BMC Genomics最新文献

{"title":"Cross-cell-line conservation-resolved interactions reveal conservation-dependent relationships among CTCF loops.","authors":"Maryam Mirabolghasemi, Mohammad Hossein Karimi-Jafari, Ali Mohammad Banaei-Moghaddam","doi":"10.1186/s12864-026-13169-w","DOIUrl":"10.1186/s12864-026-13169-w","url":null,"abstract":"<p><p>The three-dimensional organization of the genome is shaped by CTCF-mediated chromatin loops, which vary widely in strength, conservation, and cell-type specificity. A longstanding model proposes that highly conserved loops form autonomously and establish a structural scaffold that supports the subsequent formation of less conserved, cell-type-specific interactions. However, genome-wide evidence for an ordered dependency among loops of different conservation levels has remained limited.Here, we tested this hierarchical model using high-resolution CTCF ChIA-PET data from eight human cell lines. We developed a two-stage predictive framework in which high-confidence loops were first identified using sequence features, chromatin context, and cross-cell-line conservation, and then augmented with neighboring-interaction features that quantify the influence of pre-existing loops at nearby CTCF anchors. Incorporation of neighboring-interaction information resulted in only modest overall improvements in predictive performance.To directly assess hierarchical dependencies, we stratified loops into eight conservation classes based on their recurrence across cell lines and systematically evaluated how neighboring interactions from each class contributed to loop prediction in others. This conservation-resolved analysis revealed a structured pattern in predictive relationships: loops within a given conservation class were most strongly predicted by neighboring loops from adjacent conservation classes. In contrast, the most highly conserved loops showed little improvement from local loop-context information.Together, these results demonstrate that the predictive value of neighboring chromatin interactions depends strongly on loop conservation and that chromatin interaction neighborhoods contain structured conservation-dependent information. More broadly, our neighboring-interaction framework provides an interpretable approach for identifying structured associations within chromatin interaction networks and for generating hypotheses regarding the organization of three-dimensional genome architecture.</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/PMC13656712/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148468695","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":"SorghumHub: featuring the next phase for the KBCommons web portal with new molecular biology features.","authors":"Nathan Grant, Yen On Chan, Anser Mahmood, Jana Biová, Mária Škrabišová, Trupti Joshi, Kristin Bilyeu","doi":"10.1186/s12864-026-13113-y","DOIUrl":"10.1186/s12864-026-13113-y","url":null,"abstract":"<p><strong>Background: </strong>Genomic resources for underutilized crops like sorghum [Sorghum bicolor (L.) Moench] often lag behind major staples, hindering efforts to link genetic diversity to agronomic traits. Improvements in genomic sequencing and bioinformatics have advanced crop genomics, yet species-specific challenges persist in the lack of tailored genomic resources, limiting precision breeding and applied genomics applications.</p><p><strong>Results: </strong>This study presents the addition of a SorghumHub to the KBCommons web portal, an applied genomics platform for Sorghum. The core focus of this framework is the Sorghum Allele Catalog Tool, with a web-based interface enabling researchers to query, visualize, and download allelic variants from curated sorghum datasets of 988 resequenced accessions. The newly improved Allele Catalog Tool now features the ability to connect variant positions with phenotype information collected for Plant Introduction (PI) accessions in the Germplasm Resource Information Network (GRIN). On the SorghumHub, users can also find the Protein Sequence Logos, a new tool complementary to the Allele Catalog Tool, which allows users to graphically explore missense amino acid sequence changes for conservation and frequency. These custom genomic tools available on the SorghumHub enable users to query genomic variants, allele frequency, and trait-associated genotype-phenotype relationships leveraging data produced through our group's computational pipelines for variant calling and processing into curated Allele Catalog datasets.</p><p><strong>Conclusions: </strong>This research work demonstrates practical application of Sorghum Allele Catalog Tool and Protein Sequence Logos by highlighting different candidate alleles for the predicted flowering time (FT-like) gene SbFT12 (Sobic.006G047700) in Sorghum bicolor; additionally, we discovered a relatively rare missense allele of the betaine aldehyde dehydrogenase (BADH2) gene that may provide a new avenue for fragrant/scented sorghum. The tools in SorghumHub allow researchers to optimize the accession selection process with efficient trait targeting and bridge the gaps between genomics and breeding. This approach can assist breeders and researchers in the development of resilient and high yielding crop varieties with broader positive outcomes for the agricultural industry and global food security.</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/PMC13656370/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148468715","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 comparison of traditional and commercial Mehraban sheep populations reveals differences in genetic structure, linkage disequilibrium, and inbreeding patterns.","authors":"Leyla Eskandari, Ahmad Ahmadi, Reza Talebi, Masoumeh Naserkheil, Seyyedeh Azadeh Javadi Taklimi, Fatemeh Zare, Tomasz Szmatoła, Masoud Shirali, Mohammad Reza Ghaffari","doi":"10.1186/s12864-026-13177-w","DOIUrl":"10.1186/s12864-026-13177-w","url":null,"abstract":"<p><p>Understanding the genetic architecture of sheep under different breeding systems is crucial for enhancing productivity and maintaining adaptive capacity. We analyzed 145 Mehraban sheep from commercial (n = 97) and traditional (n = 48) populations utilizing the OvineSNP50 BeadChip array. The analysis revealed that the linkage disequilibrium (LD) was numerically higher on average in the traditional population at both short and long distances (mean r² = 0.249 at < 10 kb; 0.037 at 5 Mb) in comparison to the commercial population (mean r² = 0.220 and 0.027, respectively), suggesting a smaller historical effective population size (Ne). Principal component and admixture analyses validated strong genetic difference, with the commercial population showing moderate admixture from traditional lines. Principal component and admixture analysis confirmed significant genetic difference, with the commercial population exhibiting considerable admixture from traditional lines. Analysis of runs of homozygosity (ROH) revealed more numerous and longer ROH segments in commercial animals (total ROH ~ 43,768 Mb, F_ROH = 0.183 ± 0.052) compared to traditional population (11,741 Mb, F_ROH = 0.139 ± 0.066), potentially indicating a potential increase in inbreeding and prolonged artificial selection. ROH islands contained 1,586 genes in commercial population and 797 genes in traditional population, with quantitative trait loci (QTL) for muscle development, carcass yield, and milk production enriched in commercial population, whereas traditional population harbored QTL for fertility, immune response, and wool characteristics. Functional analysis further identified Hippo signaling, TCA cycle, and growth-related pathways in commercial population, as well as immune (IL-17, TNF), reproductive, and DNA repair pathways in traditional population. These findings demonstrate how breeding systems shape genome-wide diversity, inbreeding, and functionally relevant loci, highlighting the importance of traditional populations as reservoirs of adaptive alleles for sustainable improvement of commercial flocks.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13651201/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148454578","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":"Identifying sex-specific genetic effects across 733 traits in UK biobank.","authors":"Wei Jiang, Yueqian Jing, James Han, Yixuan Ye, Hongyu Zhao","doi":"10.1186/s12864-026-13164-1","DOIUrl":"10.1186/s12864-026-13164-1","url":null,"abstract":"<p><p>Sex-specificity has been reported in a wide range of diseases and complex traits. While sex-specific genetic effects have been documented for certain traits, the genetic mechanisms underlying sex differences in most traits remain largely unexplored. With its large sample size and wide range of diseases and traits, the UK Biobank-a large, prospective cohort study containing health history, phenotypic measurements, and genetic data for over 500,000 individuals-provides an opportunity to explore sexually dimorphic genetic architectures in a large number of traits and diseases. Here, we present a sex-specific analysis of 733 sex-stratified complex trait GWAS for 361,194 white British individuals in the UK Biobank. Among these 733 traits, we detected sex-specific locus in 520 of them. These 520 candidate traits with sex-specific genetic effects were classified to 270 distinct groups. Using a systematic sex-specific discovery-replication analysis, we identify 489 loci showing sex-specific effects on 127 of the candidate trait groups, among which three of them having the most numbers of traits showing replicable signals were further investigated, including fat mass related traits (12 traits), heart disease related traits (7 traits) and body impedance related traits (6 traits). We identify pathways with sex-biased enrichment patterns from exploratory enrichment analyses based on QTL-associated genes. In addition, we present further evidence for significant sex-specific genetic effects in 25 traits by comparing the prediction performance of sex-specific polygenic risk scores (PRS).</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13647673/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148454351","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":"CoReGRN: a context-aware post-processing framework for gene regulatory network inference revealing regulatory signatures in HIV-Leishmaniasis.","authors":"Emma Paul M, Jereesh A S, G Santhosh Kumar","doi":"10.1186/s12864-026-13185-w","DOIUrl":"10.1186/s12864-026-13185-w","url":null,"abstract":"<p><p>Accurate inference of gene regulatory networks (GRNs) from single-cell gene expression data is challenging due to noise, data sparsity, and variability in gene-gene associations across cells. We propose CoReGRN (Contextual Refinement of Gene Regulatory Networks), a nonparametric, context-aware post-processing framework that refines inferred GRNs by reweighting candidate regulatory interactions using Mutual Information based association strength and local network context. The method uses empirical cumulative distribution function (ECDF) based scores to assess how unusual each interaction is relative to the connectivity patterns of the genes it connects. Then combines this contextual information with the original edge confidence scores. We evaluate the CoReGRN framework on gold-standard datasets from the BEELINE benchmark suite across multiple state-of-the-art GRN inference algorithms. The results show consistent performance improvements, with average absolute gains of 0.097 in AUROC, 0.130 in AUPR, 0.133 in MCC, and 0.095 in F1-Score. We further apply the framework to a single-cell HIV-Leishmaniasis dataset, where the refined networks support the analysis of disease-specific regulatory hubs and interactions. Comparison with existing biological knowledge identifies both known and potentially novel regulatory relationships across HIV infection, HIV-Leishmaniasis, and HIV-Visceral Leishmaniasis conditions. The analysis includes hub gene identification, interaction network analysis, and literature based validation using GeneMANIA.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13651031/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148454548","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":"Distinct 5' and 3' coverage biases shape transcriptome interpretation in Nanopore direct RNA versus PCR-cDNA sequencing.","authors":"Rebecca E Lane, Eleanor Calcutt, Anandagopal Srinivasan, Vicki Gamble, Udo Oppermann, Jianfeng Sun, Adam P Cribbs","doi":"10.1186/s12864-026-13184-x","DOIUrl":"10.1186/s12864-026-13184-x","url":null,"abstract":"<p><p>Long-read RNA sequencing enables isoform-resolved transcriptomics, but library preparation introduces systematic biases that shape biological interpretation. We benchmarked Oxford Nanopore's two protocols-PCR-cDNA and direct RNA-using SKMM2 myeloma cells stimulated with interleukin-6 (IL-6) and ERCC synthetic spike-ins. Direct RNA produced longer, higher-quality reads and more high-confidence isoforms, but showed pronounced 5' coverage loss. PCR-cDNA yielded shorter fragments with 3' underrepresentation, detecting more low-abundance transcripts at reduced confidence. Protocol-specific biases had major consequences: differential expression analysis revealed limited overlap in IL-6-responsive genes, and pathway enrichment was broader in direct RNA. At the isoform level, differential transcript usage was almost entirely protocol-specific, with case studies (e.g. RPL22L1, GRB2, RNF220) illustrating concordance and divergence. ERCC controls confirmed these biases as technical rather than biological. Together, our results show that while both methods provide accurate gene-level quantification, transcript-level conclusions depend critically on protocol choice, highlighting the need for careful selection in long-read transcriptomics.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13647511/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148454525","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 analysis of the complete multi-chromosomal mitogenome of an antitussive herb Fritillaria unibracteata.","authors":"Song Lu","doi":"10.1186/s12864-026-13193-w","DOIUrl":"10.1186/s12864-026-13193-w","url":null,"abstract":"<p><strong>Background: </strong>A renowned antitussive herb, Fritillaria unibracteata P. K. Hsiao & K. C. Hsia, has long been used as the original source of many traditional Chinese medicines (TCM) prescriptions for its pharmacological effects. Currently, this species is at risk of extinction owing to overexploitation. Genomic data can provide a scientific basis for the effective protection of wild germplasm resources. Although the plastome of F. unibracteata has been released, its mitogenome remains unclear.</p><p><strong>Results: </strong>The mitogenome of F. unibracteata exhibited a sophisticated multi-chromosomal configuration containing one master circular chromosome (82,085 bp) and 21 submaster chromosomes (18,718 bp-54,256 bp). It contained 60 genes, including 44 PCGs, 13 tRNA and 3 rRNA genes. Repeat sequences, including 862 dispersed repeats, 142 simple repeats, and 23 tandem repeats, contributed more to the mitogenome size than coding genes and chloroplast-derived fragments. A total of 518 RNA editing sites were identified in 36 PCGs, with NADH dehydrogenase and cytochrome c biogenesis genes being the most prevalent. The codon usage bias is in accordance with the model for most terrestrial plants that use ATG as an initiator codon and shows an obvious A/T (U) bias in the third site of all PCGs. These results provide key insights into the F. unibracteata mitogenome.</p><p><strong>Conclusion: </strong>The assembled and annotated F. unibracteata mitogenome advanced the features and organization of multi-chromosome genomes. This provides helpful information for further research on conservation, breeding, phylogenetic, and evolutionary studies of the genus Fritillaria.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13651234/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148454576","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":"High-throughput sequencing and analysis of target genes uncover microRNA-mediated responses to low-temperature stress in Medicago falcata.","authors":"Mei Yang, Lu Chai, Yuxuan Liu, Jiuding Sun, Han Li, Kailin Qian, Lulu He, Bing Li, Pan Zhang","doi":"10.1186/s12864-026-13122-x","DOIUrl":"10.1186/s12864-026-13122-x","url":null,"abstract":"<p><strong>Background: </strong>Low temperature severely restricts plant growth and development. Medicago falcata is an important germplasm resource for alfalfa breeding because of its strong adaptability and tolerance to abiotic stresses, particularly low-temperature stress. MicroRNAs (miRNAs) are key regulators of stress-responsive genes and modulate plant adaptation to stress by directing transcript cleavage or translational repression. However, the roles of miRNAs in low-temperature response mechanisms in M. falcata remain largely unclear.</p><p><strong>Results: </strong>Here, we constructed miRNA libraries from M. falcata roots grown under normal or low-temperature conditions. High-throughput sequencing identified 442 miRNAs, including 245 known and 197 novel miRNAs. Among these, 74 were putatively upregulated and 37 were putatively downregulated under chilling and freezing treatments. Based on degradome sequencing, 193 target genes involved in diverse biological processes were predicted. The M. falcata MfbZIP transcription factor family, consisting of 41 members across six subfamilies, responded to the cold treatments. Of these, MfbZIP10, a nuclear-localized protein homologous to a bZIP transcription factor in M. truncatula, showed the most significant response to cold stress in stems and roots. miR408-5p was responsive to chilling and freezing, and could cleave MfbZIP10 transcripts in a transient assay, as determined by RLM-RACE analysis. Physiological analyses and gene expression profiling of transgenic lines further demonstrated that the miR408-5p-MfbZIP10 module plays a vital role in low-temperature stress responses, with MfbZIP10 functioning as a key regulator by modulating physiological traits and the expression of genes in multiple signaling pathways.</p><p><strong>Conclusions: </strong>Our results identified candidate cold-responsive miRNAs in M. falcata and predicted their target genes involved in diverse biological processes. miR408-5p was found to target MfbZIP transcription factors in response to cold stress. Physiological characterization and quantitative expression analyses of MfbZIP10 transgenic lines showed that the miR408-5p-MfbZIP10 module plays a crucial regulatory role in low-temperature adaptation. miRNA sequencing and target gene identification provide new insights into miRNA-mediated regulatory mechanisms in M. falcata. These findings may facilitate the development of cold-tolerant forage legume crops through genetic improvement.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13647817/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148454558","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 insights into specialized and primary metabolism gene clusters in methicillin-resistant Staphylococcus aureus from Egyptian community settings.","authors":"Ahmed Adel Aboushanab, Nehal A Saif, Salma Salem, Sama S Eltaher, Reem A Elghaish, Ben Pascoe, Samuel K Sheppard, Mohamed Elhadidy, Laila Ziko","doi":"10.1186/s12864-026-13121-y","DOIUrl":"10.1186/s12864-026-13121-y","url":null,"abstract":"<p><p>Community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) remains a major public health concern. Beyond canonical virulence determinants, biosynthetic gene clusters (BGCs) for specialized metabolites (SMs) and primary metabolic adaptations may shape fitness in community settings. In this study, we analyzed 123 CA-MRSA isolates from Egypt (2020-2021) alongside three reference genomes using a combined genomics workflow: antiSMASH and PRISM for homology-based specialized BGCs and predicted structures, GECCO for de novo BGC detection, BiG-SCAPE for gene-cluster family (GCF) networks and gutSMASH for primary-metabolism clusters detection. Assemblies were generated from Illumina MiSeq data and annotated with Prokka; sequence types and clonal complexes were assigned with FastMLST. antiSMASH identified a total of 934 BGCs (median 8 per genome), dominated by the following BGC types: NRPS-independent siderophores (NIS) (n = 312; IucA/IucC-like siderophores), non-ribosomal peptide synthetase (NRPS) (n = 132), and opine-like metallophores (n = 123). GECCO detected 415 BGCs, including 287 unclassified and 101 NRPS-associated clusters. GutSMASH recovered 582 primary metabolism gene clusters (GCs), with fumarate-to-succinate (n = 96), arginine-to-bicarbonate (n = 89; ADI) and nitrate-reductase (n = 84) energy-capturing modules being the most frequent. NRPS and NIS content varied widely among isolates, exceeding reference genome diversity, and BiG-SCAPE networks suggested multiple isolate-specific GCFs lacking MIBiG matches. Egyptian CA-MRSA displays a rich repertoire of iron-acquisition, peptide, and metallophore BGCs alongside anaerobic/energy-efficiency primary metabolism GCs that may support survival and competitiveness in community niches. While experimental validation is needed, these pathways nominate tractable targets for anti-virulence or metabolism-directed interventions and provide a genomic baseline for CA-MRSA in the North African region.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13374142/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148454606","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":"Alternative splicing serves as a molecular strategy for saliva evolution and diversification in an endoparasitoid, Pteromalus puparum.","authors":"Jiamin Shi, Chun He, Fang Wang, Gongyin Ye, Yi Yang, Qisheng Song, Xinhai Ye, Qi Fang","doi":"10.1186/s12864-026-13171-2","DOIUrl":"10.1186/s12864-026-13171-2","url":null,"abstract":"<p><strong>Background: </strong>Animal saliva represents a powerful model for investigating adaptive evolution. In parasitoid wasps, salivary proteins are known to modulate host cellular and humoral immunity. However, the functional significance of widespread alternative mRNA isoforms derived from salivary genes remains largely unexplored. To fill this gap, we applied an integrative full-length isoform sequencing and profiling pipeline in the endoparasitoid wasp Pteromalus puparum, enabling the reconstruction of a high-resolution transcriptomic landscape of salivary genes.</p><p><strong>Results: </strong>A total of 133 high-confidence salivary genes were identified, more than 75% of which produce multiple transcript isoforms. Mass spectrometry analysis suggested that alternative splicing contributes to salivary proteome diversity, with eight genes encoding distinct protein isoforms. Notably, 12 salivary genes displayed differential isoform usage with elevated expression in salivary glands relative to the carcass. A striking example is P. puparum serpin3 (PpSerpin3), whose short isoform is specifically expressed in both salivary and venom glands. Functional assays revealed that this short isoform actively suppresses host humoral melanization. Given that active components in injected venom may gradually lose their efficacy, we propose that salivary secretions function to sustain host manipulation throughout parasitization. Comparative multi-omics analyses further showed that although salivary and venom systems share a conserved core genetic toolkit, they achieve functional specialization via tissue-specific gene family co-option and extensive isoform switching.</p><p><strong>Conclusion: </strong>This study presents an isoform-resolved transcriptomic framework of the parasitoid salivary system. The findings indicate that alternative splicing contributes to salivary protein diversity by encoding distinct protein products and, further, facilitates salivary gene evolution through gland-specific isoform switching. Collectively, this work provides mechanistic insights into the diversity and evolution of salivary systems.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13651363/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148454560","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}