BMC Genomics最新文献

{"title":"Identification and expression analysis of N⁶-methyltransferase and demethylase in rapeseed (Brassica napus L.).","authors":"Xiaoyu Chen, Yu Kang, Shun Li, Bo Yang, Xiaoyan Xia, Zhonghua Wang, Lunwen Qian, Xinhua Xiong, Lei Kang, Xin He","doi":"10.1186/s12864-025-11695-7","DOIUrl":"10.1186/s12864-025-11695-7","url":null,"abstract":"<p><strong>Background: </strong>N⁶-methyladenosine (m⁶A) modification involves the addition of a methyl group to the nitrogen atom at position six of adenine in RNA. It is the most prevalent type of dynamic internal RNA methylation modification, plays an important role in plant development and abiotic stress. The m⁶A modification is facilitated by m⁶A writers (m⁶A methyltransferases), m⁶A erasers (m⁶A demethylation enzymes), and m⁶A readers (m⁶A methylated reading proteins).</p><p><strong>Results: </strong>In order to study the characterization and expression of m⁶A methyltransferases and demethylases in Brassica napus (rapeseed), we used five methyltransferases and two demethylases from Arabidopsis thaliana as reference sequences. A total of 34 methyltransferases and 12 demethylases were identified in B. napus, B. oleracea, and B. rapa. We analyzed the physicochemical properties, gene structures, conserved domains, chromosome localization, and expression pattern across all tissues, as well as the effects of hormone and stress treatments on B. napus. Our findings revealed that the methyltransferase BnaHAKAI was highly expressed during the late stages of seed development. It may be related to the synthesis of oil content and seed size in the later stage of seed growth. In contrast, the demethylase BnaALKBH10B exhibited high expression primarily in the petals, followed by the pods, buds. This expression pattern may be associated with flower development and the timing of flowering. Furthermore, BnaALKBH10B primarily responded to abiotic stresses such as salinity, drought, osmotic, cold, and freezing, as well as to hormones like jasmonic acid and gibberellins. The qRT-PCR results showed that BnaALKBH10B responded to freezing and salt stress.</p><p><strong>Conclusions: </strong>In summary, a total of 34 methyltransferases and 12 demethylases genes were identified in B. napus, B. oleracea, and B. rapa, and their phylogenetic relationships, structural domains, and expression patterns in tissues and under abiotic stress were comprehensively analyzed. This research will serve as a foundation for future studies on m⁶A in B. napus.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"526"},"PeriodicalIF":3.5,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12102800/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144141406","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":"Cross-species transcriptome-wide meta-analysis of anterior cruciate ligament rupture.","authors":"Livia Beccacece, Stefano Pallotti, Yiyun Li, Jie Huang, Leonardo Pasotti, Valerio Napolioni","doi":"10.1186/s12864-025-11702-x","DOIUrl":"10.1186/s12864-025-11702-x","url":null,"abstract":"<p><strong>Background: </strong>The Anterior Cruciate Ligament (ACL) plays a critical role in maintaining the musculoskeletal stability of the knee. Its injury has been linked to an increased risk of developing osteoarthritis. This study aims to identify cross-species responses to ACL rupture providing insights on its molecular basis. We analyzed five publicly available transcriptomic datasets from Homo sapiens, Mus musculus, Canis lupus familiaris, and Oryctolagus cuniculus. Differential gene expression analysis was performed for each dataset, producing a genome-wide transcriptional signature of fold-change significance for individual genes. Stouffer's method was used to integrate the results, identifying genes significantly deregulated across all species. Additionally, gene-set enrichment analysis revealed pathways that were consistently upregulated or downregulated.</p><p><strong>Results: </strong>A positive correlation in expression was observed between human and the other three species (r² = 0.177-0.305, p-value ≤ 2.7 × 10^- 113), identifying 210 genes as the most consistently up- and down-regulated in response to ACL rupture (p-adjusted ≤ 1.27 × 10^- 23). These genes are primarily involved in cellular mitosis, collagen pathways, and cartilage development. Furthermore, 60 pathways were found to be significantly up- or down-regulated across all species (p-adjusted ≤ 4.57 × 10^- 4). Among these, the upregulation of inhibition of bone mineralization (p-adjusted ≤ 2.99 × 10^- 6) aligns with previous findings on the reduction of subchondral bone mineral density following ACL rupture.</p><p><strong>Conclusions: </strong>This study highlights that distinct species exhibit common molecular responses to ACL rupture, underscoring the value of mice, dogs, and rabbits as potential translational model organisms for ACL rupture research. Furthermore, the identified genes and pathways highlight the molecular mechanisms underlying ACL rupture.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"524"},"PeriodicalIF":3.5,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12102845/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144131814","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":"A genome-wide association study reveals that DgFH18 and DgCMO-like are associated with flowering time in orchardgrass (Dactylis glomerata).","authors":"Miaoli Wang, Guangyan Feng, Zhongfu Yang, Lei Cao, Gang Nie, Xiaoheng Xu, Feixiang Hao, Linkai Huang, Xinquan Zhang","doi":"10.1186/s12864-025-11708-5","DOIUrl":"10.1186/s12864-025-11708-5","url":null,"abstract":"<p><strong>Background: </strong>Flowering is a tightly regulated process influencing yield and promoting plant genetic diversity and conservation. Orchardgrass (Dactylis glomerata) exhibits excellent yield traits and stress resistance, making it ideal for animal husbandry and ecological restoration. However, the molecular regulatory factors of the flowering time of orchardgrass are still unknown, limiting its molecular breeding.</p><p><strong>Results: </strong>To speed up molecular breeding to enhance flowering traits in orchardgrass, we conducted a genome-wide association study (GWAS). A diverse panel of 249 orchardgrass accessions was phenotyped for heading stage and flowering time. GWAS analysis identified 359 candidate genes that overlapped or were adjacent to effective single-nucleotide polymorphisms (SNPs), which were considered potential flowering time-related genes. Furthermore, we validated that formin-like protein 18 (DgFH18) and choline monooxygenase (DgCMO-like) was two important flowering candidate genes by overexpressing them in Arabidopsis to unravel their potential functions. Overexpression of DgFH18 and DgCMO-like positively regulated flowering time by inducing the expression of flowering-related genes. Moreover, sucrose treatment could significantly promote the expression of flavonoid pathway genes and enhance the content of total flavonoids and anthocyanins in the DgCMO-like-overexpressing lines compared to the wild type.</p><p><strong>Conclusion: </strong>These results provide valuable resources for future orchardgrass breeding programs and broaden the current comprehension of flowering time regulation in perennial grasses.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"522"},"PeriodicalIF":3.5,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12100859/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144131801","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":"RNA-Seq uncovers endogenous NO-induced hormone signal transduction and carbon metabolism in response to PEG stress in alfalfa.","authors":"Ying Zhao, Xiaofang Zhang, Yizhen Wang, Qian Ruan, Baoqiang Wang, Xiaoyue Wen, Xiaohong Wei","doi":"10.1186/s12864-025-11706-7","DOIUrl":"10.1186/s12864-025-11706-7","url":null,"abstract":"<p><strong>Background: </strong>Alfalfa (Medicago sativa L.) has the benefits of high yield and nutritional value as a sustainable forage. However, the water deficit significantly limits its growth and yield performance. Nitric oxide (NO) is a signal molecule that can enhance plant tolerance. The majority of previous studies focus on the role of exogenous NO in plant tolerance. However, the underlying mechanism of endogenous NO in alfalfa drought tolerance remains largely unexplored.</p><p><strong>Results: </strong>To explore the mechanism of the endogenous NO-mediated water deficit resistance in the alfalfa, seedlings were exposed to polyethylene glycol 6000 (PEG) and NO scavenger (cPTIO). Results showed that PEG treatment significantly augmented alfalfa endogenous NO, MDA, O₂^·-, and H₂O₂ levels. In parallel, eliminating endogenous NO under PEG stress (PEG-NO) significantly diminished NO level, exacerbated MDA and reactive oxygen species accumulation, and decreased the activities of key enzymes involved in carbon fixation and TCA cycle, such as Rubisco, FBA, PDH, α-KGDH, and SDH, as well as reduced ABA and IAA content in alfalfa leaves. RNA-Seq and bioinformatics analysis suggested that endogenous NO-responsive DEGs primarily relate to carbon metabolism and hormone signal transduction. In further studies of these DEGs, we speculated that GH3, SAUR, SnRK2, and ABF genes and FBA, GAPDH, SBP, and CS are critical genes in response to endogenous NO under PEG stress.</p><p><strong>Conclusions: </strong>In summary, our study innovatively proposes a mechanism model of how endogenous NO enhances alfalfa tolerance to water deficiency at the physiological and molecular levels. The novel candidate genes can give genetic resources for the subsequent molecular-assisted breeding of drought-resistant alfalfa crops.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"523"},"PeriodicalIF":3.5,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12101008/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144131831","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":"Prediction of lipase-specific foldase-dependence in bacterial lipase subfamilies I.1 and I.2.","authors":"Takahiro Hioki","doi":"10.1186/s12864-025-11717-4","DOIUrl":"10.1186/s12864-025-11717-4","url":null,"abstract":"<p><strong>Background: </strong>Most bacterial lipases in subfamily I.1/I.2 depend on a specific chaperone protein, lipase-specific foldase (Lif), for folding into their active form. In contrast, several Lif-independent lipases have been reported in subfamily I.1. Lif-independent lipases have the potential to be industrially useful owing to their ease of heterologous expression; however, no method has been reported to predict Lif-dependence for an arbitrary lipase. In this study, we comprehensively estimated the Lif-dependence of subfamily I.1/I.2.</p><p><strong>Results: </strong>To estimate Lif-dependence, we comprehensively analyzed the presence or absence of Lif genes in the genomes of bacteria from which the lipases were derived and integrated the results with those of phylogenetic analysis. We identified a range of lipases from the Pseudomonas fragi/Proteus vulgaris clade, which contained all known Lif-independent lipases and were enriched for lipases that did not coexist with Lif. Sequences and structural features conserved in the P. fragi/P. vulgaris clade and other lipases were identified, and the residues involved in Lif-dependence were inferred. Furthermore, we identified the Pseudoalteromonas shioyasakiensis clade, which is phylogenetically distinct from the P. fragi/P. vulgaris clade, as having no Lif in the genome of the bacterium from which the lipase was derived. The P. shioyasakiensis clade lipase, PliLip, was heterologously expressed in Escherichia coli in an active form, independent of Lif.</p><p><strong>Conclusions: </strong>In this study, we developed a method to predict Lif-dependence in any lipase belonging to subfamily I.1/I.2 and comprehensively extracted putative Lif-independent lipases from public databases. This study contributes to expand the diversity of industrially available Lif-independent lipases and provides fundamental insights into the evolution of lipases and Lif.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"520"},"PeriodicalIF":3.5,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12096544/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144118743","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":"AoUPRS: A cost-effective and versatile PRS calculator for the All of Us Program.","authors":"Ahmed Khattab, Shang-Fu Chen, Nathan Wineinger, Ali Torkamani","doi":"10.1186/s12864-025-11693-9","DOIUrl":"10.1186/s12864-025-11693-9","url":null,"abstract":"<p><strong>Background: </strong>The All of Us (AoU) Research Program provides a comprehensive genomic dataset to accelerate health research and medical breakthroughs. Despite its potential, researchers face significant challenges, including high costs and inefficiencies associated with data extraction and analysis. AoUPRS addresses these challenges by offering a versatile and cost-effective tool for calculating polygenic risk scores (PRS), enabling both experienced and novice researchers to leverage the AoU dataset for large-scale genomic discoveries.</p><p><strong>Methods: </strong>We evaluated three PRS models from the PGS Catalog (coronary artery disease, atrial fibrillation, and type 2 diabetes) using two distinct approaches in the Hail framework: MatrixTable (MT), a dense representation, and Variant Dataset (VDS), a sparse representation optimized for large-scale genomic data. Computational cost, resource usage, and processing time were compared. To assess the similarity of PRS performance between these two approaches, we compared odds ratios (ORs) and area under the curve (AUC). Lin's concordance correlation coefficient (CCC) was also computed to quantify agreement between PRS scores generated by MT and VDS.</p><p><strong>Results: </strong>The VDS approach reduced computational costs by up to 99.51% (e.g., from $32 to $0.036 for a 51-SNP score) while maintaining PRS estimates that were highly similar to those obtained using the MT approach. Across all three PRS models, AUC comparisons showed minimal differences between MT and VDS, indicating that both approaches yield consistent PRS performance. Agreement between PRS scores calculated by both approaches was further supported by Lin's CCC values ranging from 0.9199 to 0.9944, confirming strong concordance. Empirical cumulative distribution function (ECDF) plots further illustrated the near-identical distribution of PRS values across methods.</p><p><strong>Conclusions: </strong>AoUPRS enables efficient and cost-effective PRS computation within AoU, providing substantial cost savings while maintaining highly consistent PRS estimates. These findings support the use of AoUPRS for large-scale genomic risk assessment, making the AoU dataset more accessible and practical for diverse research applications. The tool's open-source availability on GitHub, coupled with detailed documentation and tutorials, ensures accessibility and ease of use for the scientific community.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"521"},"PeriodicalIF":3.5,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12096765/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144126549","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 analysis of Brassica napus Glycosyl hydrolase family 1 genes and functional analysis of BnaBGLU27.C08 in clubroot resistance.","authors":"Yiji Shi, Xiang Liu, Shunjun Bao, Ye Li, Yuqing Shi, Chen Liang, Hongyu Sha, Zihao Yu, Qing Su, Xiyu Zhang, Xiaoyan Li, Weinan Sun, Chengyu Yu, Keqi Li, Zhen Huang","doi":"10.1186/s12864-025-11638-2","DOIUrl":"10.1186/s12864-025-11638-2","url":null,"abstract":"<p><strong>Background: </strong>β-Glycosidases (BGLUs), belonging to the Glycoside Hydrolase Family 1 (GH1), play crucial roles in plant growth, development, and stress adaptation. While BGLUs have been extensively characterized in various plants, a comprehensive analysis of the BGLU family in Brassica napus has yet to be conducted.</p><p><strong>Results: </strong>In this study, we identified 131 BnaBGLU genes in B. napus and classified them into 11 subfamilies. Gene duplication analysis revealed that the expansion of the BnaBGLU family primarily resulted from segmental duplications. Structural analysis revealed high conservation within subfamilies, while promoter cis-element profiling and transcriptional studies under phytohormone treatments and abiotic stresses demonstrated BnaBGLUs respond to diverse environmental stimuli. Additionally, BnaBGLUs exhibit tissue-specific expression patterns. Notably, BnaBGLU27.C08 was significantly upregulated 96 h post-inoculation with Plasmodiophora brassicae in the root of clubroot-resistant (CR) B. napus varieties. Furthermore, overexpression of BnaBGLU27.C08 in Arabidopsis significantly enhanced resistance to clubroot disease.</p><p><strong>Conclusions: </strong>These findings establish a foundation for further investigation on the BnaBGLU family in B. napus and offer potential candidate genes for breeding CR B. napus varieties.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"515"},"PeriodicalIF":3.5,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12093868/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144118719","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, expression profiling and potential functional roles of nuclear receptors in the social aphid Pseudoregma bambucicola.","authors":"Jianjun Lu, Xiaolei Huang","doi":"10.1186/s12864-025-11724-5","DOIUrl":"10.1186/s12864-025-11724-5","url":null,"abstract":"<p><strong>Background: </strong>Nuclear receptors (NRs) constitute a superfamily of transcription factors that regulate diverse biological processes. In insects, NRs not only govern essential physiological functions including metabolism, development, and reproduction, but also play pivotal roles in regulating caste differentiation and division of labor within social insect colonies. Pseudoregma bambucicola is a species of social aphid in which adults exhibit a specialized reproductive division of labor. This unique system produces first-instar nymphs and soldiers, which share an identical genetic background yet exhibit distinct morphological and behavioral traits. Although NRs exhibit pleiotropic regulatory capacities, their roles in the unique developmental patterns of P. bambucicola remain unclear.</p><p><strong>Results: </strong>This study identified 21 NR genes based on the genomic data of P. bambucicola and analyzed the duplication and loss events of these genes through phylogenetic analysis. Additionally, differential expression of NR genes was analyzed using transcriptomic data. The TLL exhibited significant differential expression in adults with distinct reproductive behaviors, suggesting its involvement in the regulation of reproductive division of labor. E75 and HNF4 were found to be important for the post-embryonic development of soldiers. Furthermore, quantitative real-time PCR confirmed caste-specific expression patterns of HR4 and HR39, indicating their potential involvement in morphological differentiation and developmental regulation among castes.</p><p><strong>Conclusions: </strong>This study conducted bioinformatic identification of NR genes in the social aphid P. bambucicola, and investigated their potential roles in morphological differentiation and behavioral division through analysis of differential gene expression. The findings provide preliminary evidence for the functional significance of NR genes in social aphids, while offering novel insights for subsequent research exploration.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"518"},"PeriodicalIF":3.5,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12093900/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144118742","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":"Splenic comparative transcriptome analysis reveals the immunological mode of undomesticated Gayal (Bos frontalis) for adapting to harsh environments.","authors":"Ye Yu, Chunjia Jin, Runqi Fu, Lin Han, Binlong Fu, Qian Li, Yanfen Cheng, Jing Leng","doi":"10.1186/s12864-025-11718-3","DOIUrl":"10.1186/s12864-025-11718-3","url":null,"abstract":"<p><strong>Background: </strong>The utilization of transcriptome technology in the identification of pivotal regulatory genes associated with immunity is of paramount importance. Previous studies have shown that undomesticated gayal (Bos frontalis) may have higher humoral responses which is comparable to yaks. However, research on immune function of gayal is limited, and comparisons with different breeds are rarely reported. The objective of this study was to inspect the immune status and compare splenic differential expression genes (DEGs) through comparative transcriptome analysis of gayal and domesticated local cattle (Yunan yellow cattle).</p><p><strong>Results: </strong>Serum immunological status investigation showed the better humoral immune status and lower levels of pro-inflammatory cytokines of gayal when compared to the local cattle. Spleen RNA-seq showed that 708 DEGs (365 up- and 343 down-regulated genes) were obtained between the gayal and local cattle. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analysis showed that immune system pathways, immune disease pathways, and chemotaxis-related molecular function of gayal were significantly enriched, whereas T cell-related cellular component and biological process were downregulated in the gayal. Correlation analysis shown that CD1, CD36, CD38, CD179a, CD179b, CXCL8, IGCGAMMA, IGH, IGHG1, IGLL1, IL1R2, SERPINB, and SERPINB4 had positive correlations with splenic IgA, IgD, IgE, IgG, and IgM, respectively (R > 0.5, P < 0.05). ANPEP, BVD1.23, CD1E, CD3D, CD3E, CD3G, CD5, CD8 A, HBB, IDO1, LCK, MGC126945, MHC1, TRAV, TRBV, and ZAP70 had negative correlations with splenic IgA, IgD, IgE, IgG, and IgM, respectively (R < -0.5, P < 0.05).</p><p><strong>Conclusions: </strong>Our results reveal the immunological mode of gayal with high-level humoral immunity and enhanced splenic immunoglobulin gene expression and B cell differentiation, which may enable gayal to adapt to the harsh environments.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"514"},"PeriodicalIF":3.5,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12093757/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144109572","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 key genes and metabolites involved in intramuscular fat deposition in Laiwu pigs through combined transcriptomic and lipidomic analyses.","authors":"Wen Chuan Peng, Guo He Cai, Rui Rui Pan, Yong Zhen Niu, Jun Ying Xiao, Chu Xiong Zhang, Xiao Zhang, Jiang Wei Wu","doi":"10.1186/s12864-025-11669-9","DOIUrl":"10.1186/s12864-025-11669-9","url":null,"abstract":"<p><p>Pork quality is a key goal in commercial pig farming. Intramuscular fat (IMF) content in pigs serves as a critical determinant of meat quality, yet its regulatory mechanism remains unclear. In this study, two different pig breeds Chinese native breed Laiwu (fatty-type) and Yorkshire (lean-type), were selected as research subjects. The molecular regulatory mechanisms affecting IMF content were investigated through integrated transcriptomic and lipidomic analysis. We identified critical genes, including ACC1, FASN, ELOVL6, SCD, and DGAT2, and elucidated their synergistic interactions in promoting IMF deposition in Laiwu pigs. The findings reveal that the coordinated action of genes such as ACC1 and FASN promotes the increased production of palmitic acid, which was subsequently elongated and desaturated by ELOVL6 and SCD to form long-chain fatty acids necessary for TG synthesis. Additionally, DGAT2 facilitates the extensive synthesis of TG, which is stored in lipid droplets under the regulation of PLIN1. This increased triglyceride synthesis and storage capacities in Laiwu pigs, functioning as one of the key factors contributing to its high IMF content. The study highlights the importance of gene-lipid interactions in IMF deposition and offers novel insights into the genetic and molecular basis of IMF accumulation, particularly in fatty pig breeds like the Laiwu. Our research findings provide new directions for developing targeted genetic or nutritional interventions to enhance IMF content and improve meat quality.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"516"},"PeriodicalIF":3.5,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12093822/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144118740","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}