BMC Genomics最新文献

{"title":"Decoding radiation-induced transcriptomic signatures of human leukocytes using long-read RNA-seq: clinical and biodosimetric implications.","authors":"Ahmed Salah, Heinz Schmidberger, Federico Marini, Sebastian Zahnreich","doi":"10.1186/s12864-026-13475-3","DOIUrl":"10.1186/s12864-026-13475-3","url":null,"abstract":"<p><strong>Background: </strong>Gene expression profiling in radiation-exposed blood is a valuable tool for biodosimetry and clinical research. Evaluating the blood's transcriptomic radiation response provides insight into absorbed dose, hematotoxicities, and immune reactions. However, detailed analysis using long-read RNA sequencing is currently limited in its diffusion, despite the potential additional insights that could be extracted, including novel isoform discovery and on-the-field gene expression studies, owing to its portability.</p><p><strong>Results: </strong>In this study, we utilized Oxford Nanopore Technologies' long-read RNA sequencing on human peripheral blood leukocytes from three healthy donors 6 h after exposure of whole peripheral blood to 4 Gy of X-rays. Compared to sham-irradiated (0 Gy) blood samples, gene-level differential expression analysis identified 117 upregulated and 66 downregulated genes, including canonical DNA damage repair and inflammatory responses. At the transcript level, 102 transcripts were significantly upregulated, and 17 were downregulated, revealing isoform-specific regulation that was not captured at the gene level. Notably, IL32, which was not detected as significantly changed at the gene level, exhibited significant upregulation of two transcript isoforms (log2 fold-changes of 1.19 and 1.99), while WDR74, ITM2B, AK2, and RPS19 displayed changes in transcript usage following irradiation. Leveraging long-read RNA sequencing, we further identified novel candidate isoforms, including protein-coding isoforms of PHPT1 and FBXO22 as well as non-coding candidates. Notably, the FBXO22 isoform showed evidence of altered protein domain architecture relative to the reference isoform.</p><p><strong>Conclusions: </strong>This study is the first to systematically investigate differential transcript usage in the leukocyte fraction of irradiated human whole blood using long-read RNA sequencing. We confirmed known radiation-response signatures at the gene level and identified transcript-level regulatory events and novel candidate isoforms that can be masked in gene-level analyses and conventional short-read pipelines. These findings demonstrate the potential of long-read RNA sequencing to provide a more detailed view of radiation-induced transcriptomic alterations, with potential applications in biodosimetry and clinical settings.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"27 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13678912/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149223259","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 pool sequencing reveals genomic variation in field Haemonchus contortus isolates in Sweden.","authors":"Nanxing Liu, Paulius Baltrušis, Åsa Ohlsson, Johan Höglund, Sofia Mikko","doi":"10.1186/s12864-026-13449-5","DOIUrl":"10.1186/s12864-026-13449-5","url":null,"abstract":"<p><strong>Background: </strong>Haemonchus contortus is a major gastrointestinal parasite of small ruminants worldwide. Its large effective population size, high fecundity, and extensive genetic variation promote rapid adaptation and the development of anthelmintic resistance. Resolving genome-wide genetic variation in H. contortus within and among populations is essential for tracking variant distribution, interpreting resistance-associated markers, and informing parasite control strategies. Although reduced representation and targeted marker approaches have provided important insights into population structure, whole genome sequencing is required to fully characterise population differentiation. This study aimed to characterise genome-wide variation within and between field-derived H. contortus populations in Sweden, using whole genome sequencing of pools of individuals from 12 sheep farms.</p><p><strong>Results: </strong>Field-derived H. contortus isolates from Swedish farms showed high genomic diversity within populations (nucleotide diversity (Pi) = 0.0211-0.0253) and relatively low genomic differentiation among most populations (fixation index (F_ST) < 0.1). However, three population pairs displayed higher genomic differentiation (F_ST = 0.144-0.157) combined with lower genomic nucleotide diversity (Pi = 0.0211-0.0227), with divergence concentrated on chromosomes 4, 5, and X. Significantly differentiated single nucleotide polymorphisms were linked to a limited set of annotated genes involved in regulatory, signalling, and nervous system-related functions. However, the biological basis of these patterns remains unclear and will require further investigation using phenotype-linked data and farm-management metadata.</p><p><strong>Conclusions: </strong>This work establishes the first genome-wide baseline for field-derived H. contortus populations across multiple Swedish sheep farms and shows that pooled-sample whole-genome sequencing (Pool-seq) is a useful method for describing broad population-genomic patterns in this species. Our findings indicate relatively low genomic variation between Swedish H. contortus populations and high genomic variation within them. This study provides a valuable foundation for future research on parasite adaptation, resistance, surveillance, and control.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"27 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13678931/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149223335","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":"Systematic assessment of sequencing depth requirements for Hi-C-derived metrics.","authors":"Alexander Granovsky, Kirill Polovnikov","doi":"10.1186/s12864-026-13455-7","DOIUrl":"10.1186/s12864-026-13455-7","url":null,"abstract":"<p><strong>Background: </strong>Hi-C experiments produce genome-wide chromatin contact maps from which structural features can be quantified across multiple genomic scales, ranging from megabase-scale compartments to kilobase-scale boundaries and chromatin loops. Although high-resolution analyses commonly rely on hundreds of millions of sequenced read pairs, the minimum sequencing depth required for different classes of Hi-C-derived features has not been systematically established. We therefore sought to determine these depth requirements systematically.</p><p><strong>Results: </strong>We performed progressive random subsampling of twelve Hi-C libraries representing multiple cell types and experimental protocols. Loop-density and loop-size inference from the P(s) log-derivative was evaluated across all libraries, whereas compartment, insulation, and boundary analyses were performed on a subset of nine libraries with comparable full-depth coverage. Rather than defining a \"sufficient depth\" as an arbitrary fraction of the full-depth value, we introduced a biologically motivated criterion based on the variability of the metric between independent biological replicates. The required sequencing depth for each metric was defined as the point at which the subsampling scatter first reached the variability observed between independent biological replicates, representing the accuracy that additional sequencing cannot improve upon. Using this criterion, the genome-average loop-density estimate reached its biological floor at approximately 7 million read pairs, the genome-average loop-size estimate at approximately 20 million, insulation scores at approximately 80 million, and compartment eigenvectors at 100-kilobase resolution at approximately 110 million read pairs.</p><p><strong>Conclusions: </strong>Different Hi-C-derived metrics require substantially different sequencing depths to achieve biologically meaningful accuracy. For all metrics, depth-induced variability fell below biological replicate variability well before full sequencing depth was reached. These thresholds apply to genome-averaged characteristics, not local metrics of specific loci. They therefore provide practical guidance for genome-wide experimental design and sequencing budget allocation, suggesting that increasing the number of biological replicates is likely to improve the inference of global biophysical features more effectively than sequencing individual libraries to greater depth.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"27 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13670550/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149191331","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":"ERMA: a harmonizing epicPCR data analysis tool.","authors":"Adrian Dörr, Svjetlana Dekić Rozman, Lina Viktoria Duncker, Jan Kehrmann, Jan Buer, Marko Virta, Folker Meyer, Ivana Kraiselburd","doi":"10.1186/s12864-026-13418-y","DOIUrl":"10.1186/s12864-026-13418-y","url":null,"abstract":"<p><strong>Background: </strong>EpicPCR links functional genes to taxonomic markers at the single-cell level and has become an important method in microbial ecology and antimicrobial resistance research. However, the lack of missing standardized data analysis workflows limits reproducibility and comparability across studies. Existing analyses are often based on custom, unpublished scripts, complicating cross-study benchmarking and reuse.</p><p><strong>Results: </strong>We present ERMA, an open-source, Snakemake-based pipeline that enables an automated, standardized, reproducible, and scalable epicPCR data analysis with minimal user input. ERMA supports both Illumina and ONT sequencing data and integrates quality control, database preparation, dual similarity searches against taxonomic and functional reference databases, results integration, filtering, and visualization. The pipeline is adaptable to a broad range of research questions beyond AMR due to modular database preparation and integration of specific UniRef queries. We evaluated ERMA using five publicly available epicPCR datasets covering diverse sample sources and sequencing depths. Across these datasets, ERMA achieved mean concordance rates of approximately 70-83% with the taxonomic results reported in the respective publications. In addition, validation using a defined five-member mock community spiked into clinical wastewater demonstrated full recovery of mock genera, with 85% of ERMA-detected genera also detected by independent 16S rDNA gene analysis of the same wastewater sample. Attrition analysis showed inconsistent filtering patterns across studies, reflecting dataset-specific quality differences.</p><p><strong>Conclusion: </strong>While large-scale reference datasets for epicPCR remain limited, validation using both publicly available studies and a defined mock community shows strong, interpretable performance across heterogeneous datasets. By providing a transparent, modular, and reproducible workflow, ERMA contributes toward harmonized epicPCR data analysis and establishes a foundation for future methodological standardization and benchmarking efforts as reference datasets improve.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"27 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13660262/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149164587","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":"Beyond two alleles: multiallelic genotypic selection and its estimation from time-series data.","authors":"Nikolas Vellnow, Toni I Gossmann, David Waxman","doi":"10.1186/s12864-026-13411-5","DOIUrl":"10.1186/s12864-026-13411-5","url":null,"abstract":"<p><p>Genetic diversity is central to evolutionary change, with both natural selection and random genetic drift depending on variation within a population. An individual in a diploid population carries two alleles per locus, yet the population as a whole can harbour many alleles, giving rise to a rich spectrum of homozygous and heterozygous genotypes. Such multiallelic variation is common at biologically and medically important loci such as the major histocompatibility complex, the ABO blood group system, and genes underlying monogenic diseases. However, much of population genetic theory and data analysis has focussed on biallelic loci. Here, we introduce a matrix representation of the genotypic selection acting at a multiallelic locus. This exploits the common mathematical structure underlying selection and drift, and separates the effects of genetic diversity and fitness. The representation accommodates diverse selection regimes, including additive, multiplicative, frequency-dependent, and temporally varying selection, as well as heterozygote advantage. We show how, under specific assumptions, genotype-specific fitness-effects can be estimated from allele frequency trajectories over microevolutionary timescales. Applying this estimation procedure to time-series data from experimental yeast evolution illustrates how multiallelic fitness interactions, including heterozygote advantage, may be characterised from haplotype frequency data. More broadly, this work provides a practical foundation for analysing evolutionary dynamics at multiallelic loci in experimental and natural populations.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"27 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13651084/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149147119","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 sequencing enables high-accuracy mitochondrial heteroplasmy detection in Parkinson's disease.","authors":"Theresa Lüth, Susen Schaake, Christoph Much, Mary Megan Belyea, Philip Seibler, Anne Grünewald, Patrick May, Christine Klein, Hansi Weissensteiner, Joanne Trinh","doi":"10.1186/s12864-026-13426-y","DOIUrl":"10.1186/s12864-026-13426-y","url":null,"abstract":"<p><strong>Background: </strong>Low-frequency heteroplasmic mitochondrial DNA (mtDNA) variants are associated with aging and neurological diseases, including Parkinson's disease (PD). Targeted deep mtDNA sequencing using PacBio HiFi long reads has the potential to resolve heteroplasmy across the full mitochondrial genome with high accuracy.</p><p><strong>Methods: </strong>To validate Vega PacBio sequencing for detecting mtDNA heteroplasmy, we analyzed four predefined mixtures of two mtDNA haplotypes. We generated a single long-range PCR amplicon covering the entire mitochondrial genome. These amplicons were mixed at predefined ratios (minor mixture haplotype component: 5%, 2%, 1%, and 0.1%). Variant calling was performed using Mutserve2, and accuracy was assessed by calculating the F₁ score from comparisons between expected and detected variants. Full-length mtDNA PacBio sequencing was applied to explore heteroplasmy across fibroblast passages derived from five LRRK2 p.Gly2019Ser variant carriers (n = 3 affected with PD and n = 2 unaffected carriers). Changes in mtDNA heteroplasmy level and variant load were assessed longitudinally using a linear mixed model as a proof-of-principle.</p><p><strong>Results: </strong>The single-amplicon approach enabled full-length haplotype resolution without amplification bias associated with overlapping PCR strategies. The F₁ score of the predefined mixtures was 1.0 for heteroplasmy levels between 5% and 1% and remained high (0.91) at 0.1%. At the specifically lowered calling threshold applied to the 0.1% mixture, n = 10/62 additional variants discordant with the Illumina reference were observed, but sensitivity remained very high at 1.00 in that mixture. Detected minor variants closely matched expected heteroplasmy levels, with average variant levels of 0.057 (5%), 0.022 (2%), 0.011 (1%), and 0.001 (0.1%). Across twelve fibroblast passages, we observed fewer mtDNA heteroplasmic variants. In this small proof-of-principle experiment, heteroplasmic variant load was higher in affected (n = 3) than in unaffected (n = 2) LRRK2 variant carriers and with older age. Notably, we observed distinct patterns of heteroplasmic variants that either increased or decreased in heteroplasmy level across passages.</p><p><strong>Conclusion: </strong>PacBio HiFi sequencing, combined with a single-amplicon strategy, enables accurate full-length mtDNA heteroplasmy detection and longitudinal analysis, providing a valuable tool for studying mitochondrial variation and dynamics in disease.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"27 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13651137/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149134992","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":"On the hunt for candidate genes involved in host-adaptation in Pseudomonas aeruginosa using comparative genomics.","authors":"Agata Marchi, Marcus Wenne, Vi Varga, Johan Bengtsson-Palme","doi":"10.1186/s12864-026-13405-3","DOIUrl":"https://doi.org/10.1186/s12864-026-13405-3","url":null,"abstract":"<p><strong>Background: </strong>Pseudomonas aeruginosa is an opportunistic pathogen responsible for causing severe hospital-acquired infections, largely due to its adaptability, diverse range of virulence factors and drug resistance mechanisms. Despite extensive research, a substantial portion of the genome of P. aeruginosa remains functionally uncharacterized. The aim of this study was to identify candidate host-adaptation genes, including potential virulence factors, among these numerous uncharacterized genes.</p><p><strong>Results: </strong>We performed a comparative genomic analysis of P. aeruginosa strains isolated from human clinical sources versus those from natural environments to identify clusters of homologous proteins significantly enriched with sequences from bacteria isolated from humans. Our analysis revealed that approximately 3% of all protein clusters showed significant enrichment in sequences from human isolates. Functional characterization of 45 selected clusters with particularly large enrichment of human isolates showed that these clusters contained genes with roles primarily related to host interaction and horizontal gene transfer. Notably, twelve of the 45 selected clusters consisted of genes with unknown function, suggesting the existence of potentially novel virulence factors or genes involved in the infection process within human-derived isolates.</p><p><strong>Conclusions: </strong>Our findings highlight specific uncharacterized protein clusters as promising targets for future investigation. The identification of both known virulence-associated functions and uncharacterized proteins among human-enriched clusters demonstrates the ability of our comparative genomics approach to detect established as well as potentially novel candidate host-adaptation genes. These findings further suggest that this strategy may be broadly applicable to the study of other opportunistic pathogens.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"27 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13637380/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149103936","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":"Genetic marker analysis of RAPGEF6 gene and covariance structure modelling for egg.","authors":"Mohammad Taghi Zarrinnia, Karim Hasanpur, Sadegh Alijani, Arash Javanmard, Majid Olyayee","doi":"10.1186/s12864-026-13373-8","DOIUrl":"10.1186/s12864-026-13373-8","url":null,"abstract":"<p><strong>Background: </strong>Egg production sustainability is economically critical for layer farms. The Marandi chicken, an indigenous breed from northwestern Iran (Azerbaijan region), possesses significant potential for efficient egg production, yet its genetic potential remains underexplored. This study aimed to investigate the association between single nucleotide polymorphisms (SNPs) in the RAPGEF6 gene and productive and reproductive traits in the Marandi chicken population.</p><p><strong>Methods: </strong>Performance and reproductive data were collected from 153 Marandi hens. Genotyping was performed using PCR-RFLP. Data were analyzed using two complementary approaches in SAS: a repeated-measure model (with eight covariance structures) for repeated egg weight measurements, and Generalized Linear Models (GLM) for the remaining growth and performance traits. Genotype frequencies for the studied SNPs were determined. Post-hoc statistical power analysis was conducted using GLMPOWER in SAS to evaluate the ability of the current sample size to detect observed effect sizes.</p><p><strong>Results: </strong>A significant association between one SNP and Maturity Weight (P = 0.014) was found in the present work, while no significant associations were found for the other 16 traits (P > 0.05). However, post-hoc power analysis revealed that the study had only 5% power to detect this effect, indicating that this finding is statistically unstable. The ARMA (1,1) model demonstrated good performance in accounting for the repeated egg weight measurements.</p><p><strong>Conclusions: </strong>Polymorphisms in the RAPGEF6 gene may influence growth traits in Marandi chickens, offering insights into the genetic underpinnings of performance. However, given the single-SNP design, the small sample size, and the severely limited statistical power (5%), all findings should be interpreted as exploratory and preliminary, warranting validation in independent, well-powered populations. No recommendations for marker-assisted selection can be made based on the current data. The optimal ARMA (1,1) covariance structure enhanced repeated-record analysis precision for egg-laying performance, facilitating a more consistent and reliable assessment of egg production patterns.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"27 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13670638/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149191315","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":"Genetic divergence and signatures of historical isolation of the traditionally harvested Amolops marmoratus from the Darjeeling Hill Region in the Himalaya Biodiversity Hotspot.","authors":"Kumaresh Mandal, Shishir Tamang, Soni Subba, Divya Rai, Saptaparni De, Shailesh Desai, Shristi Subba, Amit Singha Mahapatra, Noor A Nargis, Kaushik Deuti, Gyaneshwer Chaubey, Rakesh Tamang","doi":"10.1186/s12864-026-13367-6","DOIUrl":"https://doi.org/10.1186/s12864-026-13367-6","url":null,"abstract":"<p><strong>Background: </strong>The Darjeeling Hill Region (DHR) has numerous freshwater bodies, such as hill streams, springs, and temporary water pools. It receives abundant rainfall and has extensive forest cover, which together play vital roles in sustaining frog diversity. Amolops marmoratus is among the notable hillstream frogs, known for its wide geographic distribution and status as a local delicacy. Thus, A. marmoratus is an important subject for studying genetic divergence and population structure along with anthropogenic pressure. This research investigates the standard morphological characteristics and genetic relationships of A. marmoratus globally using 16S rRNA and COI gene sequences.</p><p><strong>Results: </strong>Our results revealed low estimates of nucleotide and gene diversity in A. marmoratus from the DHR, whereas comparatively higher values were observed in Southeast Asia, China, and Myanmar. Higher F_ST values were noted between the DHR populations and those from other Asian regions, whereas lower F_ST values were found among populations from Myanmar and Southeast Asia. However, these comparisons warrant caution given unequal sample sizes and the potential for cryptic lineage diversity within this taxonomically complex group. Phylogenetic analysis indicated distinct clades corresponding to different regions, with comparatively shorter branches and limited founders in the DHR group. The significantly negative Fu's Fs value, along with a unimodal mismatch distribution, indicated a deviation from demographic equilibrium reflecting a historical post-founder demographic expansion.</p><p><strong>Conclusion: </strong>These findings indicate strong regional differentiation for A. marmoratus. The inherently reduced genetic diversity of A. marmoratus in the DHR is consistent with historical demographic processes and geographic isolation. Furthermore, local frog-eating practices may act as a severe contemporary stressor on this already genetically depauperate population. We recommend framing conservation guidelines and increasing awareness among locals to promote a balanced ecosystem and ensure the long-term survival of A. marmoratus in the DHR.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"27 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13628901/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149103962","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 autotetraploid origin of the stress-tolerant wild beet Beta corolliflora.","authors":"Katharina Sielemann, Nicola Schmidt, Jonas Guzik, Natalie Kalina, Boas Pucker, Prisca Viehöver, Sarah Breitenbach, Tony Heitkam, Daniela Holtgräwe","doi":"10.1186/s12864-026-13276-8","DOIUrl":"10.1186/s12864-026-13276-8","url":null,"abstract":"<p><strong>Background: </strong>Most crop plants, including sugar beet (Beta vulgaris subsp. vulgaris), suffer from domestication bottlenecks and low genetic diversity caused by extensive selection for few traits. However, crop wild relatives (CWRs) harbour useful traits relevant for crop improvement, including enhanced adaptation to biotic and abiotic stresses. Especially polyploids are interesting from an evolutionary perspective as the genome undergoes reorganisation after the polyploidisation event. Through neo- and subfunctionalisation, novel gene functions emerge, which enable plants to cope with changing environments and extreme/harsh conditions. To introduce such resilience traits into breeding material, CWRs have already been identified as an important source for sustainable breeding. For beets, the section Corollinae contains the tetraploid species Beta corolliflora (2n = 4x = 36) that is believed to harbour salt and frost tolerances as well as a wealth of pathogen resistances. The number of beneficial traits of B. corolliflora is increased compared to those of the known diploids in this section (all 2n = 2x = 18). Nevertheless, neither the parental relationships of B. corolliflora have been resolved, nor are genomic resources available to steer sustainable, genomics-informed breeding.</p><p><strong>Results: </strong>To benefit from the resources offered by (polyploid) beet wild relatives, we generated and evaluated genome resources and assemblies for four different sugar beet wild relatives - Beta corolliflora (tetraploid), Beta lomatogona (diploid), Beta macrorhiza (diploid), and as an outgroup Patellifolia procumbens (diploid). We combined cytogenetic, k-mer-, and gene-based approaches that present strong evidence for the parental relationship of the B. corolliflora wild beet as an autotetraploid emerging from B. macrorhiza. Together with the publicly available genome sequences of two additional wild beets, we identified genomic regions absent from the cultivated beet, providing a sequence database harbouring traits relevant for future breeding endeavours.</p><p><strong>Conclusion: </strong>The provided evidence for the evolutionary history of wild beets, especially Beta corolliflora`s derivation from the diploid B. macrorhiza, resolves long-standing questions and highlights how genomic data can clarify crop evolution and support breeding.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"27 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13616124/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149058337","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}