGs). Functional enrichment analysis revealed that the DEGs were significantly associated with key signaling pathways, including neuroactive ligand-receptor interactions, the cAMP signaling pathway, and the calcium signaling pathway, suggesting their critical roles in pituitary-regulated reproductive functions. Based on integrative analysis of ATAC-seq and RNA-seq, we revealed several potentially key genes involved in gonadotropin secretion, such as CMKLR1, TAFA1, and PPP1R17. Furthermore, we identified novel transcription factors (TFs), including NR4A2 and MEF2, which may influence pituitary hormone secretion by modulating chromatin accessibility and gene expression.</p><p><strong>Conclusions: </strong>This study systematically delineated the gene expression and chromatin accessibility of the pituitary and identified some key regulatory genes associated with gonadotropin secretion in sheep. Our integrated multi-omics analysis identifies critical molecular markers that may contribute to the genetic improvement of reproductive efficiency in ovine species.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"508"},"PeriodicalIF":3.5,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12090423/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144109497","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":"Identification of regulatory loci and candidate genes related to body weight traits in broilers based on different models.","authors":"Na Luo, Keqi Cai, Limin Wei, Huanxian Cui, Jie Wen, Bingxing An, Guiping Zhao","doi":"10.1186/s12864-025-11651-5","DOIUrl":"10.1186/s12864-025-11651-5","url":null,"abstract":"<p><strong>Background: </strong>Growth traits are crucial for the economic viability in broiler production, as they significantly contribute to the cost of rearing. Maximizing body weight (BW) while minimizing feed intake is key to enhancing the efficiency of broiler breeding. Identifying the genetic architecture associated with BW trait is therefore a critical step in enhancing breeding strategies.</p><p><strong>Results: </strong>We conducted a genome-wide association study (GWAS) using two statistical approaches: single-trait GWAS and longitudinal GWAS. The study was performed on the BW trait at five developmental stages (72, 81, 89, 113, and 120 days) and mid-test metabolic weight (MWT) across four growth cycles. Transcriptome sequencing analysis was also included to investigate the differential expression of candidate genes identified through the GWAS models, particularly linked to BW and MWT traits. Utilizing the chicken 55K single nucleotide polymorphism (SNP) array, we identified 52,060 SNPs in the genomic data of 4,493 Wenchang chickens. The single-trait GWAS model revealed 42 BW-associated SNPs, corresponding to 18 potential genes. For MWT, 47 SNPs were associated, mapping to 31 candidate genes. The longitudinal GWAS model identified 34 BW-linked SNPs, annotated with 22 candidate genes, and 21 MWT-linked SNPs, annotated with 10 candidate genes. Notably, 16 SNPs on chromosome 4 were associated with both BW and MWT, located within the 73.08Mb-76.82Mb region. Nine genes were annotated from this region, including STIM2, SEL1L3, SEPSECS, LGI2, SOD3, KCNIP4, NCAPG, FAM184B, LDB2. Notably, there are 32 overlapping SNPs identified in both the single-trait and longitudinal GWAS models, suggesting consistent associations for both BW and MWT. These overlapping SNPs represent robust loci that may influence both traits across different statistical approaches. Transcriptome sequencing indicated differential expression of LDB2 and SEL1L3 between high and low BW groups.</p><p><strong>Conclusion: </strong>Our study has uncovered novel candidate genes that are potentially involved in growth traits, providing valuable insights for broiler breeding. The identified SNPs and genes could serve as genetic markers for selecting broilers with improved growth efficiency, which may lead to more cost-effective and productive broiler farming.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"513"},"PeriodicalIF":3.5,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12093760/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144109566","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":"Application of multi-omics technology in pathogen identification and resistance gene screening of sheep pneumonia.","authors":"Kai Huang, Lvfeng Yuan, Jia Liu, Xiaolong Li, Dan Xu, Xiaoxue Zhang, Jie Peng, Huibin Tian, Fadi Li, Weimin Wang","doi":"10.1186/s12864-025-11699-3","DOIUrl":"10.1186/s12864-025-11699-3","url":null,"abstract":"<p><strong>Background: </strong>Pneumonia constitutes a major health challenge in sheep, severely compromising growth rates and overall productivity, and resulting in considerable economic losses to the sheep industry. To address this issue, the development of disease-resistant breeding programs based on the identification of genetic markers associated with pneumonia susceptibility is of critical importance. This study investigated a sheep population on a farm where pneumonia was endemic. The purpose was to use multi-omics methods to rapidly identify the principal pathogens responsible for pneumonia outbreaks, and to screen for genetic loci and key genes related to pneumonia resistance, thereby providing a scientific basis for the implementation of targeted breeding strategies for pneumonia resistance.</p><p><strong>Results: </strong>Here, we assessed the impact of pneumonia on sheep growth by evaluating the pneumonia phenotypes of 912 sheep. High-throughput transcriptome sequencing of 40 lungs was conducted to obtain exogenous RNA fragments for microbial sequence alignment. Additionally, 16S rRNA sequencing was performed on lung tissues from 10 healthy and 10 diseased sheep to identify biomarkers associated with phenotypic differences. Mycoplasma ovipneumoniae was identified as the primary pneumonia pathogen, and its presence was further validated by load quantification and immunohistochemical analysis. Integration of genome-wide association study (GWAS) data from 266 lung pathological scores with transcriptome-based differentially expressed genes analysis enabled the identification of five single nucleotide polymorphisms (SNPs) and three potential candidate genes associated with Mycoplasma pneumonia. Subsequent genotyping and phenotype association analyses confirmed the significance of two SNPs and established a strong association between the FOXF1 gene and resistance to Mycoplasma pneumonia.</p><p><strong>Conclusions: </strong>High-throughput sequencing technologies have enabled the rapid and accurate identification of the causative pathogen of sheep pneumonia. By integrating multi-omics data, two genomic loci significantly associated with Mycoplasma pneumonia were screened, as well as an anti-Mycoplasma pneumonia key gene, FOXF1.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"507"},"PeriodicalIF":3.5,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12090697/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144109493","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":"DNA methylation regulates growth traits by influencing metabolic pathways in Pacific white shrimp (Litopenaeus vannamei).","authors":"Xin Zhang, Chaoqun Hu, Ting Chen, Pengying Li, Yehui Tan, Chunhua Ren, Yanhong Wang, Xiao Jiang, Bo Ma, Jiayue Yin, Yunyi Huang, Liyan Liu, Huo Li, Peng Luo","doi":"10.1186/s12864-025-11688-6","DOIUrl":"10.1186/s12864-025-11688-6","url":null,"abstract":"<p><strong>Background: </strong>DNA methylation is a critical epigenetic modification that dynamically regulates gene expression associated with economic traits. Pacific white shrimp (Litopenaeus vannamei) is one of the most important aquatic species for culturing, and growth trait is one of the most important economic traits for its production. However, research on DNA methylation regulation of growth traits is still at an early stage. This study explored DNA methylome dynamics and their associations with the regulatory mechanism behind growth traits using full-subfamily individuals with discrepant growth performance.</p><p><strong>Results: </strong>The DNA methylation-related genes in L. vannamei were identified, and the expression of DNA methylation genes showed significantly higher levels in the slow growth (SG) group compared to the fast-growing (FG) individuals. The Whole Genome Bisulfite Sequencing (WGBS) analysis revealed that the methylation levels in the muscles of shrimp were notably decreased in SG individuals compared to FG individuals. A total of 532 differentially methylated promoters and 2,067 differentially methylated regions were identified. Through integrative analysis of DNA methylation and transcriptomic data from SG and FG group shrimp, a total of 47 genes were screened out with differential methylation levels (DMGs) and expression levels (DEGs). Functional enrichment analysis revealed that the overlapping DEGs/DMGs were enriched mainly in metabolic pathways, starch and sucrose metabolism, linoleic acid metabolism, ascorbate and aldarate metabolism, pentose and glucuronate interconversions.</p><p><strong>Conclusions: </strong>DNA methylation plays a role in the regulation of growth traits in L. vannamei. The level of DNA methylation was found to be negatively correlated with growth traits. Through comprehensive analysis, it was discovered that DNA methylation predominantly affects growth performance by up-regulating the expression of genes involved in metabolic pathways, such as glucose metabolism and amino acid metabolism in L. vannamei. This suggests a higher metabolism activity in SG individuals derived DNA methylation to cope with some unknown internal stress or environmental stress rather than being allocated for growth.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"511"},"PeriodicalIF":3.5,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12093746/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144109533","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 analysis of lncRNA m6A methylation in the mouse cortex after repetitive mild traumatic brain injury.","authors":"Rongrong Zhong, Chen Chen, Yingao Zhang, Conglin Wang, Meimei Li, Fanglian Chen, Lu Wang, Qiang Liu, Ping Lei","doi":"10.1186/s12864-025-11696-6","DOIUrl":"10.1186/s12864-025-11696-6","url":null,"abstract":"<p><p>N6-methyladenosine (m6A), a prevalent post-transcriptional modification in eukaryotic RNA, plays a significant role in regulating sensory experiences, learning, and injury in the mammalian central nervous system. However, the pattern of lncRNA m6A methylation in the mouse cortex following repetitive mild traumatic brain injury (rmTBI) has not been explored. This study conducted a genome-wide analysis of lncRNA m6A methylation in the mouse cortex using methylated RNA immunoprecipitation sequencing (MeRIP-Seq). We identified 43,103 differentially methylated peaks. Notably, the expression of m6A peaks indicated altered methylation and expression levels of 423 lncRNAs after rmTBI. In addition, employing METTL3 inhibitor STM2457 demonstrated that functional METTL3 was essential for repairing neural damage caused by rmTBI and influenced spatial learning and memory in rmTBI-model mice. Thus, the m6A methylation pattern of lncRNA in the mouse cortex after rmTBI identifies METTL3 as a potential intervention target for epigenetic modification following such injuries. Clinical trial number Not applicable.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"509"},"PeriodicalIF":3.5,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12090626/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144109537","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 cataloging and orthology analysis of long noncoding RNA expression in three species of Anopheles mosquito.","authors":"Waseem Akram Malla, Kuldeep Singh, Niha Ayman, Chandini Boro, Naorem Chaoba Devi, Priyanka Mech, Nida Siddiqui, Anupkumar R Anvikar, Praveen Kumar Bharti","doi":"10.1186/s12864-025-11687-7","DOIUrl":"10.1186/s12864-025-11687-7","url":null,"abstract":"<p><strong>Background: </strong>Long noncoding RNAs (lncRNAs) are versatile regulatory molecules that affect cellular phenotypes through context-specific expression. While their role in controlling cellular pathways is well-established in insects, investigating lncRNA expression in Anopheles in a tissue- and species-specific manner could add to our understanding of malaria transmission by this important vector.</p><p><strong>Methodology: </strong>We performed de novo transcriptome assembly of Anopheles minimus, Anopheles albimanus, and Anopheles arabiensis utilising publicly available RNA-Seq datasets of male reproductive tissues, male carcasses, female reproductive tissues, and female carcasses. Various bioinformatics tools were subsequently used for lncRNA identification, conservation analysis, and differential expression analysis across sexes and tissues.</p><p><strong>Results: </strong>We identified 9331, 5372, and 5256 lncRNA transcripts in An. albimanus, An. arabiensis, and An. minimus, respectively. Compared with An. albimanus lncRNAs, conservation analysis revealed that a total of 1964 and 1400 lncRNAs were conserved in An. arabiensis and An. minimus; however, only 283 and 253 lncRNAs presented sequence-level conservation. Differential expression (DE) analysis revealed that the carcasses presented the lowest difference in lncRNA expression, whereas in each comparison, the reproductive tissues (whether male or female) presented relatively high levels of differential expression. Additionally, 69 lncRNAs were found to be conserved at the sequence level in all 3 species. These lncRNAs were almost exclusively upregulated in males (reproductive tissue as well as carcasses) and exclusively downregulated in female carcasses.</p><p><strong>Conclusions: </strong>The genes in the vicinity of differentially expressed, conserved lncRNAs were found to be involved in critical pathways such as nuclear structure, chromatin remodelling, protein and RNA metabolism, and cell cycle in each of these species. Future studies on these lncRNAs can provide useful insights into how these functions control sexually-dimorphic physiological phenomena such as host-seeking and biting behaviour of female mosquitoes, blood meal metabolism, reproductive behaviour, and disease-carrying capacity.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"510"},"PeriodicalIF":3.5,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12090406/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144109561","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":"Dissection of genetic basis underlying heat stress response of Apis cerana.","authors":"Ao-Mei Li, Chun-Xiu Pang, Xiao-Lin Cai, Fu-Chang Zhuo, Bo Hu, Xue-Hua Huang, Jia-Xiang Huang, Yu-Ming Lu","doi":"10.1186/s12864-025-11714-7","DOIUrl":"10.1186/s12864-025-11714-7","url":null,"abstract":"<p><p>The honeybee Apis cerana as an important pollinator contributes significantly to ecological diversity. In recent years, it has been used as a common pollinator in greenhouses, but it is highly susceptible to heat stress, which affects its behavior, physiology, survival, and gene expression. Here, we conducted transcriptomic analysis to identify differentially expressed genes (DEGs) and reveal the associated biological processes in the queen head and ovary of honeybee A. cerana under different temperatures. Differential expression analysis revealed 116 DEGs (72 upregulated, 44 downregulated) in the head and 106 DEGs (78 upregulated, 28 downregulated) in the ovary after 24 h of heat stress. At 96 h, 29 DEGs (17 upregulated, 12 downregulated) were identified in the head, and 44 DEGs (34 upregulated, 10 downregulated) in the ovary. After 168 h, the number of DEGs increased significantly: 846 DEGs (567 upregulated, 279 downregulated) in the head, 479 DEGs (296 upregulated, 183 downregulated) in the ovary, and 582 DEGs (338 upregulated, 244 downregulated) in the thorax. DEGs associated with metabolic processes, signaling, and transport pathways were significantly altered under heat stress, potentially contributing to the reduced reproductive and growth capacity of bees. Additionally, genes related to antioxidant activity, nutrient metabolism, heat shock proteins, zinc finger proteins, and serine/threonine-protein kinases were differentially expressed across treatments. Overall, the head and ovaries of honeybee queens show a significant response to heat shock, and these responses are related to antioxidant genes, heat shock proteins, and metabolic regulation, our findings provide genetic information for the breeding of heat-resistant bee strains.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"512"},"PeriodicalIF":3.5,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12093875/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144109505","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":"Unveiling the evolutionary and transcriptional landscape of ERF transcription factors in wheat genomes: a genome-wide comparative analysis.","authors":"Liwen Wang, Hongjun Zhao, Runfang Li, Rumei Tian, Kaihua Jia, Yongchao Gong, Song Hou, Nana Li, Yanyan Pu","doi":"10.1186/s12864-025-11671-1","DOIUrl":"10.1186/s12864-025-11671-1","url":null,"abstract":"<p><p>Ethylene response factors (ERFs), belonging to the AP2/ERF superfamily, play vital roles in plant growth, development, and stress responses. The evolutionary and expression features of the members of the ERF gene family have not yet been extensively analyzed through comprehensive comparative genomics across various diploid, tetraploid, and hexaploid wheat genomes. In this study, we identified a total of 2,967 ERF genes across one diploid, two tetraploid, and five hexaploid wheat genomes using the characteristics of conserved domains of ERF proteins. Phylogenetic analysis revealed that ERF genes clustered into two main groups. Analyses of expansion of the ERF gene family indicated that the members of IIIc and IX (sub)groups were observed to show the expansion in tetraploid and hexaploid wheat compared to diploid wheat. Tandem duplication was identified as a key mechanism for ERF gene family expansion, with varying proportions across different wheat genomes. Ancient evolutionary evidence was traced using Amborella trichopoda as a reference, revealing the retention of gene copies in both tetraploid and hexaploid wheat. Then, we analyzed the expression of ERF genes under salt stress in Triticum aestivum, identifying 86 consistently up-regulated and 14 down-regulated ERF genes, and reported the stress tolerant and disease resistant ERF genes in hexaploid wheat. These findings provide valuable insights into the evolutionary dynamics and functional features of ERF genes in wheat, paving the way for genetic breeding and molecular improvement of wheat species.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"503"},"PeriodicalIF":3.5,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12090403/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144101090","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}