BMC Genomics最新文献

{"title":"Genome-wide characterization of the bZIP gene family in Rattus norvegicus and expression profiling analysis during brain development.","authors":"Pan Lu, Zongjun Zhu, Yuanyuan Guan, Ya Wang, Ruiquan Chen, Hongbo Xiao","doi":"10.1186/s12864-026-13180-1","DOIUrl":"10.1186/s12864-026-13180-1","url":null,"abstract":"<p><strong>Background: </strong>The brown rat (Rattus norvegicus) serves as a cornerstone model organism in biomedical research, particularly for understanding physiological homeostasis and stress responses. The basic leucine zipper (bZIP) transcription factor family is a pivotal regulatory network involved in growth, organogenesis, and neurodevelopment. Despite its importance, a systematic characterization of the bZIP gene family in rats has remained elusive.</p><p><strong>Results: </strong>In this study, we performed a genome-wide identification of 61 RnbZIP genes, which were categorized into 10 distinct subfamilies based on phylogenetic relationships and chromosomal localization. Structural analysis revealed conserved motif arrangements within subfamilies, while collinearity analysis identified significant gene duplication events-predominantly tandem and segmental duplications-that have driven the evolutionary expansion of the RnbZIP family. Quantitative analysis showed that members within the same subfamily shared 45%-92% sequence similarity (calculated using the BLOSUM62 scoring matrix), and all duplicated gene pairs underwent strong purifying selection (Ka/Ks < 1). Comparative genomics across seven rodent species further underscored the evolutionary conservation and divergence of these factors. Expression profiling across diverse organs and brain developmental stages indicated that RnbZIP genes exhibit high tissue specificity. Notably, 10 candidate genes, including RnbZIP01, RnbZIP02, and RnbZIP08, demonstrated dynamic expression patterns during brain maturation, suggesting their essential roles in neurodevelopmental processes.</p><p><strong>Conclusions: </strong>Our findings provide a comprehensive structural and evolutionary framework for the RnbZIP gene family, highlighting their potential regulatory functions in rat organogenesis and brain development. This study establishes a valuable resource for further functional characterization of specific bZIP members in mammalian neurological systems.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"27 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13551848/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148910787","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":"SNP genotyping in Pseudotsuga menziesii and Pinus radiata using targeted genotyping-by-sequencing (GBS): improved Bayesian SNP calling using a beta-binomial distribution and other optimized input parameters.","authors":"Jia Guo, Gancho Slavov, Liam W Gilson, Douglas A Maguire, Anna C Magnuson, Natalie Graham, Tancred Frickey, Glenn T Howe","doi":"10.1186/s12864-026-13099-7","DOIUrl":"10.1186/s12864-026-13099-7","url":null,"abstract":"<p><strong>Background: </strong>Single-nucleotide polymorphism markers (SNPs) have important applications in gene conservation, breeding, and fundamental genetics research. Our long-term goal is to develop routine approaches for SNP genotyping in forest trees. Ideally, these approaches would be inexpensive, able to accommodate a wide range of samples and SNPs, available through commercial providers, and produce high-quality SNP data.</p><p><strong>Results: </strong>Using targeted genotyping-by-sequencing (GBS), we developed SNP assays for two highly heterozygous tree species, Douglas-fir (Pseudotsuga menziesii) and radiata pine (Pinus radiata). Using Douglas-fir haploid and diploid data, we optimized Bayesian SNP calling by testing four input parameters: (1) allele and genotype prior probabilities, (2) Rho, the beta-binomial dispersion parameter, (3) estimated read error (BayesReadError), and (4) the logPO cutoff used to filter low confidence SNP calls. logPO is the Bayesian posterior odds ratio for a called SNP. Compared to assuming a binomial distribution of read counts (Rho = 0), the beta-binomial distribution (Rho = 0.33) substantially reduced call error and heterozygote undercalling. Compared to the other Bayesian parameters, genotype priors had little effect on genotyping success. For Douglas-fir, we tested 5,360 SNP assays, and then studied the performance of the best 4,000. For radiata pine, we tested 6,000 SNP assays, and then studied the performance of the best 4,570. In Douglas-fir and radiata pine, our Bayesian approach resulted in median call rates of 95% to 98% for the top-ranked SNPs, with an estimated call error of 1.60% for known homozygous genotypes and 2.27% for known heterozygotes. In radiata pine, median and mean call rates were above 91% for GBS and SNP genotyping using an Axiom fixed genotyping array. Additionally, the median correspondence between the GBS and Axiom genotypes was about 98% overall (mean 96%).</p><p><strong>Conclusions: </strong>By optimizing Bayesian SNP calling, selecting the best 4-5 K SNPs, and excluding samples with low DNA amounts, we substantially reduced call error and heterozygote undercalling, resulting in SNP genotypes that were nearly identical to genotypes obtained using the Axiom array. Furthermore, genotyping performance should increase even further if our SNP rankings were used to develop less complex probe pools that target fewer SNPs.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"27 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13536811/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148872832","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A hybrid and cost-efficient barcoding strategy for full-length 16S rRNA gene nanopore sequencing of environmental samples.","authors":"Ida Romano, Edoardo Pasolli, Jean-Claude Walser, Valeria Ventorino, Sonja Reinhard, Giuseppina Magaraci, Olimpia Pepe, Natacha Bodenhausen","doi":"10.1186/s12864-026-13239-z","DOIUrl":"10.1186/s12864-026-13239-z","url":null,"abstract":"<p><strong>Background: </strong>Accurate species-level identification of bacteria in complex environmental samples is essential for applications in biotechnology, ecological monitoring, and clinical diagnostics. Short-read platforms such as Illumina frequently truncate the 16S rRNA gene, limiting taxonomic resolution. In this work, we applied Oxford Nanopore Technology (ONT) long-read sequencing to full-length 16S rRNA amplicon in samples from natural soil amended with lignocellulosic biomass and a simplified microbial community derived from cultures grown on selective and differential carboxymethyl cellulose (CMC)-based substrates, with the aim to evaluate the difference in performance between a real, complex community and a less complex system. To reduce consumable costs, we substituted the standard ONT Barcoding kits with an in-house hybrid barcoding workflow. Specifically, PacBio PCR-based barcoding protocol was used for sample indexing, followed by library preparation using the ONT Ligation Sequencing Kit. This simplified approach retained compatibility with MinION and Flongle flow cells and supported accurate downstream demultiplexing while lowering barcode costs substantially. Additionally, a new bioinformatic workflow tailored to ONT data was implemented.</p><p><strong>Results: </strong>Overall, the hybrid protocol significantly reduced per-sample barcoding costs while preserving high sequencing quality and throughput. The sequencing run yielded over 5 Gb of quality-filtered data (Q-score ≥ 10). Furthermore, the new bioinformatic workflow allowed taxonomic assignment at the species level for 49.38% of annotated taxa, compared to just 4.59% using Illumina NovaSeq sequencing of the V3-V4 region. ONT also recovered 2.3 times more genera and 1.3 times more families. Although 16S rRNA gene sequencing often cannot distinguish between closely related species, particularly within taxonomically complex groups, in this work, full-length reads substantially improved both taxonomic resolution and database matching.</p><p><strong>Conclusions: </strong>These results show that full-length 16S rRNA sequencing with ONT, paired with a low-cost barcoding strategy, enhanced taxonomic resolution compared to short-read workflows. This approach also offers a scalable and cost-effective option for high-resolution microbiome profiling in research and applied settings.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"27 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13551857/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148904566","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A rapid one-step NGS-based system integrating microhaplotypes and SNPs for forensic identification","authors":"Linyu Shi, Jiaxuan Hao, Jingjing Xu, Mengyang Zhao, Anjie Wei, Xinyi Zhang, Haoliang Fan, Jiangwei Yan","doi":"10.1186/s12864-026-13237-1","DOIUrl":"https://doi.org/10.1186/s12864-026-13237-1","url":null,"abstract":"Short tandem repeats (STRs) have limited performance in analysing challenging forensic samples owing to the relatively long amplicon lengths of a subset of STR loci and the presence of stutter artefacts. While single nucleotide polymorphisms (SNPs) offer advantages for degraded DNA analysis through shorter amplicons, microhaplotypes (MHs) provide higher allelic diversity per locus than diallelic SNPs, thereby improving the statistical power of mixture deconvolution. To address these needs, we developed a novel next-generation sequencing (NGS)-based MHs and SNPs system, integrating 24 MHs, 80 SNPs, and a Y-Indel marker. Additionally, we developed a rapid, one-step library preparation method, reverse-probe-guided direct amplification. This method efficiently constructs targeted NGS libraries within 2.5 h by integrating target amplification and adapter ligation in a single tube, eliminating intermediate transfers to minimise contamination risks. We conducted comprehensive forensic validation, including population genetics parameters (total discrimination power = 1–2.0265 × 10 –39 ), performance on severely degraded DNA (degradation index: 10–15, quantified by qPCR; likelihood ratios supporting suspect contribution in 1:9 mixtures with a known victim > 2.26 × 10 15 ), performance on formalin-fixed paraffin-embedded tissues (our panel achieved 100% genotyping accuracy, whereas capillary electrophoresis-STR exhibited > 38% allelic dropout), species specificity (six common non-human species: chicken, cattle, pig, mouse, rabbit and sheep, all yielded no interpretable typing data), and inhibitor resistance (evaluated against three common forensic inhibitors: humic acid, indigo and EDTA, at varying concentrations). Taken together, the developed one-step library preparation workflow and integrated MH-SNP panel offer a rapid, reliable approach for individual identification across common challenging forensic samples, including degraded DNA, degraded mixtures, FFPE tissues and inhibitor-contaminated specimens.","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148861228","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":"Conservation of Long G4-rich (LG4) genomic enhancer regulations.","authors":"Michael H Shaw, Jeffrey D DeMeis, Claire A Arnold, Makala R Cox, Tien C Duong, Kyle A Gaviria, Grace K McDavid, Jose M Villegas, Margaret L Weimer, Suhas S Patil, Shahem Y Alqudah, Glen M Borchert","doi":"10.1186/s12864-026-13154-3","DOIUrl":"10.1186/s12864-026-13154-3","url":null,"abstract":"<p><p>Long G4-rich regions (LG4s) are defined as DNA sequences containing a high density of guanine triplets capable of forming non-B DNA structures called G-quadruplexes (G4s). These regions frequently overlap with enhancers, which are regulatory DNA elements that modulate gene expression by interacting with DNA regions that dictate where transcription is initiated known as promoters. While LG4s have now been well-characterized in the human genome, neither LG4 occurrence, nor the ability of LG4s to function as enhancers, in other species has been described. To address this, we screened the genomes of 16 different species from various taxa to identify LG4s and then determined if they were conserved, and additionally, we show the ability of one of the conserved LG4s to interact with its cognate promoter in vitro is functionally maintained across species. Our analyses characterized a number of previously unreported LG4s in the human genome as well as LG4s in 13 additional species. Of note, we identified a highly conserved LG4 enhancer predicted to regulate over 40 genes. This LG4 is embedded in the MAZ (Myc-Associated Zinc finger protein) locus, and we find this LG4 possesses the ability to directly interact with the same target promoter in both human and mouse. In summary, this work describes LG4s in the genomes of both unicellular and multicellular species including vertebrates, invertebrates, plants, and fungi, and finds many of these LG4 sequences highly conserved.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"27 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13556083/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148910707","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":"Divergent host adaptation in Marburg virus: a hypothesis-generating framework for prioritizing non-traditional reservoirs.","authors":"Qi Chen, Jingjing Hu, Siru Hu, Yuxi Wang, Weijie Chen, Shuiping Lu, Jiaxu Chen, Sijia Zhuang, Zhong Sun, Karuppiah Thilakavathy, Lufang Jiang, Chenglong Xiong","doi":"10.1186/s12864-026-13256-y","DOIUrl":"10.1186/s12864-026-13256-y","url":null,"abstract":"<p><strong>Background: </strong>Although Rousettus aegyptiacus is the primary natural reservoir of Marburg virus (MARV), recent atypical outbreaks and viral genomic diversification suggest a highly complex host-pathogen ecology. Here, we systematically evaluated the molecular homologies between MARV and diverse mammalian taxa to identify putative reservoir hosts and guide targeted surveillance.</p><p><strong>Methods: </strong>A multi-dimensional molecular characterization of the Marburg virus (MARV) genome was performed using an integrative suite of computational approaches. Distant sequence homology was interrogated via BLAST in conjunction with a null model framework, supplemented by granular analyses of codon usage bias, nucleotide composition, and dinucleotide frequencies. For comparative genomic context, we evaluated a cohort of 63 mammalian species across the orders Rodentia, Primates, Chiroptera, and Perissodactyla.</p><p><strong>Results: </strong>Multidimensional molecular profiling showed varied genomic similarity between MARV and mammalian groups, with stable convergence observed in Perissodactyla and certain rodents across multiple codon usage indices. Notably, the effective number of codons (ENC) in Equus caballus (52.43) nearly matched MARV (52.44), and Equus asinus exhibited the lowest average RSCU Manhattan distance to the virus (0.25). Additionally, MARV's CpG suppression ([Formula: see text] = 0.48) was consistent with the CpG depletion levels characteristic of the studied mammalian taxa.</p><p><strong>Conclusion: </strong>Through the lens of computational biology, this study identifies putative host cohorts within the orders Perissodactyla and Rodentia that share distinct genomic, codon-usage, and dinucleotide-frequency homologies with MARV. These findings establish high-priority targets for downstream ecological field monitoring, seroepidemiological surveys, and experimental validation, ultimately providing a scientific blueprint to refine zoonotic surveillance networks under the global 'One Health' paradigm.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"27 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13589372/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149001218","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 characteristics and geographical distribution of uncultivated soil prokaryotes.","authors":"Álvaro Rodríguez Del Río, Yongxing Cui, India Mansour, Matthias C Rillig","doi":"10.1186/s12864-026-13092-0","DOIUrl":"10.1186/s12864-026-13092-0","url":null,"abstract":"<p><p>Most soil prokaryotic species remain uncultivated, limiting our understanding of the terrestrial microbiome. Metagenomic sequencing, and particularly the study of metagenome-assembled genomes (MAGs), represents an unprecedented opportunity to characterize the genomic features and biogeography of uncultivated prokaryotic taxa at the large scale. Here, we analyze 40,039 genomic bins from cultivated and uncultivated soil taxa within the SMAG catalog, and examine the occurrence of uncultivated prokaryotes in 9,012 metagenomic samples from the Sandpiper resource. Compared to genera with cultivated representatives, uncultivated soil prokaryotes show smaller genomes, lower G + C content, tendency to acidophilic, non-alkaline, thermophilic and host-associated lifestyles, and slower growth rates, with the latter having the highest predictive power for cultivation status. Uncultivated soil microbes also show unique gene repertoires, characterized by a depletion of biosynthetic and motility genes. We also show that completely uncultivated genera are more abundant in tropical and arctic soils, indicating substantial hidden diversity in these regions. Our work emphasizes that current cultivation efforts systematically fail to capture a particular fraction of soil prokaryotic diversity, and provides guidelines for future cultivation strategies.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"27 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13445660/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148676965","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":"Phylogenetic analysis of the bacterial intracellular R-body killer proteins indicates extensive horizontal gene transfer and signature Reb sequence motifs.","authors":"Lennart Dörr, Robin Ghosh, Michael Schweikert","doi":"10.1186/s12864-026-13231-7","DOIUrl":"10.1186/s12864-026-13231-7","url":null,"abstract":"<p><p>The fascinating spiral proteinaceous structures named 'R-bodies' can be produced by a number of bacterial species and are known to cause the so-called 'killer-effect' in paramecia. The genetic determinants of the R-bodies are the 'reb genes', which are widespread among diverse proteobacteria, presumably due to horizontal gene transfer. However, the extent of their taxonomic spread, genetic sequence diversity, and gene cluster synteny has not been analyzed exhaustively using the present genetic databases. In this study we have performed an extensive genetic survey for Reb homologous proteins, including those in previously unknown taxa. Our study reveals key amino acids of Reb protein sequences that are highly conserved and may hint at the biological role of the individual Reb proteins. We also show that the genetic synteny of reb gene clusters is diverse but can be clustered into distinct groups. Further, we analyze possible horizontal gene transfer events and pathways for reb genes and indicate context with the bacterial habitat. By identifying key aspects of R-body spread and functionality with our genetic analysis we pave the way for more targeted lab experiments that will allow R-bodies to be used for biotechnological or biomedical applications.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"27 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13430693/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148667955","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":"Long-read RNA-seq maps the isoform landscape of the trigeminal ganglion in an allergic rhinitis mouse model.","authors":"Zhiyao Han, Beirui Yu, Maoqia Shen, Ziyuan Tang, Xinran Li, Mingyang Wang, Fengxian Li, Xiaolong Cao","doi":"10.1186/s12864-026-13024-y","DOIUrl":"10.1186/s12864-026-13024-y","url":null,"abstract":"<p><strong>Background: </strong>The trigeminal ganglion (TG) plays a key role in allergic rhinitis (AR), mediating symptoms like nasal itching and sneezing via sensory neuron activation. Yet, the underlying transcriptomic mechanisms remain unclear. While short-read RNA-seq struggles to accurately capture complex transcript isoforms, long-read sequencing offers full-length coverage but limited quantitation. Here, we combine both technologies to comprehensively profile the TG transcriptome in an AR mouse model.</p><p><strong>Results: </strong>We identify 25,988 high-confidence full-length isoforms from 13,011 known and 237 novel genes, including 7,543 (29.02%) novel isoforms absent from reference databases. These are enriched in RNA splicing and processing genes. Alternative first exons are the most common splicing event and are especially frequent among novel isoforms. AR induces shifts in gene expression, splicing dynamics, and promoter activity, suggesting neuro-immune crosstalk. Single-cell RNA-seq integration further reveals that while some genes lack cell type-specific expression, their alternative splicing patterns are highly cell type-specific, suggesting that AS may play a crucial role in diversifying gene function across different cell types.</p><p><strong>Conclusions: </strong>The findings provide a comprehensive full-length transcriptome dataset, facilitating in-depth exploration of the interplay between sensory alterations and AR in trigeminal ganglion.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"27 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13589356/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149001268","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 genomics of nicotinic acetylcholine receptors reveals early divergence of the α6 subunit in cryptic Anopheles species.","authors":"Caroline Fouet, Desiree E Rios, Fred A Ashu, Matthew J Pinch, Cesar A Hernandez, Marilene M Ambadiang, Basile Kamgang, Colince Kamdem","doi":"10.1186/s12864-026-12994-3","DOIUrl":"https://doi.org/10.1186/s12864-026-12994-3","url":null,"abstract":"<p><strong>Background: </strong>Nicotinic acetylcholine receptors (nAChRs) are pentameric ligand-gated ion channels that mediate fast cholinergic transmission in the insect central nervous system and serve as targets for several widely used classes of insecticides. nAChR-targeting formulations are being deployed in malaria vector control programs to mitigate widespread resistance to pyrethroids. However, the extent of genetic variation at insecticide target sites that may facilitate evolutionary responses to chemical exposure among vector species remains poorly understood.</p><p><strong>Results: </strong>Here, we used whole-genome and Sanger sequencing to examine amino acid substitutions across all 11 nAChR subunits in sibling species of the Anopheles gambiae complex in Africa. The gene family is highly constrained, with only 33 nonsynonymous mutations detected at very low frequency in wild populations throughout the continent. No substitutions were observed at canonical ligand-binding residues within orthosteric domains, suggesting that acetylcholine and neonicotinoid binding affinities are unlikely to differ between the cryptic species. However, despite the evolutionary constraint, we identified two linked amino acid substitutions in the α6 subunit indicating early divergence of the receptor between species.</p><p><strong>Conclusions: </strong>These findings show that relaxed constraint can enable subtle amino acid changes in specific subunits of a conserved receptor family. The role of these mutations in shaping heterogeneous responses to insecticide exposure among mosquito species warrants further investigation.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"27 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13471630/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148762396","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}