BMC Genomics最新文献

{"title":"Chromosome-level genome assembly of the coral grouper, Epinephelus corallicola and its evolutionary insights into Eupercaria.","authors":"Baojun Zhao, Chaofan Jin, Yuhan Jiang, Chunren Huang, Yuting Yang, Mingjian Liu, Haizhan Tang, Da Zheng, Zhenmin Bao, Bo Wang, Jingjie Hu","doi":"10.1186/s12864-025-11996-x","DOIUrl":"10.1186/s12864-025-11996-x","url":null,"abstract":"<p><strong>Background: </strong>Epinephelus corallicola, also known as the coral grouper, is an economically valuable grouper species widely distributed in Southeast Asia. However, its genomic information and phylogenetic status remain unclear. Furthermore, despite substantial genomic resources accumulated for Eupercaria, integrated analyses of phylogenetic relationships and genome evolution based on these resources remain scarce.</p><p><strong>Results: </strong>In this study, we generated high-quality haplotype-solved genomes of E. corallicola, with total lengths of 1.086 Gb and 1.083 Gb for the two haplotypes, and contig N50 values of 44.94 Mb and 43.86 Mb, respectively. Phylogenomic analyses placed the Perciformes at the basal position of the Eupercaria, with an estimated divergence time of 88.55 Mya. And the phylogenetic topology supported the previous proposal to elevate Epinephelinae to the family level as Epinephelidae, distinct from Serranidae. Ancestral karyotype evolution analyses based on chromosomal genomes of 33 species revealed that E. corallicola serves as a representative model for the 24 ancestral linkage groups (ALGs) of Eupercaria, enabling the tracing of ancient chromosomal evolution across lineages. Within the Epinephelidae, the whole-genome average nucleotide identity (ANI) among species ranged from 84.16% to 96.97%. Gene family expansion and contraction analyses revealed 285 significantly expanded and 618 contracted gene families. Notably, the expanded gene families were significantly enriched in immune-related genes, including MHCIIα, MHCIIβ, and RFX5, which may contribute to the adaptive evolution of E. corallicola.</p><p><strong>Conclusions: </strong>Our results provide important genomic resources for Epinephelidae, advancing aquaculture and selective breeding programs for groupers, while offering new insights into the phylogeny and ancestral chromosomal karyotype evolution of Eupercaria.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"832"},"PeriodicalIF":3.7,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12465458/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145173311","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":"Genetic variation landscape of sheep GDF9 gene from global ewes breeds and their association with gestation days.","authors":"Peiyao Liu, Yejun Pan, Xiangding Wang, Chunna Cao, Ran Li, Chuanying Pan, Qingfeng Zhang, Xianyong Lan","doi":"10.1186/s12864-025-12000-2","DOIUrl":"10.1186/s12864-025-12000-2","url":null,"abstract":"<p><p>Growth differentiation Factor 9 (GDF9) has been confirmed to be closely related to the reproductive capacity of sheep. This study systematically investigated the genetic variation of the GDF9 gene across 75 global sheep breeds (n = 2,409) and explored its association with gestation days in Australian White sheep (AUW, n = 120). Through whole-genome sequencing and SNP analysis, 49 SNPs (26 located in introns, 22 in exons, and 1 in the 3' UTR region) and 20 InDel loci were identified within GDF9 gene. Haplotype analysis revealed six major haplotypes strongly correlated with geographical population distribution. Association studies in Australian White sheep demonstrated a significant difference between three SNPs loci (g.42115010T > C, g.42115254T > C, and g.42114509T > C) and gestation days: primiparous ewes with the CC genotype at g.42,115,010 exhibited the shortest gestation days (146.42 ± 2.57 days, P = 0.030), while fourth-parity ewes with the AG genotype at g.42,114,509 showed an abnormally prolonged gestation (155.00 ± 12.81 days, P = 0.030). Key missense mutations (e.g., E241K, R87H) were predicted to alter protein 3D structure, suggesting functional impacts on reproductive regulation. Despite limited sample sizes in certain parity groups, suggests that GDF9 may serve a potential genetic marker for optimizing reproductive efficiency, offering molecular strategies to shorten primiparous gestation and uncovering its evolutionary role in sheep domestication.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"820"},"PeriodicalIF":3.7,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12465990/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145173388","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":"Selection and validation of RT-qPCR reference genes for multi-tissue gene expression normalization in two honeybee subspecies across post-emergence developmental stages.","authors":"Xuanpeng Liu, Ting Yang, Jilian Li, Chuan Ma","doi":"10.1186/s12864-025-12020-y","DOIUrl":"10.1186/s12864-025-12020-y","url":null,"abstract":"<p><strong>Background: </strong>The western honeybee (Apis mellifera) represents a pivotal model organism for investigating social organization and phenotypic plasticity. Behavioral specialization in worker bees induces tissue-specific molecular adaptations, particularly in sensory and secretory tissues. Although real-time quantitative PCR (RT-qPCR) has been extensively employed to quantify gene expression dynamics in these tissues, systematic evaluation of optimal reference genes for RT-qPCR data normalization remains undressed.</p><p><strong>Results: </strong>We systematically assessed nine candidate reference genes across three tissues (antennae, hypopharyngeal glands, and brains) in adult honeybees at three developmental stages (newly emerged bees, nurses, and foragers) from two subspecies (A. m. ligustica and A. m. carnica). Using five statistical algorithms (geNorm, NormFinder, BestKeeper, ΔC_T method, and RefFinder), we identified ADP-ribosylation factor 1 (arf1) as the most stable reference gene across all experimental conditions, followed by ribosomal protein L32 (rpL32). Their stability was confirmed by experimental validation through normalization of major royal jelly protein 2 (mrjp2) expression patterns. Notably, three conventional housekeeping genes (α-tubulin, glyceraldehyde-3-phosphate dehydrogenase, and β-actin) displayed consistently poor stability, disqualifying their application in quantitative analyses under these experimental conditions.</p><p><strong>Conclusions: </strong>Our findings provide validated reference genes for precise quantification of tissue-specific gene expression patterns during adult honeybee development. These reference genes facilitate identification of candidate genes associated with honeybee development, social behavior, and productivity traits.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"822"},"PeriodicalIF":3.7,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12465390/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145173515","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":"From benchmarking alignment of genome assemblies to IMGT annotation: the paradigm of the bovine Bos taurus T cell receptor (TRG) locus.","authors":"Hao Zhou, Chimari Jiko, Christoph Gerle, Marie-Paule Lefranc, Kazutaka Katoh, Daron M Standley","doi":"10.1186/s12864-025-12081-z","DOIUrl":"10.1186/s12864-025-12081-z","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"809"},"PeriodicalIF":3.7,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12462221/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145147622","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":"Integrative assessment of RNA sequencing and in silico analysis to pinpoint mRNAs, lncRNAs, and circRNAs interactions with miRNAs underlying arsenic-induced neurotoxicity.","authors":"Sana Sarkar, Anuj Pandey, Bushra Khan, A B Pant","doi":"10.1186/s12864-025-11970-7","DOIUrl":"10.1186/s12864-025-11970-7","url":null,"abstract":"<p><strong>Background: </strong>The acquisition of neurodegeneration hallmarks necessitates molecular changes at multiple levels of functional genomics. Regulatory RNAs, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), play crucial roles in modulating messenger RNAs (mRNAs) expression and are potential molecules that regulate multifactorial neurotoxicity mechanisms. Integrated studies of regulatory RNAs' functions are still lacking to portray the complete picture. In this study, we carried out a detailed analysis of mRNA, lncRNA, and circRNA profiles in differentiated SH-SY5Y cells exposed to arsenic, a well-known neurotoxicant, using the Illumina Novaseq6000 platform. Subsequently, employing a bioinformatics approach, we identified specific interactions between these RNA molecules and potential miRNAs, unraveling intricate regulatory networks.</p><p><strong>Results: </strong>Among significantly deregulated transcripts, we identified 2487 mRNA transcripts, 1192 lncRNA transcripts, and 20 circRNA transcripts in arsenic-treated cells compared to control. Functional enrichment analysis indicated their involvement in numerous pathways underlying neurotoxicity. Further, these regulatory molecules displayed strong interactions with multiple miRNAs implicated in neuronal damage.</p><p><strong>Conclusion: </strong>Our findings revealed intricate molecular alterations in response to arsenic exposure, emphasizing the crucial role of multi-omics technologies in understanding neurodegeneration. This approach has enabled the identification of potential targets for future exploration, emphasizing the precise modulation of regulatory RNA networks to mitigate the effects of arsenic.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"813"},"PeriodicalIF":3.7,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12465176/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145147612","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":"Genomic diversity in Chinese Holstein cattle and genome-wide association study for body conformation traits.","authors":"Jinpeng Wang, Yaran Zhang, Chunhong Yang, Zhihua Ju, Yao Xiao, Qiang Jiang, Wenhao Liu, Xiuge Wang, Xiaochao Wei, Yaping Gao, Xiuxin Zhao, Lingling Wang, Yundong Gao, Jianbin Li, Jinming Huang","doi":"10.1186/s12864-025-12002-0","DOIUrl":"10.1186/s12864-025-12002-0","url":null,"abstract":"<p><strong>Background: </strong>The genomic diversity of Chinese Holstein cattle remains insufficiently characterized, and the identification of genes associated with body conformation traits is still limited. In this study, we aimed to explore the genome-wide diversity and population structure, and to identify candidate genes associated with 20 body conformation traits in Chinese Holstein cattle from six farms using the GGP Bovine 50 K single nucleotide polymorphism (SNP) chip.</p><p><strong>Results: </strong>We analyzed runs of homozygosity and population admixture across farms and observed genetic diversity differences among herds. A genome-wide association study identified 21 significant SNPs linked to five body conformation traits. Notably, a missense mutation in TJP1 (BovineHD2100008355) was associated with foot heel depth. Ten SNPs within intronic regions of genes such as GABRG3, NEGR1, and CDH2 were associated with various udder and leg traits. The remaining ten SNPs were located in intergenic regions and influenced transcription factor binding sites. Among them, BovineHD2100013266, BovineHD0500004109, and BTB-00042676 were shown to regulate transcriptional activity through dual-luciferase reporter assays.</p><p><strong>Conclusions: </strong>Our findings offer valuable insights for managing genetic inbreeding in cattle farms, enhancing the understanding of the genetic architecture underlying body conformation traits in Holstein cattle, and accelerating the genomic selection process in Chinese Holsteins.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"811"},"PeriodicalIF":3.7,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12465292/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145147562","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 HS-SPME-GC/MS and RNA sequencing analysis reveals metabolic differences of flavor compounds of muscle tissues with different intramuscular fat contents from Tibetan sheep.","authors":"Xiayang Jin, Wu Sun, Yuhong Ma, Yan Zhang, Shike Ma","doi":"10.1186/s12864-025-11997-w","DOIUrl":"10.1186/s12864-025-11997-w","url":null,"abstract":"<p><strong>Background: </strong>A key factor used to evaluate the quality of meat is intramuscular fat (IMF) content, which has a strong association with the flavor of meat. To date, however, the influence of IMF content on the volatile profiles of ovine meat has not been clarified.</p><p><strong>Results: </strong>We used headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC/MS) to study the aroma characteristics of low-IMF (L-IMF) and high-IMF (H-IMF) content in muscle tissue and to identify volatile compounds in L-IMF and H-IMF groups. Thirteen of 557 volatile compounds identified were significantly different between the groups (Odor Activity Values > 1, VIP values > 1), of which aldehydes, ketones, and esters were the predominant volatile compounds. We conducted RNA-seq analysis and found 985 differentially expressed genes (DEGs) in the L-IMF and H-IMF groups. The weighted gene coexpression network analysis (WGCNA) showed that DEGs associated with muscle aroma characteristics were enriched in lipolysis regulation in adipocytes, PPAR signaling, AMPK signaling, arachidonic acid metabolism, and the biosynthesis of unsaturated fatty acids (UFAs). These pathways played a role in regulating energy metabolism and muscle lipid metabolism functions in Tibetan sheep. The combined results of DEGs, WGCNA, and gene-aroma compound interactions revealed ADIPOQ, FABP4, FADS2, GPD2, HSL, LEP, PEPCK and PLIN4 to be potential candidate genes affecting IMF and aroma compounds content.</p><p><strong>Conclusion: </strong>In this study, we established profiles of the transcriptome and volatile compounds of L-IMF and H-IMF ovine muscle tissues. The findings suggested that HSL, FABP4 and PLIN4, along with the lipolysis regulation in adipocytes and PPAR signaling pathways, contributed to the difference in lipid metabolism within muscle tissues, and biosynthesis of the UFA pathway may influence the production of volatile compound precursors in muscles. These results offer important information about regulating genes that pertain to ovine meat flavor compounds.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"812"},"PeriodicalIF":3.7,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12465669/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145147629","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":"Integrative analysis of mRNA, lncRNA, circRNA, and miRNA to investigate the anti-fibrotic activity of silibinin in TGF-β2-treated human trabecular meshwork cells.","authors":"Jinfeng Liu, Xueping Wu, Junhong Guo, Lina Zhou, Xin Liu, Lei Zhu, Lan Ma, Jiantao Wang","doi":"10.1186/s12864-025-12027-5","DOIUrl":"10.1186/s12864-025-12027-5","url":null,"abstract":"<p><strong>Background: </strong>TGF-β-induced fibrogenic changes in human trabecular meshwork (HTM) cells contribute to intraocular pressure elevation in glaucoma. Silibinin, a natural polyphenolic flavonoid from milk thistle seeds, has been well investigated for its function to inhibit fibrosis. The transcriptomic changes in noncoding RNAs contributing to the pro-fibrotic effect of TGF-β2 and the anti-fibrotic activity of silibinin in HTM cells remain unknown.</p><p><strong>Methods: </strong>RNA sequencing was conducted to characterize the transcriptomic profiles (mRNA, lncRNA, circRNA, and miRNA) in TGF-β2-stimulated HTM cells, with or without silibinin treatment. Pathway enrichment analysis of the differentially expressed RNAs was conducted. Competing endogenous RNA networks were constructed.</p><p><strong>Results: </strong>TGF-β2 upregulated 1119 mRNAs, 319 lncRNAs, 383 circRNAs, and 30 miRNAs in HTM cells, of which 545 mRNAs, 183 lncRNAs, 265 circRNAs, and 22 miRNAs were reversed by silibinin. These rescued mRNAs, including COL1A1 and α-SMA, were enriched in pathways including cell migration, cell adhesion, and extracellular matrix. Furthermore, TGF-β2 downregulated 1165 mRNAs, 212 lncRNAs, 449 circRNAs, and 15 miRNAs, of which 395 mRNAs, 54 lncRNAs, 104 circRNAs, and 7 miRNAs were reversed by silibinin. These rescued mRNAs were enriched in cytokine-mediated signaling pathway and inflammatory response. By predicting the binding of differentially expressed mRNAs, lncRNAs, and circRNAs to miRNAs via miranda (v 3.3a) software, we constructed lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA networks that might be involved in the effects of TGF-β2 and silibinin in HTM cells.</p><p><strong>Conclusions: </strong>Silibinin mitigated TGF-β2-induced alterations in the coding and noncoding RNA profiles of HTM cells, presumably contributing to its anti-fibrotic activity. To our knowledge, this is the first study to illustrate the lncRNA and circRNA changes induced by TGF-β2 in HTM cells, and the first study to investigate silibinin's anti-fibrotic effects in HTM cells from the perspective of noncoding RNAs. Our work deepened the understanding of gene regulation by noncoding RNAs in the TGF-β2-induced fibrogenic changes and the anti-fibrotic activity of silibinin in HTM cells.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"814"},"PeriodicalIF":3.7,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12465171/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145147588","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":"MitoDelta: identifying mitochondrial DNA deletions at cell-type resolution from single-cell RNA sequencing data.","authors":"Haruko Nakagawa, Yasuyuki Shima, Yohei Sasagawa, Itoshi Nikaido","doi":"10.1186/s12864-025-11931-0","DOIUrl":"10.1186/s12864-025-11931-0","url":null,"abstract":"<p><strong>Background: </strong>Deletion variants in mitochondrial DNA (mtDNA) are associated with various diseases, such as mitochondrial disorders and neurodegenerative diseases. Traditionally, mtDNA deletions have been studied using bulk DNA sequencing, but bulk methods average signals across cells, thereby masking the cell-type-specific mutational landscapes. Resolving mtDNA deletions at single-cell resolution is beneficial for understanding how these mutations affect distinct cell populations. To date, no specialized method exists for detecting cell-type-specific mtDNA deletions from single-cell RNA sequencing data. Notably, mtDNA possesses unique molecular features: a high copy number, stable transcription, and compact structure of the mitochondrial genome. This results in a relatively high abundance of mtDNA-derived reads even in single-cell RNA sequencing data, suggesting the possibility of detecting mtDNA deletion variants directly from transcriptomic data.</p><p><strong>Results: </strong>Here, we present MitoDelta, a computational pipeline that enables the detection of mtDNA deletions at cell-type resolution solely from single-cell RNA sequencing data. MitoDelta combines a sensitive alignment strategy with robust statistical filtering based on a beta-binomial distribution model, allowing accurate identification of deletion events even from noisy single-cell transcriptomes. To capture cell-type-specific deletion patterns, MitoDelta analyzes reads pooled by annotated cell types, enabling quantification of deletion burden across distinct cellular populations. We benchmarked MitoDelta against existing mtDNA deletion detection tools and demonstrated superior overall performance. As a practical application, we applied MitoDelta to a published single-nucleus RNA sequencing dataset for Parkinson's disease and revealed distinct mtDNA deletion burdens across neuronal subtypes.</p><p><strong>Conclusions: </strong>MitoDelta enables the transcriptome-integrated, cell-type-specific detection of mtDNA deletions from single-cell RNA sequencing data alone, offering a valuable framework for reanalyzing public datasets and studying mitochondrial genome alterations at cell-type resolution. This integrated approach enables insights into how mtDNA deletions are distributed across specific cell types and cellular states, providing new opportunities to investigate the role of mtDNA deletions in cell-type-specific disease mechanisms. The tool is available at https://github.com/NikaidoLaboratory/mitodelta .</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"810"},"PeriodicalIF":3.7,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12465547/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145147543","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":"HKDE-LACM: a hybrid model for lactic acid bacteria classification via k-mer and DNABERT-2 embedding fusion with cyclic DE-BO optimization.","authors":"Jie Zou, Weichi Liu, Jinhui Dai, Gaifang Dong","doi":"10.1186/s12864-025-12009-7","DOIUrl":"10.1186/s12864-025-12009-7","url":null,"abstract":"<p><strong>Background: </strong>Lactic acid bacteria (LAB) play vital roles in food production and clinical applications. Accurate classification of LAB strains facilitates their functional development and targeted utilization. Although machine learning and deep learning methods have been widely applied to genome sequence classification, challenges remain in capturing comprehensive feature representations and enhancing model generalizability.</p><p><strong>Results: </strong>We present HKDE-LACM, a hybrid classification model that integrates high-dimensional k-mer frequency features with contextual embeddings derived from DNABERT-2. To optimize model hyperparameters, we introduce a Cyclic Differential Evolution and Bayesian Optimization with Failure Avoidance (C-DBFA) framework. We conducted 10-fold cross-validation on three LAB datasets and evaluated performance. Experimental results demonstrate that HKDE-LACM outperforms existing methods in terms of both classification accuracy and robustness.</p><p><strong>Conclusions: </strong>HKDE-LACM overcomes the limitations of traditional k-mer features by incorporating semantic embeddings, thereby enriching the representation of genomic sequences. In addition, the model can automatically identify optimal combinations of feature extractors and classifiers through the C-DBFA optimization framework. These advantages effectively enhance the model's generalization ability, making it a promising tool for genome-based LAB classification and related tasks.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"815"},"PeriodicalIF":3.7,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12465904/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145147617","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}