BMC Genomics最新文献

{"title":"High-efficiency 14-plex cSNP SNaPshot assay for forensic peripheral blood identification.","authors":"Yixia Zhao, Yuting Sun, Siyi Wei, Qinglin Liu, Anquan Ji, Caixia Li, Bofeng Zhu","doi":"10.1186/s12864-026-13173-0","DOIUrl":"10.1186/s12864-026-13173-0","url":null,"abstract":"<p><p>The analysis of body fluid stains found at criminal scenes requires not only DNA profiles but also identification of the composition of these stains, particularly in mixed stains. Prior studies have demonstrated that forensic body fluids can be differentiated by their mRNA biomarkers.In this study, we screened a panel including 14 cSNPs located on four peripheral blood mRNA biomarkers (CD3G, ANK1, SPTB, and GYPA) and developed a multiplex assay for forensic blood identification using the SNaPshot method. Particularly, a one-step multiplex reverse transcription PCR (RT-PCR) strategy was used to generate cDNA amplicons from the corresponding mRNA by reverse transcription. The sensitivity, specificity, and capability of the multiplex SNaPshot assay for blood identification were systematically assessed. These results showed that the panel of 14 cSNPs successfully realized peripheral blood identification, including single-source body fluid as well as mixed samples. However, several peripheral blood cSNP markers were detected at low expression levels in menstrual blood and vaginal secretions. The detection sensitivity of the multiplex assay reached 1 ng total RNA input. Furthermore, 14 cSNP loci were genotyped across 19 peripheral blood samples, yielding 100% concordance between DNA- and RNA-derived profiles. Using allele frequencies of 14 cSNP loci in 100 unrelated Han individuals from northern China, the cumulative discrimination power of the 14 cSNPs was calculated to be 0.98303.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13644189/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148418433","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":"Insertion sequence elements associated with Staphylococcus epidermidis evolution in persistent orthopaedic device-related infections.","authors":"James C Littlefair, Carolin M Kobras, Virginia Post, Ben Pascoe, David J Baker, Christoph Erichsen, Mathew Stracy, Fintan Moriarty, Samuel K Sheppard","doi":"10.1186/s12864-026-13148-1","DOIUrl":"10.1186/s12864-026-13148-1","url":null,"abstract":"<p><strong>Background: </strong>Staphylococcus epidermidis is a major cause of orthopaedic device-related infections (ODRIs), which are often challenging to treat due to their extensive antimicrobial resistance (AMR) and biofilm formation. It has been hypothesised that S. epidermidis may rapidly adapt to the medical device niche, enhancing persistence, but direct evidence of within-host pathoadaptive evolution remains limited.</p><p><strong>Results: </strong>To investigate within-host evolution during chronic infection by S. epidermidis, we analysed isolates from patients with confirmed ODRIs and used a rat infection model to examine the evolution of strains from two distinct epidemic lineages (ST2 and ST23). Our analysis revealed that the replicative transposition of insertion sequence (IS) elements within the accessory genome was the predominant mechanism of genetic diversification. This was largely driven by the IS256 family, which accounted for approximately 25% of all mutational events. However, other than SCCmec deletions resulting in the loss of mecA, no mutations, including those which exhibited parallel evolution, were predicted or observed to influence AMR or biofilm formation. These findings suggest that the strains investigated in this study, which already exhibited high-level multidrug resistance and biofilm-forming ability, were likely pre-adapted epidemic S. epidermidis clones well suited to establishing persistent ODRIs.</p><p><strong>Conclusions: </strong>Our findings highlight the prominent role of IS elements in driving genetic diversification in S. epidermidis, underscoring the need for closer examination of their contribution to pathoadaptation during persistent infection.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13640169/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148418418","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":"Bioinformatics analysis of the sodium-dependent neurotransmitter transporter family in Bursaphelenchus xylophilus.","authors":"Caijin He, Shichao Wang, Haixiang Li, Na Pu, Wangyang Liao, Jie Chen, Xin Hao","doi":"10.1186/s12864-026-13150-7","DOIUrl":"10.1186/s12864-026-13150-7","url":null,"abstract":"<p><p>Pine wilt disease (PWD), caused by Bursaphelenchus xylophilus, poses a significant threat to global pine forests. The sodium-dependent neurotransmitter transporter (SNF) plays a critical role in the reuptake of neurotransmitters from the synaptic cleft, thereby terminating neural signal transmission and maintaining nervous system homeostasis. This study aimed to comprehensively identify all members of the SNF in B. xylophilus and elucidated their roles in nematode development and nervous system function. Through genome-wide data analysis, we identified 18 SNFs in B. xylophilus and thoroughly characterized their physicochemical properties, conserved motifs, protein structures, and gene expression profiles across different developmental stages. Phylogenetic analysis revealed evolutionary relationships with SNF homologs from other nematodes, suggesting lineage-specific functional adaptations. Chromosomal localization revealed that the SNF genes are distributed across five chromosomes with numbers ranging from 1 to 18. Expression analysis showed that Bx-snf-2, Bx-snf-6, Bx-snf-7, Bx-snf-9, Bx-snf-10 were highly expressed in adult males, while Bx-snf-1 and Bx-snf-4 were enriched during the egg stage. Additionally, Bx-snf-12 and Bx-snf-18 exhibited peak expression in fourth-stage larvae (L4). Notably, the upregulation of specific Bx-snfs during the dauer stage indicates potential roles in mediating stress adaptation and survival under adverse conditions. This study provides the first systematic characterization of the BxSNFs, revealing unique gene structures and specialized expression profiles. These findings offer potential molecular targets for developing novel control strategies against pine wilt disease by interfering with neurotransmitter reuptake.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13640315/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148418194","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 the GDSL esterase/lipase (GELP) family in banana (Musa acuminata) and functional validation of MaGELP81 as a candidate positive regulator associated with resistance to Fusarium oxysporum f. sp. cubense tropical race 4.","authors":"Dandan Tian, Zhangfei He, Jiahui Chen, Liping Wei, Baoshen Li, Quyan Huang, Di Wei, Wei Zhou, Shaolong Wei, Sumei Huang, Jialin Li, Liuyan Qin, Chaosheng Li","doi":"10.1186/s12864-026-13114-x","DOIUrl":"10.1186/s12864-026-13114-x","url":null,"abstract":"<p><strong>Background: </strong>Fusarium wilt is among the most destructive diseases threatening global banana production and severely undermines the industry's sustainability. GDSL-type esterase/lipase proteins (GELPs) are lipid-hydrolyzing enzymes with diverse substrate specificities that catalyze the generation and transduction of lipid-derived signals, playing key roles in plant defense responses.</p><p><strong>Results: </strong>Here, we systematically identified members of the GELP gene family in the banana genome and conducted an integrated analysis of their phylogeny, gene structures, and promoter cis-elements. After manual correction of incorrectly annotated gene structures, a total of 92 MaGELP genes were identified and found to be unevenly distributed across 11 chromosomes, with most located near chromosome ends. Phylogenetic analysis combined with collinearity evidence indicated that the family is evolutionarily conserved. Promoter analysis revealed an enrichment of cis-elements associated with light responsiveness and MeJA-mediated signaling. Expression profiling showed that MaGELP81 is strongly up-regulated (fold change > 1.5) by infection with Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) and by SA, JA, and ET treatments, with pronounced differential expression between resistant and susceptible cultivars (fold change > 1.6). Subcellular localization assays demonstrated that MaGELP81 resides at the vacuolar membrane. When MaGELP81 was overexpressed in Arabidopsis thaliana, three independent high-expression lines exhibited better growth after Foc TR4 inoculation and significantly reduced disease incidence, severity scores, and disease index compared with the wild type, suggesting that MaGELP81 may be associated with enhanced resistance to Foc TR4.</p><p><strong>Conclusion: </strong>Collectively, this study provides a comprehensive view of the composition and evolutionary features of the banana GELP family, elucidates their potential roles in responses to Foc TR4 stress, and pinpoints MaGELP81 as a key candidate gene. These findings offer foundational insight into the molecular interplay between lipid metabolism and plant immune signaling and provide valuable genetic resources for the molecular breeding of Foc TR4-resistant banana.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13640102/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148418329","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":"D3aist: data-driven detection of atypical interactions in spatial transcriptomics.","authors":"Teresa León, Juan Domingo, Guillermo Ayala, Angela Riffo-Campos","doi":"10.1186/s12864-026-13147-2","DOIUrl":"10.1186/s12864-026-13147-2","url":null,"abstract":"<p><p>Tissues exhibit complex spatial organization that governs cellular function and interactions, yet traditional transcriptomic methods fail to capture this context. Spatial transcriptomics preserves cellular locations while profiling gene expression, enabling high-resolution mapping of tissue architecture. Molecule-resolved spatial transcriptomics data, in which individual transcript detections are associated with spatial coordinates and gene identities, can be naturally modeled as multitype point patterns within the framework of spatial statistics. Second-order summary statistics, such as the Ripley cross K-, cross L-, and pair correlation functions, are commonly used to characterize spatial interactions; however, systematic comparison across multiple types remains challenging. We propose a data-driven method, termed D3AIST, based on empirical envelopes constructed via a leave-one-pair-out strategy over the set of observed functions. Each gene-pair type is evaluated by comparing its second-order summary functions against an empirical envelope constructed from the corresponding functions of all other pairs, excluding the one under evaluation. This allows the detection of atypical spatial interactions without relying on classical null models or asymptotic results. D3AIST provides a global comparative scheme across all type pairs, facilitating the identification of singular interaction patterns within a fully empirical framework. We applied D3AIST to transcript-level Xenium data from two publicly available studies. In a primary colorectal cancer case study based on GSE280318/GSE280314, D3AIST identified atypical spatial interaction networks across expert-defined tumor microenvironment regions. An independent external evaluation using the GSE267680 Xenium dataset further illustrated the applicability of the framework in a distinct pancreatic intraepithelial neoplasia context. Controlled simulations and computational benchmarking were additionally used to evaluate empirical error behavior and scalability. Overall, D3AIST provides a descriptive and hypothesis-generating framework for prioritizing atypical transcript-level spatial associations in molecule-resolved spatial transcriptomics data.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13644092/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148418116","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":"Reversible jumps for the joint modeling of the dimension of pseudo-functional models in chromosomal windows in genome-wide selection.","authors":"Ernandes Guedes Moura, Carlos Pereira da Silva, Luciano Antonio de Oliveira, Marcio Balestre, Júlio Sílvio de Sousa Bueno Filho","doi":"10.1186/s12864-026-13073-3","DOIUrl":"10.1186/s12864-026-13073-3","url":null,"abstract":"<p><strong>Background: </strong>With the advance of large-scale genotyping and the high availability of single nucleotide polymorphism (SNP) markers, genomic selection (GS) has become fundamental for plant and animal breeding. However, this technique faces three classical problems: multicollinearity, high marker dimensionality, and high computational cost. To address these problems, mixed models or Bayesian inference methods are generally used. More recently, bin-based genomic window approaches have been widely used, as they can group redundant markers, reducing dimensionality and mitigating the effects of multicollinearity. However, the performance of these methods depends, among other factors, on the number, size, and location of the bins. In general, existing approaches group markers based on linkage disequilibrium (LD) patterns or use fixed-size genome partitions.</p><p><strong>Results: </strong>A transdimensional method was proposed to jointly infer the dimension, location, and composition of genomic compartments, as well as the parameters associated with the model, through reversible jump Markov chain Monte Carlo (RJ-MCMC) sampling. The method was evaluated in simulated F2 and F10 populations under oligogenic and polygenic architectures, as well as in human SNP data from the HapMap project with simulated phenotypes and real eucalyptus data. In the simulated datasets, the method achieved the best results under oligogenic architectures (F2 and F10). In more complex polygenic scenarios and real data, performance was satisfactory and comparable to that of rr-BLUP, Bayes B, and Hu, considering mean squared error (MSE), mean absolute error (MAE), and coefficient of determination (R²).</p><p><strong>Conclusions: </strong>The proposed method incorporates model complexity as an inferential component, allowing the automatic estimation of the number, location, and composition of genomic compartments jointly with the model effects. The method demonstrated robust predictive performance, in addition to improving the ability to identify causal regions, which may represent a promising methodological alternative for both genomic selection and QTL mapping.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13644038/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148418496","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":"Novel iflavirus species discovered through virome analysis of cotton field-collected aphids.","authors":"Chaoyang Zhao, Isabella Owens, Alana L Jacobson, Cesar Escalante, Raman Bansal, Kathleen M Martin, Kipling S Balkcom","doi":"10.1186/s12864-026-13132-9","DOIUrl":"10.1186/s12864-026-13132-9","url":null,"abstract":"<p><strong>Background: </strong>Insect-associated viruses (viromes) shape insect biology and agroecosystems, yet aphid viromes remain undercharacterized. The cotton aphid, Aphis gossypii, is a globally distributed pest with a broad plant host range and demonstrated virus-vector competence, making it well suited for investigating virome composition at the plant-insect-virus interface. In this study, we profiled the virome of field-collected aphid alates, which were dominated by A. gossypii but included additional aphid species in some samples, across 15 cotton fields in Alabama, USA, to assess taxonomic diversity, relative viral abundance, and focal aphid-associated viruses.</p><p><strong>Results: </strong>Metatranscriptomic sequencing of aphid alates revealed differences in taxonomic composition among county-level libraries, including viruses and diverse prokaryotic and eukaryotic taxa. Fifty-eight viral contigs > 1 kb were assembled, of which 20 were assigned to seven families: Dicistroviridae, Iflaviridae, Mitoviridae, Nudiviridae, Partitiviridae, Phasmaviridae, and Solemoviridae. Representative contigs from six families (all except Phasmaviridae) and five additional family-unassigned viruses were validated by PCR and Sanger sequencing. Three iflaviruses (RrIV, AgIV1, and AgIV2), positive-sense single-stranded RNA viruses, were discovered, including one associated with Rhopalosiphum rufiabdominale and two with A. gossypii. Their complete genomes were determined using PCR-based resequencing and 5'/3' RACE, each comprising a single open reading frame that encodes a polyprotein. Sequence identity and phylogenetic analyses indicate that the newly identified viruses are putative new species and form a distinct clade together with previously reported aphid iflaviruses within Iflaviridae. AgIV1 and AgIV2, despite being associated with the same host species, were not monophyletic within this clade, consistent with cross-species transmission among aphid hosts. Strand-specific RT-PCR detected negative-strand RNA for AgIV1 and AgIV2, suggesting replication in aphids. Given their low field prevalence, we propose the names Iflavirus furtiva (RrIV), Iflavirus obscurata (AgIV1), and Iflavirus rarivira (AgIV2).</p><p><strong>Conclusions: </strong>The aphid virome is taxonomically diverse and shows county-level differences in relative viral contig abundance. We identified seven viral families and three complete iflavirus genomes, providing a foundation for further investigating their host range, transmission, and potential impacts on aphid biology and cotton production.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13637338/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148418470","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":"Profiling chromatin accessibility responses to seasonal heat stress in Angora rabbit testes.","authors":"Haisheng Ding, Yuanlang Wang, Huiling Zhao, Dongwei Huang","doi":"10.1186/s12864-026-13133-8","DOIUrl":"10.1186/s12864-026-13133-8","url":null,"abstract":"<p><strong>Background: </strong>Seasonal heat stress negatively impacts spermatogenesis, yet the underlying molecular mechanisms remain poorly understood. To investigate the epigenetic responses to heat stress in Angora rabbit spermatogenesis, we performed an Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) on testicular tissues collected during spring and summer.</p><p><strong>Results: </strong>High-quality sequencing data were obtained, yielding 196 to 310 million clean reads per sample with mapping rates exceeding 97%. Chromatin accessibility signals were predominantly enriched near transcription start sites, and principal component analysis (PCA) clearly segregated the spring and summer samples, revealing distinct epigenetic landscapes across seasons. We identified 416 differentially accessible chromatin regions (DARs), comprising 346 up-regulated and 70 down-regulated peaks in the summer group compared to the spring group. Motif analysis of these regions revealed enrichment of binding sites for transcription factors (TFs) such as E-box, MITF, and Usf2. Genes associated with these DARs were significantly enriched in reproduction-related biological processes and critical signaling pathways, including p53, TGF-beta, MAPK, Wnt, and mTOR. Integrating the ATAC-seq data with RNA-seq profiles identified 88 overlapping differentially expressed genes, among which BAX, CDK4, UBB, and TNP2 exhibited consistent or complementary alterations in both chromatin accessibility and gene expression. These key genes are intrinsically involved in spermatogenesis, stress response, and apoptosis, and are potentially regulated by the transcription factors identified in this study.</p><p><strong>Conclusions: </strong>Our findings provide novel insights into the epigenetic regulation of testicular function under heat stress, highlighting essential candidate genes and pathways for further functional studies.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13637228/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148418430","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 DNA methylation analysis in pigs using long-read sequencing unveils high-altitude adaptation and allele-specific regulation.","authors":"Yi-Fan Jiang, Yi Guo, Wen-Ye Yao, Ao Qiu, Chong-Long Wang, Ru-Hai Xu, Qin Zhang, Ling-Zhao Fang, Xiang-Dong Ding","doi":"10.1186/s12864-026-13117-8","DOIUrl":"10.1186/s12864-026-13117-8","url":null,"abstract":"<p><strong>Background: </strong>The advent of third-generation sequencing, particularly Oxford Nanopore Technologies (ONT), has revolutionized epigenetic studies by enabling direct detection of DNA methylation modifications and single-base resolution profiling of methylation patterns. While this technology has been predominantly utilized in human and bacterial research, its applications in livestock and poultry remain limited. In this study, we employed ONT sequencing to construct comprehensive 5-methylcytosine modification maps for ten representative pig breeds, explored the mechanism of high altitude adaptive methylation and allele-specific methylation events in these pigs.</p><p><strong>Results: </strong>Through genome-wide integration of sequencing data, we identified 27,857,021 CpG sites, with 71.5% (19,836,456) shared across pigs. Comparative differential methylation analysis between high-altitude and low-altitude pigs revealed four candidate genes (CALM1, HBB, PRKCQ and RAMP1) and the Sp1 transcription factor as potential key regulators of hypoxic adaptation. Notably, Tibetan pigs exhibited promoter hypomethylation patterns at the CALM1 locus, correlating with its consistently elevated expression confirmed by public transcriptomic databases. Allele-specific methylation (ASM) analysis integrated with transcriptomic profiles demonstrated significant enrichment of ASM events in promoters or exons of allele-specific expression (ASE) genes, suggesting synergistic regulatory mechanisms between epigenetic modifications and allelic expression patterns.</p><p><strong>Conclusions: </strong>Our results provided a high-resolution DNA methylation atlas based on long-read sequencing encompassing ten representative pigs across Eurasia, and identified hypoxic adaption-related genes (CALM1, etc.) and a transcription factor (Sp1) based on the unique physiological characteristics of Tibetan pigs. Further, combined with transcriptome data, it was demonstrated ASM and ASE events are synergistic and expressions of ASE genes may be regulated by ASM. This study offers valuable insights into the epigenetic mechanisms underlying adaptation and gene regulation in pigs.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13637240/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148418497","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 and metabolic divergence of the primary symbiont Candidatus Portiera between Bemisia tabaci and other whitefly species.","authors":"Teng Lei, Yong-Jing Fan, Hong-Da Song, Xin-Jia Zhang, Hua-Ling Wang, Chao Song, Yin-Quan Liu, Xin Qi","doi":"10.1186/s12864-026-13143-6","DOIUrl":"10.1186/s12864-026-13143-6","url":null,"abstract":"<p><strong>Background: </strong>The primary symbiont Candidatus Portiera is essential for nutrient provisioning in whiteflies. Genomic instability is a hallmark of Bemisia tabaci-associated Portiera, but the specific molecular evolutions and their metabolic consequences compared to Portiera from other whiteflies remain unclear.</p><p><strong>Results: </strong>To overcome the limited sampling of previous studies, we assembled novel Portiera genomes from seven additional B. tabaci cryptic species. Comparative genomic, phylogenetic, and species delimitation analyses were conducted with other publicly available Portiera genomes. Branch-model selection analysis identified differentially evolved genes in the B. tabaci-associated Portiera, which were significantly enriched in amino acid biosynthetic pathways. The composition of essential amino acids biosynthetic pathways was systematically analyzed across Portiera, host nuclear, and secondary symbiont genomes. B. tabaci-associated Portiera formed a monophyletic lineage with larger genomes, lower coding density, and accelerated evolutionary rates, classified as a single species distinct from Portiera in other whiteflies. Twenty-two genes showed significantly different evolutionary rates with enrichment in amino acid biosynthetic pathways. Key genes for lysine and arginine biosynthesis were lost or pseudogenized in B. tabaci-associated Portiera but remained intact in other whiteflies like Trialeurodes vaporariorum. The synthesis of most other essential amino acids was similarly incomplete across all Portiera, relying on host or secondary symbiont genes for pathway completion.</p><p><strong>Conclusions: </strong>The B. tabaci-associated Portiera represents a unique symbiotic metabolic architecture where host horizontally transferred genes may potentially compensate for Portiera's genomic erosion, contrasting with the more autonomous Portiera in other whiteflies. This study reveals divergent evolutionary trajectories and metabolic integration strategies in whitefly symbiotic systems.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13637331/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148418458","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}