BMC Genomics最新文献

{"title":"Global profiling of the protein lactylome in porcine liver.","authors":"Shuhao Fan, Shunyao Lu, Jinyu Guan, Yu Li, Wei Li, Yueyun Ding, Xianrui Zheng, Zongjun Yin, Xiaodong Zhang","doi":"10.1186/s12864-026-13200-0","DOIUrl":"10.1186/s12864-026-13200-0","url":null,"abstract":"<p><p>Given the significant physiological and metabolic similarities between pig liver and human liver, along with the importance of pigs as excellent clinical models (successful xenotransplantation and survival in humans), this study presents for the first time a comprehensive lactylation map of the pig liver, revealing that protein lactylation (Kla) is a widespread and functionally important modification in this metabolically active organ. Through high-resolution mass spectrometry, we conducted a global analysis of lactylated proteins and sites in healthy pig liver, identifying 4,110 Kla sites on 1,486 proteins. Bioinformatics feature analysis indicated that these proteins are mainly located in the cytoplasm, mitochondria, and nucleus, and are significantly enriched in core metabolic pathways including glycolysis, the tricarboxylic acid cycle, and the pentose phosphate pathway. Motif analysis identified specific sequence patterns around lactoylated lysines. Comparative analysis showed that specific histone lactylation sites (such as H3K23, H2AK96, H2BK5) are conserved in pigs, mice, and humans, while also revealing tissue-specific characteristics compared to pig ovarian cells. These findings emphasize the close connection between liver lactylation and cellular energy metabolism, and provide a valuable comparative framework for studying the role of lactylation in human liver physiology and disease.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13663148/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148534882","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":"Impact of M and E protein mutations in SARS-CoV-2 Omicron variants on reduced antibody binding and increased structural stability: a bioinformatics study (2021-2023).","authors":"Maryam Sadat Pishva, Behzad Shahbazi, Ladan Mafakher, Nesa Amirpour, Hamed Gouklani, Khadijeh Ahmadi","doi":"10.1186/s12864-026-13206-8","DOIUrl":"10.1186/s12864-026-13206-8","url":null,"abstract":"<p><strong>Background: </strong>First identified in late 2021, the Omicron variant of SARS-CoV-2 accumulated substantially more mutations than previously circulating variants. This study investigated the genomic characteristics and structural consequences of mutations in the membrane (M) and envelope (E) proteins of dominant Omicron lineages circulating in southern Iran between March 2021 and March 2023.</p><p><strong>Methods: </strong>A total of 528 clinical samples were analyzed using next-generation sequencing (NGS), Nextclade lineage assignment, and complementary bioinformatics approaches. The structural effects of selected mutations were further evaluated using protein-protein docking, PDBe PISA interface analysis, MM/GBSA binding free energy calculations, and 100-ns molecular dynamics simulations.</p><p><strong>Results: </strong>Between 2021 and 2023, BA.5.2 accounted for 32.4% of sequenced isolates, whereas XBB.1.9.1 became the predominant lineage during the later phase of the study (14.2%). Structural analysis demonstrated that the interaction interface between the M protein dimer and the Fab fragment remained largely conserved across all investigated variants. However, MM/GBSA calculations revealed mutation-dependent differences in binding energetics, with the BA.5 (Q19E, A38S, A63T) variant exhibiting the least favorable binding free energy despite preservation of the overall interaction interface. Molecular dynamics simulations further showed that the investigated E protein variants maintained compact conformations with reduced conformational fluctuations relative to the wild-type protein throughout the simulation.</p><p><strong>Conclusions: </strong>Combined genomic surveillance and structural analyses demonstrated that the investigated Omicron-associated mutations largely preserved the overall architecture of the M protein-Fab interaction interface while modulating residue-level energetic contributions and the conformational dynamics of the E protein. These findings indicate that the investigated mutations primarily affect interaction energetics and protein dynamics rather than inducing major structural rearrangements. The integrated computational framework presented in this study provides a useful approach for evaluating the structural consequences of newly emerging SARS-CoV-2 variants and prioritizing mutations for future experimental validation.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13670851/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148535075","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 and genomic insights into a plant probiotic Bacillus subtilis strain CF1 isolated from Protaetia brevitarsis frass.","authors":"Hongyu Wang, Xiaolong Hu, Junling Zhang, Yan Qin, Chenpu Wu, Shuan Zhao, Mian Hou, Beibei Cao, Jie Zhang, Changlong Shu, Kui Wang","doi":"10.1186/s12864-026-13174-z","DOIUrl":"10.1186/s12864-026-13174-z","url":null,"abstract":"<p><strong>Background: </strong>Plant probiotic bacteria offer a sustainable strategy for enhancing crop health and productivity. Insect frass has emerged as a unique niche for isolating beneficial microorganisms with novel traits. In this study, we isolated a bacterial strain CF1 from the frass of Protaetia brevitarsis and characterized its biocontrol and plant growth‑promoting potential against Fusarium crown rot of wheat.</p><p><strong>Results: </strong>Based on whole‑genome analysis, strain CF1 was identified as Bacillus subtilis. CF1 exhibited strong antagonistic activity against Fusarium graminearum and F. asiaticum, with inhibition rates of 34.67% and 33.95%, respectively. Its cell‑free filtrate showed dose‑dependent antifungal activity, reaching 43.70% inhibition against F. graminearum at a 5‑fold dilution. Phenotypic characterization confirmed its ability to produce IAA equivalents, siderophores, and solubilized phosphate. In pot experiments, CF1 effectively suppressed Fusarium crown rot, achieving a biocontrol efficacy of 43.47%, comparable to that of the well‑characterized strain B. velezensis SQR9 (44.07%). The inoculation of CF1 also promoted wheat growth, increasing plant height and plant biomass. Whole-genome sequencing revealed a 4.11 Mb genome encoding 4,277 genes, with 11 biosynthetic gene clusters for secondary metabolites, including bacillaene, fengycin, bacillibactin, surfactin, bacilysin, subtilomycin, subtilosin A, and pulcherriminic acid, along with three biosynthetic gene clusters of unknown function, suggesting potentially unique bioactivities. Genome mining further uncovered numerous genes associated with plant growth promotion, rhizosphere colonization, stress resistance, and volatile organic compound production.</p><p><strong>Conclusions: </strong>B. subtilis CF1 is a promising microbial agent that combines strong antifungal activity, plant growth‑promoting traits, and a diverse set of genetic features that may confer unique properties, warranting further field validation for sustainable wheat production.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13663132/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148535014","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":"Multi-omics integration of F_st, GWAS, TWAS and transcriptomics revealed candidate genes and pathways associated with pneumonia lesion scores in pigs.","authors":"Guankai Zhao, Yanzhen Yin, Junzhao Han, Jianmei Chen, Mengyu Li, Xiangyu Han, Jinfeng Ma, Jianghui Yu, Jin Zhou, Chifeng Chen, Ruihua Huang, Pinghua Li, Qingbo Zhao","doi":"10.1186/s12864-026-13203-x","DOIUrl":"10.1186/s12864-026-13203-x","url":null,"abstract":"<p><strong>Background: </strong>Respiratory diseases significantly impair pig growth performance by reducing average daily gain and feed conversion efficiency. Pneumonia lesion score (PLS) is a reliable phenotypic indicator for detecting respiratory issues in pig herds, including subclinical infections that often remain undiagnosed. In this study, PLS data was collected from 327 Large White pigs, and whole-genome resequencing (WGS) was performed. Lung tissue samples from pigs with extremely high and low PLS values were subjected to transcriptomic sequencing and Fixation Index (F_st) analysis. Additionally, a transcriptome-wide association study (TWAS) was conducted using FarmGTEx prediction models based on blood and lung tissues.</p><p><strong>Results: </strong>By integrating F_st, Genome-Wide Association Study (GWAS), TWAS, and transcriptomic data, we identified key genomic regions and pathways associated with PLS variation, including immune regulation, inflammation, and metabolic adaptation. Candidate genes, RAB11FIP2 and SLC18A2 are implicated in immune modulation: RAB11FIP2 enhances TLR4 signaling and phagocytosis, whereas reduced SLC18A2 expression may compromise monoamine-mediated immune regulation. FBXL13 and ALPK2, identified via F_st and transcriptomic analysis, are linked to macrophage migration and Wnt/β-catenin signaling. Similarly, Genes like TRAF3IP1 and ASB1, highlighted by F_st and GWAS, contribute to ciliary transport, epithelial defense, and regulation of NF-κB and MAPK signaling. Moreover, GWAS and TWAS pinpointed RAMP1, as a novel candidate gene influencing immune modulation and airway responses through CGRP signaling, vascular tone regulation, and neuro-immune interactions, these findings have not been previously reported in PLS studies.</p><p><strong>Conclusions: </strong>Overall, this study provides novel insights into the genetic mechanisms underlying porcine lung lesions and offers a foundation for breeding strategies aimed at improving respiratory disease resistance and herd health.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13670770/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148535066","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":"Global phylogenomics of Bordetella pertussis ST2 reveals regional heterogeneity in China and lineage-specific genome evolution.","authors":"Meng Qi, Wangxiao Zhou, Huili Ye, Deru Lei, Xu Dong, Xinmei Wu","doi":"10.1186/s12864-026-13189-6","DOIUrl":"10.1186/s12864-026-13189-6","url":null,"abstract":"<p><strong>Background: </strong>Bordetella pertussis sequence type 2 (ST2) is widely detected in China and in public genome datasets, yet the evolutionary relationships, dissemination patterns, and genomic features that distinguish its major lineages have not been systematically characterized.</p><p><strong>Results: </strong>In this study, we conducted a comprehensive genomic analysis of 580 ST2 genomes from 24 countries between 1942 and 2024, integrating 46 newly sequenced clinical isolates from Wenzhou, China. Phylogenetic reconstruction showed that the Wenzhou isolates were not homogeneous but comprised two distinct clades, including a dominant macrolide-resistant ptxP1-associated lineage and a smaller ptxP3-associated lineage. At the global scale, the ST2 population resolved into two major clades and three subclades; the dominant ptxP1-associated Wenzhou lineage was assigned to subclade I, whereas the smaller ptxP3-associated Wenzhou lineage belonged to global clade II, with one isolate placed in subclade III. Two China-enriched subclades were strongly associated with 23S rRNA A2047G mutations, whereas a geographically widespread subclade lacked this determinant. Chinese isolates were distributed across multiple phylogenetic positions, supporting repeated introductions followed by local expansion. Comparative analyses further revealed lineage-specific differences in detected insertion sequence (IS) elements and pseudogene accumulation. IS481 was the predominant IS family, and intergenic insertions were more common than intragenic events across lineages. Clade-specific SNPs and stable pseudogene patterns together indicated partially distinct adaptive trajectories among ST2 clades.</p><p><strong>Conclusions: </strong>These findings define the local and global population structure of ST2, highlight marked regional heterogeneity in contemporary Chinese pertussis, and show that ongoing diversification of this lineage is shaped by both geographic spread and lineage-specific genome evolution.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13479600/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148496928","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":"Development and application of whole genome SNP markers in mango.","authors":"Feng Liu, Chunyuan Wu, Jingping Liu, Quansheng Yao, Ru-Lin Zhan","doi":"10.1186/s12864-026-13182-z","DOIUrl":"10.1186/s12864-026-13182-z","url":null,"abstract":"<p><strong>Background: </strong>Mango (Mangifera indica L.) is a globally significant fruit over the world. The precise identification of germplasm resources is of great significance for the breeding of new mango cultivars. Traditional methods based on phenotypic characterization are time-consuming, labor-intensive, and often lack accuracy in distinguishing and identifying accessions. In contrast, DNA fingerprinting utilizing single nucleotide polymorphism (SNP) markers offers an efficient and accurate alternative for germplasm identification and variety protection. However, applications of such SNP-based systems remain relatively limited in mango research.</p><p><strong>Results: </strong>In this study, 438,322 SNP sites of SNP-InDel information were obtained by GATK software filtering. After filtered by minimum allele frequency (MAF) > 0.4; mismatch rate < 0.25; heterozygosity rate < 0.5; no other mutations within 70 bp on either side of the SNP site, 272 high-quality SNP sites was identified. Then 85 novel PARMS-SNP markers were developed. Based on the 85 novel PARMS-SNP markers, 145 mango germplasm accessions were grouped to three major categories. Based on the polymorphism results, 16 SNP markers were selected as the core markers to construct the DNA fingerprints of 145 mango germplasms. The results showed that 145 mango germplasms had unique genotyping and strong identification ability, indicating that there was no misidentification in the germplasm. At the same time, it provided a basis for the accurate identification of mango germplasm resources and the breeding of new varieties. In addition, 85 SNP markers were screened and 3 specific SNP markers of \"Keitt\" (KT) × \"Renong No.1\" (RN) were mined, which could effectively distinguish parents and control materials. The most important thing was to realize the rapid identification of mango parent-child relationship.</p><p><strong>Conclusions: </strong>To the best of our knowledge, this represents the first attempt to establish SNP markers in genomic wide. The objective is to conduct genetic diversity analysis and construct DNA fingerprint of mango germplasm resources, thereby providing a foundation for germplasm utilization and molecular marker-assisted breeding.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148468644","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Coding regions are rarely predefined in the eukaryotic genomes: a note on simplified models of gene architecture.","authors":"Qi Cao, Ziyi Wang, Yuange Duan","doi":"10.1186/s12864-026-13181-0","DOIUrl":"10.1186/s12864-026-13181-0","url":null,"abstract":"<p><strong>Background: </strong>The pedagogical depiction of eukaryotic gene structure seems to assume that coding sequences (CDSs) are predefined in the genome, with transcript diversity arising mainly from exon shuffling. However, whether such \"predefined CDS\" model is universal remains untested.</p><p><strong>Methods: </strong>We systematically analyzed seven representative eukaryotic genomes to classify protein-coding genes (PCGs) into four classes based on the positional consistency of CDS start/stop sites. Both strict and loose criteria were applied, followed by cross-species comparisons of genomic feature and functional enrichment.</p><p><strong>Results: </strong>Predefined CDS genes (Class 1) were unexpectedly rare, comprising < 10% of PCGs in most species but exceeding 25% in Drosophila. Class 1 genes displayed more exons, longer CDSs, but minimal splicing isoforms, indicating purifying selection on molecular diversity. Class 1 genes are enriched in housekeeping terms like neuronal and developmental processes, whereas highly variable Class 4 genes (with distinct CDS start/end positions across different transcripts) are associated with fast-evolving processes like metabolism and reproduction.</p><p><strong>Conclusions: </strong>In contrast to the pedagogical simplification, our results show that CDSs are rarely predefined in the genome. The differential roles of predefined versus variable CDS architectures may reflect how natural selection balances molecular stability and functional innovation.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13663203/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148496918","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":"Population genomics of the Japanese oak wilt pathogen reveals genetic structure mirroring its beetle vector and informs biosecurity risk assessment.","authors":"John T Dobbs, Rachel Koch-Bach, Christine Stone, Jo Anne Crouch","doi":"10.1186/s12864-026-13167-y","DOIUrl":"10.1186/s12864-026-13167-y","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Japanese oak wilt (JOW), caused by the fungus Dryadomyces quercivorus, has caused mass mortality of healthy oak trees in urban and landscape forests in Japan since the 2000s. The expanding geographic range of the pathogen, vectored by the ambrosia beetle Platypus quercivorus, threatens oak-dominated ecosystems and the timber industry globally. While variation in virulence among isolates has been described based on canker formation within Japanese oak species, there is limited understanding of the genetic variation of D. quercivorus that may underpin this virulence variation. Understanding the genetic variation represents a critical component to determining the capacity of this species to evolve novel virulences or overcome management strategies. In this study, improved hybrid assemblies of the JOW pathogen and closely related species including the Korean oak wilt pathogen (D. quercus-mongolicae) and the Mediterranean oak borer fungal symbiont (D. montetyi) were generated using Oxford Nanopore Technology long reads and Illumina short reads. To understand the genetic variation among JOW fungal populations, 32 isolates from two beetle lineages (A and B) across the Japanese archipelago were sequenced to assess population structure, genetic diversity, and evolutionary potential.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;High-quality genomes were generated for D. quercivorus, D. quercus-mongolicae, and, for the first time, D. montetyi. DAPC, phylogenetic, and distance-based analyses, together with ADMIXTURE patterns at K = 2, revealed two biologically meaningful genetic groupings that broadly corresponded to beetle lineage. Isolates from beetle lineage B, primarily collected in a previous study on the eastern coast of Japan, clustered separately from most isolates associated with beetle lineage A, which were collected across other regions of Japan. Notably, this genetic structure did not correlate with previously reported virulence levels. Window-based Tajima's D values were generally positive, a pattern consistent with weak bottlenecking and/or structured genetic variation rather than recent population expansion. Furthermore, evidence for sexual recombination was found. Both mating-type idiomorphs were present, and their overall frequency did not significantly deviate from a 1:1 ratio.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusions: &lt;/strong&gt;This research shows that the major genetic structure observed in this ambrosia fungus broadly parallels that of its beetle vector lineages. This co-structuring, together with evidence consistent with sexual recombination, suggests that beetle-mediated introductions could transport multiple pathogen genotypes with the potential for recombination. This information is critical for biosecurity risk assessment and will be useful for tracking incursions of this pathogen outside of Japan and for developing effective management strategies, including the use of the genomic resources generated here for rapid diagnostics.&lt;/","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/PMC13663286/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148468658","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":"Decoding the genome of the basidiomycetous yeast Vishniacozyma victoriae D19: a promising fungal model for biotechnology.","authors":"Bartosz Wąsik, Patryk Kupaj, Paweł Moroz, Anna Kancelista, Przemyslaw B Kowalczuk, Zbigniew Lazar, Cécile Neuvéglise, Hugo Devillers","doi":"10.1186/s12864-026-13178-9","DOIUrl":"10.1186/s12864-026-13178-9","url":null,"abstract":"<p><strong>Background: </strong>Vishniacozyma victoriae is a ubiquitous yeast isolated from various regions across the globe, especially in extreme environments. It can produce several interesting extracellular compounds, including carotenoids and cold-active hydrolytic enzymes, that confer high potential for industrial production and biotechnological applications. However, insufficient knowledge in its biology, genetics and genomics are the primary obstacle of its development as a new chassis. The aim of this study was to provide a high-quality genome assembly and an in-depth genome analysis of V. victoriae strain D19.</p><p><strong>Results: </strong>We isolated V. victoriae D19 (CBS 19383) from Trondheimfjordens, Norway. Here we present its high-quality genome assembly, along with comprehensive structural and functional annotation of the genome. The assembly consists of 10 nuclear scaffolds with a cumulative size of 18.1 Mb, an N50 value of 1.7 Mb (L50 = 3) and a complete circular mitochondrial genome. A total of 7,853 protein-coding genes were predicted. Intron structure and other features, such as rRNA, tRNA, transposable elements, telomeric repeats were also analyzed to contribute to a deeper understanding of the V. victoriae genome architecture. Functional gene annotation, performed using the go-FAnnoT and BlastKOALA tools, enabled the reconstruction of key metabolic pathways, providing potential functions for 6,434 and 3,626 proteins, respectively. Moreover, the analysis of protein targeting and in silico secretome analysis, followed by CAZymes identification, helped us to understand the metabolic potential of this yeast.</p><p><strong>Conclusion: </strong>These genomic resources establish a valuable foundation for future functional studies and provide keys for developing a new chassis for potential industrial applications.</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/PMC13660059/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148468730","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":"Transcriptome analysis of brown adipose tissue in Brandt's vole treated with tannic acid under cold exposure.","authors":"Qiu-Yi Shen, Kai-Xin Chen, Xu-Wei Ma, Sheng-Mei Yang, Wan-Hong Wei, Feng-Ping Yang, Xin Dai","doi":"10.1186/s12864-026-13187-8","DOIUrl":"10.1186/s12864-026-13187-8","url":null,"abstract":"<p><strong>Background: </strong>Tannic acid (TA) is a hydrolysable plant secondary metabolite known to influence multiple physiological processes in animals; however, its role in regulating brown adipose tissue (BAT) thermogenesis remains poorly understood. Notably, the overwinter food caches of Brandt's voles predominantly consist of Artemisia species, which are rich in TA. This study aimed to determine whether TA contributes to cold tolerance in Brandt's voles by activating BAT thermogenesis. Adult male voles were administered TA, after which the masses of BAT and inguinal white adipose tissue (iWAT) were measured, and temperature changes in BAT, the body surface, and the rectum were recorded following exposure to - 20 °C. In addition, transcriptomic analyses of BAT were performed, and the expression and protein levels of key thermogenic markers were assessed.</p><p><strong>Results: </strong>The results showed that TA reduced iWAT mass while exerting minimal effects on BAT mass. TA-treated voles exhibited significantly elevated temperatures in BAT, the body surface, and the rectum after cold exposure. Histological analyses revealed that TA treatment reduced adipocyte area in iWAT while increasing the number of nuclei in brown adipocytes in BAT. In BAT, differentially expressed genes (DEGs) in voles receiving a low TA dose were significantly enriched in pathways related to fat digestion and absorption and peroxisome proliferator-activated receptor (PPAR) signaling. In contrast, DEGs in voles administered a high TA dose were predominantly associated with brown adipocyte differentiation and the upregulation of cold-induced thermogenesis. Moreover, TA administration increased the expression of FFAR4 and UCP1, as well as the protein levels of PGC-1α, PPARγ, and UCP1 following cold exposure.</p><p><strong>Conclusions: </strong>Collectively, these findings demonstrate that TA enhances cold tolerance in Brandt's voles by promoting thermogenic gene expression and stimulating brown adipocyte differentiation in BAT, providing novel insights into the role of plant secondary metabolites in mammalian cold adaptation and herbivore-plant interactions.</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/PMC13531749/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148468720","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}