BMC Genomics最新文献

{"title":"Deep sequencing of single Pleurotus ostreatus strain revealed mixed infection of seven RNA viruses.","authors":"Jiayi Gao, Guoqiang He, Jin Kang Wei, Yong Pan, Congliang Deng, Xiju Shi, Caige Lu, Yongqiang Li","doi":"10.1186/s12864-026-13166-z","DOIUrl":"10.1186/s12864-026-13166-z","url":null,"abstract":"<p><strong>Background: </strong>As a globally cultivated edible fungus, Pleurotus ostreatus is highly nutritious and rich in proteins, vitamins, minerals, and amino acids. However, viral infections cause significant losses in quality and yield during cultivation. In our survey, weakened growth and malformed fruiting bodies were observed in Sanbaoxiang Agricultural Technology Park, which is located in Tongzhou District of Beijing, but the associated viruses were not clear.</p><p><strong>Results: </strong>The mycelia were isolated, purified and used for ribosomal RNA-depleted total RNA deep sequencing. A total of 118,973,697 clean reads were obtained and subsequently assembled into 53,864 contigs. BLAST analysis indicated that most contigs originated from the host P. ostreatus; however several contigs showed high amino acid sequence identities to known mycoviruses. Further complete genome sequencing with RT‒PCR and rapid amplification of cDNA ends for the terminal sequences revealed that mixed infection with seven RNA viruses was associated with the observed symptoms: four reported viruses, including oyster mushroom spherical virus, pleurotus ostreatus deltaflexivirus 2, pleurotus ostreatus alpha-like virus, and pleurotus ostreatus ambivirus 2, and three new viruses tentatively named pleurotus ostreatus deltaflexivirus 3, pleurotus ostreatus ambivirus 3 and pleurotus ostreatus lentinuvirus 1. The sequence characterization, genomic structure and phylogenetic relationships of these new viruses with other known viruses were also characterized. Further virus distribution patterns were explored with RT-PCR analysis of different strains isolated from different locations.</p><p><strong>Conclusions: </strong>In this study, a mixed infection with seven RNA viruses from a P. ostreatus strain was identified via deep sequencing, and their genomes were characterized. These findings advance our understanding of the diversity of viruses infecting P. ostreatus and provide critical insights for further research on virus‒host interactions and the development of viral elimination strategies.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13660232/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148468735","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":"Transcriptomics-based analysis to explore the effects of culture media and cell models on the function of B. pseudocatenulatum strains of intestinal origin.","authors":"Peng Du, Rong Guo, Ya Dong Yao, Jun Min Zhu, Jian Gang Feng, Hui Sun, Jie Mao","doi":"10.1186/s12864-026-13067-1","DOIUrl":"10.1186/s12864-026-13067-1","url":null,"abstract":"<p><strong>Background: </strong>The gut microbiota plays a pivotal role in maintaining host health by modulating metabolic pathways and immune functions. Although its biological significance is well recognized, systematic research into the functional characterization of intestinal bacteria remains scarce, particularly concerning the impact of culture environments and host cell model selection on functional assessment. This study focused on a strain of Bifidobacterium pseudocatenulatum isolated from the feces of healthy individuals. The objective was to investigate the regulatory effects of its metabolites, produced under different medium conditions, on gene expression across multiple host cell models.</p><p><strong>Results: </strong>Metabolomic analysis revealed that the choice of culture medium (BHI vs. GAM) significantly reshaped the metabolic profiles of B. pseudocatenulatum. Transcriptomic data demonstrated that metabolites induced by different media led to markedly distinct gene expression patterns within the same host cell line. Furthermore, even under identical metabolite exposure conditions, the four cell models (MODE-K, NCM460, Henle-407, and HEK-293T) exhibited highly divergent and cell-line-specific regulatory responses.</p><p><strong>Conclusions: </strong>These findings highlight the decisive influence of both medium composition and cell model selection on the outcomes of functional studies concerning gut commensal bacteria. This research not only provides a scientific basis for optimizing experimental designs in microbial functional studies but also underscores the necessity of rigorously evaluating culture conditions and model suitability in microbiota research.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13663047/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148468704","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":"The neuronal A-to-I RNA editome of Solenopsis invicta expands conserved recoding repertoire between two ant species.","authors":"Jiyao Liu, Ling Ma, Qiuhua Xie, Wanzhi Cai, Hu Li, Fenghao Liu, Youming Hou, Lu Peng, Yuange Duan","doi":"10.1186/s12864-026-13199-4","DOIUrl":"10.1186/s12864-026-13199-4","url":null,"abstract":"<p><strong>Background: </strong>A-to-I RNA editing expands proteomic diversity and may contribute to caste-specific phenotypic plasticity in eusocial insects. However, the quantity-accuracy trade-off in editing detection usually hinders comprehensive characterization of the RNA editome.</p><p><strong>Materials and methods: </strong>To overcome the quantity-accuracy trade-off, we first perform de novo identification of the neuronal A-to-I editome of the red imported fire ant Solenopsis invicta, and then apply an orthology-based strategy to project candidate editing sites to another ant species Acromyrmex echinatior.</p><p><strong>Results: </strong>We obtain nearly 3000 editing sites in S. invicta, including 91 nonsynonymous (recoding) sites enriched in neuronal functions such as synaptic transmission, ion channels, and circadian rhythms. The orthology-based strategy substantially expands the previously known recoding repertoire in the leaf-cutting ant A. echinatior, reveals many previously missed recoding sites and edited genes, and uncovers additional caste-specific recoding events between gynes and workers, highlighting conserved, potentially functional editing targets across ant evolution. Representative recoding sites are validated by Sanger sequencing.</p><p><strong>Conclusion: </strong>Our work expands ant RNA editome resources and identifies conserved recoding candidates that may facilitate future studies of eusocial caste diversification, neuronal function, and phenotypic plasticity.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13663048/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148468688","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":"scFANCL: Dual contrastive learning with false-negative correction at cell level for single-cell RNA-seq clustering.","authors":"Gunho Choi, Minsik Oh","doi":"10.1186/s12864-026-13179-8","DOIUrl":"10.1186/s12864-026-13179-8","url":null,"abstract":"<p><strong>Background: </strong>Single-cell RNA sequencing (scRNA-seq) enables cellular characterization at single-cell resolution. However, its high dimensionality, sparsity, and noise make clustering challenging. Approaches utilizing contrastive learning and data augmentation have been introduced to improve representation quality for scRNA-seq clustering. In particular, dual contrastive frameworks combining instance- and cluster-level objectives can capture both cell-cell similarities and inter-cluster variations. However, existing dual contrastive frameworks focus primarily on discrete cluster boundaries, neglecting the biological continuity inherent in scRNA-seq data.</p><p><strong>Methods: </strong>We propose scFANCL, a dual contrastive framework designed to capture biological continuity in scRNA data. Rather than treating all non-augmented samples as negatives, scFANCL applies a cosine-similarity-based threshold to exclude cells of the same type from the negative pool, preserving continuous transcriptional relationships among them while maintaining inter-cluster separation.</p><p><strong>Results: </strong>Extensive experiments across seven publicly available scRNA-seq datasets demonstrated that scFANCL achieves competitive clustering performance compared with existing baseline methods, consistently yielding high ARI and NMI scores across datasets of varying size and complexity. Ablation studies further confirmed the contribution of the false negative filtering component, showing measurable improvements over variants without filtering. Downstream analyses further suggest that the learned embeddings may reflect biologically meaningful transcriptional transitions, including continuous differentiation trajectories within related cell types. The source code is available at https://github.com/mjuailab/scFANCL .</p><p><strong>Conclusions: </strong>scFANCL addresses a key limitation of conventional contrastive learning by applying a cosine-similarity-based threshold to exclude cells of the same type from the negative pool, thereby preserving biological continuity within cell types while maintaining inter-cluster separation. Evaluations across seven benchmark scRNA-seq datasets demonstrate competitive clustering performance, with learned embeddings capturing biologically meaningful transcriptional structure and characteristics of rare cell populations.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13563771/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148468671","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":"Molecular characterization in elite rock climbers: insights from multi-omics analysis.","authors":"Rongqi Liang, Jingjing Li, Long Cao, Cheng Wang, Shaoqin Zhang, Xing Ye","doi":"10.1186/s12864-026-13192-x","DOIUrl":"10.1186/s12864-026-13192-x","url":null,"abstract":"<p><strong>Objective: </strong>Elite rock climbing is characterized by sustained upper-limb-dominant loading and complex systemic demands. However, the molecular signatures associated with elite climbing-related adaptation remain poorly defined. This study integrates physiological, functional, transcriptomic, and metabolomic profiling to characterize the potential mechanisms underlying these adaptations.</p><p><strong>Design: </strong>This is a cross-sectional study comparing the molecular profiles of elite rock climbers and matched non-climbers.</p><p><strong>Methods: </strong>A total of 40 participants were recruited, comprising 20 elite rock climbers certified as National Master Sportsmen (athlete group) and 20 age, sex, and body mass matched non climbers (control group). Participants underwent functional assessments for vascular reactivity via flow-mediated dilation and climbing specific forearm endurance through dead hang and intermittent grip tests. Fasting venous blood samples were analyzed for biochemical markers, while integrated transcriptomic and metabolomic profiles were established to identify molecular signatures. Data were analyzed using differential expression profiling, functional enrichment, and joint pathway analysis, with results validated by qRT-PCR.</p><p><strong>Results: </strong>The athlete group exhibited significantly superior functional performance characterized by enhanced vascular endothelial function and prolonged forearm endurance alongside widespread systemic adaptations, as reflected by elevated levels of cortisol, creatine kinase, blood urea nitrogen, hemoglobin, plasma volume and total hemoglobin mass (p < 0.05). RNA sequencing identified 850 differentially expressed genes (|log₂FC| ≥ 1, FDR < 0.05), which were predominantly enriched in cAMP, Apelin, PPAR, TNF, and HIF-1 signaling pathways. Metabolomics detected 71 differential metabolites (VIP ≥ 1, |log₂FC| ≥1.5, FDR < 0.05), enriched in Insulin secretion, glycolysis/gluconeogenesis, fatty acid degradation, and amino acid metabolism. Integrated transcriptomic and metabolomic analyses revealed that elite climbers exhibited multidimensional molecular adaptation signatures associated with the specific demands of climbing, mainly characterized by enhanced metabolic flexibility, vascular regulation, and optimized metabolic homeostasis. These changes collectively optimized metabolic flexibility, redox homeostasis and controlled inflammation. Validation via qRT-PCR confirmed the RNA-Seq results.</p><p><strong>Conclusions: </strong>Elite rock climbers exhibited multilayered physiological, transcriptional, and metabolic features associated with energy homeostasis, redox balance, inflammatory modulation, and neuromuscular performance. These insights establish a molecular blueprint for evidence-based training optimization and personalized sports interventions.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13673920/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148468650","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":"Study on the molecular mechanism of colony strength of Apis cerana cerana based on transcriptomics.","authors":"Lina Guo, Xiaoyin Deng, Ke Sun, Yu Zhang, Kai Xu, Yuan Guo","doi":"10.1186/s12864-026-13183-y","DOIUrl":"10.1186/s12864-026-13183-y","url":null,"abstract":"<p><p>Apis cerana cerana exhibits highly sensitive olfactory capabilities, resistance to cold and heat, and strong foraging abilities. It plays a critical role in sustaining ecosystem stability and enhancing agricultural productivity and economic yields of farmers in mountainous areas. Given that colony strength is fundamental to the reproductive capacity and productivity of Apis cerana cerana, maintaining strong colonies is essential for enhancing their disease resistance, survival, and productivity. In this study, Apis cerana cerana in Zizhou County of the Lvliang Mountains was used as the research object. To investigate the molecular mechanisms underlying colony strength differences, we performed transcriptome sequencing on the head and thorax of worker bees from strong and weak colonies, with the goal of identifying differentially expressed genes and regulatory pathways associated with sensory perception in the head and energy metabolism in the thorax.The results showed that 751 differentially expressed genes were identified between the heads of strong and weak colonies, primarily enriched in odorant-binding protein, royal jelly major protein, taste receptor gene, olfactory receptor family genes, and others. A total of 852 differentially expressed genes were identified between the thorax of different colonies, mainly enriched in cytochrome P450, zinc finger protein, serine / threonine kinase, and cytochrome C oxidase family genes. Gene function enrichment analysis revealed that the strength of colony is associated with growth and immune response pathways, such as macromolecular biosynthesis, organic nitrogen biosynthesis, and ribosome metabolism in the head of bees, as well as energy metabolism pathways, including sugar metabolism, lipid metabolism, and amino acid metabolism in the thorax of bees, which have been previously associated with extended lifespan in other insect models, suggesting a potential link to individual longevity in strong colonies. The strength of the colony is significantly related to energy metabolism, immunity, heat stress, and phosphorylation regulation, Worker bees in strong colony exhibit stronger antioxidative stress, energy metabolism, resistance to external environmental temperature and harmful substances, and anti-inflammatory and antibacterial capabilities.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13663140/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148468706","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":"Whole-genome resequencing reveals population genetic structure and selective sweeps in Bombus waltoni.","authors":"Rui Zhang, Chengbo Liang, Wenrui Jiao, Lei Si, Daoxin Liu, Jingyan Yan","doi":"10.1186/s12864-026-13175-y","DOIUrl":"10.1186/s12864-026-13175-y","url":null,"abstract":"<p><strong>Background: </strong>Bombus waltoni is a typical alpine bumblebee species and an important indicator species of the Qinghai-Tibetan Plateau. However, whole-genome studies of bumblebees from this region remain limited. In this study, we investigated the genetic diversity, population structure, and adaptive genomic variation of B. waltoni, providing essential genomic resources for understanding its population genetic structure and signatures of local adaptation.</p><p><strong>Results: </strong>Based on whole-genome SNP data, genetic diversity was relatively similar across B. waltoni populations, with expected heterozygosity (He) ranging from 0.2265 to 0.2601, unbiased expected heterozygosity (uHe) from 0.2517 to 0.2729, and nucleotide diversity (π) from 0.00104504 to 0.00113178. Genetic diversity was significantly associated with elevation after correction for multiple testing. Population structure analyses consistently resolved the 18 populations into two major genetic clusters corresponding to northeastern and southwestern regions, a pattern supported by ADMIXTURE, PCA, and phylogenetic analyses. Although overall genetic differentiation was low, a significant pattern of isolation by distance was detected. Multiple gene flow analyses suggested that population differentiation was inconsistent with complete isolation. Selective sweep analyses identified distinct sets of candidate genes and functional enrichment patterns between the two clusters.</p><p><strong>Conclusion: </strong>Significant but low genetic differentiation was detected among B. waltoni populations within the northeastern Qinghai-Tibetan Plateau, and populations showed relatively similar levels of genetic diversity. Gene flow signals suggested that population differentiation was inconsistent with complete isolation, while multiple genomic regions under selection suggest potential adaptive responses to elevation- and latitude-associated environmental heterogeneity. These results provide genomic evidence for population differentiation and local adaptation in a high-altitude pollinator, offering a scientific basis for region-specific conservation and management.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13656426/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148468693","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":"Ex Situ Diversity of Sorghum bicolor (L.) moench collections and derived wide crosses (sorghum x maize) based on DArTSeq markers.","authors":"Tadeo Kaweesi, Alexander Bombom, Maphosa Mcebisi, Paul Asiimwe, Emilio Ovuga","doi":"10.1186/s12864-026-13162-3","DOIUrl":"10.1186/s12864-026-13162-3","url":null,"abstract":"<p><p>Sorghum is an important crop in sub-Saharan Africa sustaining many livelihoods. However, despite its importance, sorghum continues to have limited research attention and priority and is categorized as one of the Neglected and Underutilised Species. The paucity of current information on genetic diversity and structure of sorghum accessions being cultivated, improved, introduced, and or conserved across east and southern Africa remains limited. Ex situ genetic diversity and population structure for 177 sorghum accessions from diverse sources was studied using high throughput Diversity Array Technology markers. A total of 15,220 DArTseq SNP markers were generated with over 90% call rate and 95% reproducibility. DArTseq SNP markers had an average polymorphic information content of 0.21 indicating the discriminatory power of DArTSeq markers. Genetic relationships estimated using discriminant analysis of principal components and ancestry coefficients revealed eight populations. Observed heterozygosity was lower than the expected heterozygosity across populations with a mean inbreeding coefficient (F_IS) of 0.82. Analysis of molecular variance found 83% of the variation to be attributed to within-population variance. A high divergence (F_st = 0.16) obtained from AMOVA suggests high genetic differentiation among populations. Genetic diversity indices Shannon-wiener index (H) (3.37-3.95), Stoddard and Taylor index (G) (29-52) and Simpson's index (λ - Lambda) (0.90-0.99) were high across populations. Nei's unbiased gene diversity ranged from 0.13 to 0.23. The results suggest a high differentiation among sorghum accessions under study. Implications with respect to insights to guide identification, selection and testing of plant genetic resources for food and agriculture with unique genes and traits to address demand-led crop improvement and market needs, conservation, and deployment in farmer fields are shared.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13656433/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148468668","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":"Chromosome-scale genome of Ormosia hosiei provides insights into legume tree genome evolution.","authors":"Yi Wang, Minhao Liu, Liang Shi, Binhao Yang, Linli Dai, Hanbo Yang, Jinwu Li, Huimin Zhao, Xingcui Xiao, Hongying Guo, Yunjie Gu, Jian Peng","doi":"10.1186/s12864-026-13195-8","DOIUrl":"10.1186/s12864-026-13195-8","url":null,"abstract":"<p><strong>Background: </strong>Ormosia hosiei, commonly known as the \"Chinese love bean tree\" for its traditional symbolic association with love and longing in Chinese literature, is an economically and ecologically important leguminous tree species endemic to China, prized for its high-density hardwood and its vital ecological functions in subtropical forests. However, the limited availability of genomic resources has hindered in-depth molecular studies, constraining both genetic improvement efforts-such as those targeting wood formation-and conservation strategies.</p><p><strong>Results: </strong>In this study, we present a high-quality genome assembly of O. hosiei with a total size of 2.14 Gb and a scaffold N50 of 255.85 Mb, and annotated 39,309 protein-coding genes. Extensive identification and characterization of Gypsy and Copia LTR retrotransposon subfamilies revealed their major contribution to genome size expansion. Whole-genome duplication (WGD) analysis revealed that O. hosiei has experienced two WGD events: an ancient event shared broadly across leguminous species, and a more recent duplication likely shared within the Genistoid clade, including multiple Ormosia species. Furthermore, we identified 117 NAC and 176 MYB transcription factors in O. hosiei, including VND-like and MYB46-/83-like genes that are central regulators of secondary cell wall biosynthesis. These genes likely contribute to wood formation and the development of straight trunk architecture.</p><p><strong>Conclusions: </strong>Overall, the O. hosiei reference genome provides a valuable genomic resource for understanding legume evolution and offers essential support for functional genomics studies, molecular breeding, and conservation of this precious timber species endemic to China.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13663118/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148468641","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative mitogenomic analysis of Lygaeoidea (Hemiptera: Heteroptera): insights into genomic features, phylogenetic relationships, and divergence times.","authors":"Mengcheng Wan, Changjun Meng, Liu'er Yang, Qi Xie, Cuiqing Gao","doi":"10.1186/s12864-026-13188-7","DOIUrl":"10.1186/s12864-026-13188-7","url":null,"abstract":"<p><strong>Background: </strong>Lygaeoidea represents one of the most diverse superfamilies of true bugs. However, the phylogenetic relationships among its major lineages remain to be fully resolved, and the evolutionary history of this group has not been thoroughly investigated, largely due to limited molecular data.</p><p><strong>Results: </strong>To address this, we sequence 17 complete mitogenomes representing 10 families of Lygaeoidea, including new data for species from Heterogastridae and Cymidae. This study aims to expand mitogenomic resources and explore the evolutionary history of this superfamily. Across all analyzed species, including the 17 newly sequenced mitogenomes, we observed consistently high A + T content, conserved codon usage bias, and purifying selection acting on protein-coding genes (PCGs), with cox1 being the most conserved and atp8 the most variable. Phylogenetic analyses using 12 PCGs from 73 mitogenomes robustly support Lygaeoidea as monophyletic and delineate three clades: Clade I ((Heterogastridae + Pachygronthidae) + Lethaeidae), Clade II (Artheneidae + (Oxycarenidae + Piesmatidae)), and Clade III comprising the remaining families. Divergence time estimation suggests that Lygaeoidea originated in the Early Cretaceous (~ 133.9 Ma), with major familial diversification events occurring from the latest Early Cretaceous through the Paleogene.</p><p><strong>Conclusions: </strong>This study provides valuable mitogenomic datasets and novel evolutionary insights into Lygaeoidea molecular evolution, phylogeny, and validates the independent familial rank of Lethaeidae. Our findings improve the understanding of evolutionary dynamics in forest-dwelling true bugs and accumulate essential baseline data for subsequent taxonomic and systematic investigations.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13651057/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148454571","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}