BMC Genomics最新文献

{"title":"Genome-wide association analysis reveals genetic variations and candidate genes associated with tannin and starch contents in sorghum.","authors":"Xinqi Fan, Du Liang, Chenchen Wang, Yizhong Zhang, Qi Guo, Huiyan Wang, Chunhong Li, Xinlian Shen, Qingshan Liu, Peng Xu","doi":"10.1186/s12864-026-12914-5","DOIUrl":"https://doi.org/10.1186/s12864-026-12914-5","url":null,"abstract":"<p><strong>Background: </strong>Sorghum is the key grain for brewing distilled liquors. Grain composition, particularly tannin and starch levels, is closely linked to the sensory characteristics and yield of the final product. Developing elite sorghum cultivars with suitable tannin and elevated starch content is thus essential for producing liquors with diverse and distinct aroma profiles. Investigating the natural variations of grain composition in sorghum germplasms and identifying underlying genetic loci can facilitate the improvement of sorghum's nutritional value.</p><p><strong>Results: </strong>This study established near-infrared reflectance spectrometer (NIRS) non-destructive calibration models for determining sorghum tannin and starch contents based on phenotypic identification of 214 representative sorghum cultivars. A genome-wide association study (GWAS) of tannin and starch contents was performed based on two years and two locations of phenotypic data. A total of 18 associations with 338 single nucleotide polymorphisms (SNPs) scattered over 4 chromosomes were detected significantly associated with tannin and starch contents. Among these, two associations for tannin content and two associations for starch content were expressed in different environments, indicating that they were likely to be stable quantitative trait loci (QTLs). Through linkage disequilibrium (LD) block and haplotype analysis, a promising gene, Sobic.003G118266, which encodes chalcone synthase (CHS), was identified as orthologous to structural genes in known tannin synthesis pathways; while another promising gene, Sobic.004G353100, annotated as a glucose-6-phosphate translocator (G6PT), was determined to be a putative regulatory node in plant starch synthesis.</p><p><strong>Conclusion: </strong>These results provided important genetic variations and candidate genes to accelerate the improvement of sorghum breeding for liquor-brewing quality related traits.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147810870","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":"Single cell RNA sequencing reveals transitional states and signaling shifts in nephron progenitor cells of the late-gestation rhesus macaque kidney.","authors":"Kairavee Thakkar, Sunitha Yarlagadda, Lyan Alkhudairy, Andrew Potter, Konrad Thorner, Praneet Chaturvedi, Cristina Cebrian, Kyle W McCracken, Nathan Salomonis, Raphael Kopan, Meredith P Schuh","doi":"10.1186/s12864-026-12908-3","DOIUrl":"https://doi.org/10.1186/s12864-026-12908-3","url":null,"abstract":"<p><strong>Background: </strong>Human nephrogenesis is complete at 34-36 weeks gestation, with 60% of nephrons forming during the third trimester through lateral branch nephrogenesis (LBN). Currently, no mechanism exists for LBN as there are no late gestation human kidney transcriptional datasets. We hypothesized that an induced but dividing population of nephron progenitor cells (NPCs) would contribute to the amplification of nephrons in late gestation. We used the rhesus macaque, an established model of LBN, to help identify potential mechanisms.</p><p><strong>Methods: </strong>Single-cell RNA-sequencing (scRNA-Seq) was performed on cortically-enriched fetal rhesus kidneys (n = 9) from late second trimester and third trimester during LBN. This data was integrated with publicly available human scRNA-seq datasets from 8-18 weeks gestation kidneys (n = 8) using Harmony package. Differentially expressed genes and ligand-receptor interactions were assessed and validated using RNAScope™ on human and rhesus archival tissue.</p><p><strong>Results: </strong>Label transfer of previously defined kidney cell populations was performed on scRNA-seq data from 64,782 rhesus cells, including 7,879 nephron progenitor cells (NPCs) identified based on marker gene expression. Pseudotime analyses identified a late gestation-specific lineage branch of induced NPC in rhesus that was not observed in mid-gestation humans. Differential expression analyses identified increased SFRP1, FZD4, and TLE2 and decreased FZD7, SHISA2, SHISA3, and TLE4 within the late-gestation rhesus NPC compared to mid-gestation human NPC and increased SEMA3D within the rhesus ureteric bud (UB) tip, suggesting a compositional shift in WNT and SEMA signaling components within the naive NPC population during LBN.</p><p><strong>Conclusion: </strong>The rhesus macaque uniquely enables molecular studies of late-gestation primate nephrogenesis. Our study suggests the hypothesis that a transitional state of self-renewing NPCs supported by compositional shifts in key pathways may underlie the switch from branching phase nephrogenesis to lateral branch nephrogenesis and support ongoing nephron formation in late gestation. However, it remains to be determined if these changes within the late gestation NPC are time-dependent or species-dependent.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147810889","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":"Linking somatic mutations in cancer to the electronic properties of DNA.","authors":"Benoît de Witte, Cyril Karamaoun, Pauline Hermans, Maxime Tarabichi, Fabrizio Pucci, Marianne Rooman","doi":"10.1186/s12864-026-12879-5","DOIUrl":"https://doi.org/10.1186/s12864-026-12879-5","url":null,"abstract":"<p><p>Oxidative stress, generated by both endogenous and exogenous agents, can cause DNA lesions that, if not repaired, accumulate as somatic mutations and can contribute to cancer initiation. Here, we explored this problem through the lens of DNA electronic properties, quantified by the vertical ionization potential (vIP) of nucleobase motifs, which reflects their susceptibility to oxidation. We analyzed genome-wide experimental data on oxidative DNA damage and found that the highest damage levels occur in regions with low vIP values, suggesting a causal link between them. The analysis of cancer mutational signatures and their annotated aetiologies revealed strong anticorrelations between mutation frequency and vIP values, particularly in cancers driven by oxidative DNA damage, such as lung cancer. We further computed anticorrelations between vIP values and the frequencies of mutated motifs across coding and non-coding regions and across different mutation types, observing the strongest anticorrelations for silent mutations, consistent with their reduced selective pressure. Moreover, similar anticorrelations were observed for somatic mutations in cancer and normal tissues, as well as for germline mutations, suggesting that they arise from similar mutagenesis processes. This work clarifies how oxidative damage, DNA electronic properties and carcinogenesis are related and help identify genomic regions more prone to mutations.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147810817","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":"Genome-resolved metagenomics reveals unexpected diversity and host range of Candidatus Lariskella (Rickettsiales: Midichloriaceae).","authors":"Arno Hagenbeek, Yumiko Masukagami, Pradeep Palanichamy, Filip Husnik","doi":"10.1186/s12864-026-12881-x","DOIUrl":"https://doi.org/10.1186/s12864-026-12881-x","url":null,"abstract":"<p><p>The intracellular endosymbiont Candidatus Lariskella (Alphaproteobacteria, Candidatus Midichloriaceae) has been found across a wide diversity of terrestrial arthropods, including ticks, true bugs, beetles, fleas, wasps and moths. Despite its prevalence, little is known about the biology of Ca. Lariskella, nor do we grasp the full extent of its host range. Here, we report the first known occurrence of Ca. Lariskella infecting a population of free-living marine nematodes (Enoplida, Thoracostomopsideae). This novel nematode-infecting Ca. Lariskella was found to be closely related to insect-infecting strains, despite the drastic shift in both host taxonomy and habitat. TEM and FISH microscopy showed Ca. Lariskella is localized within both the nematode somatic cells and developing oocytes, confirming its status as a nematode endosymbiont and strongly suggesting maternal transmission. This finding led us to reassess the host range of Ca. Lariskella. We screened the SRA database for Ca. Lariskella sequences and performed genome-resolved metagenomics on SRA entries positive for Ca. Lariskella. We recovered 16 novel Ca. Lariskella metagenome-assembled genomes from SRA entries, including from novel hosts such as ants and treehoppers. However, we did not encounter further instances of Ca. Lariskella within nematodes or marine invertebrates, which we attribute to the relatively poor sampling of these groups. Overall, our findings illustrate the ability of Ca. Lariskella to infect both arthropods and nematodes as well as hosts from both terrestrial and marine environments.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147810867","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":"Identification of TSHB gene expression profile in Duolang sheep and its functional role in granulosa cells.","authors":"HuiPing Sun, LeXiao Zhu, GulMuhammad Shahbaz, RuoHuai Gu, ChengLong He, ShuXin Chen, ChaoFan Wang, Feng Xing, XiangLin Yan","doi":"10.1186/s12864-026-12757-0","DOIUrl":"https://doi.org/10.1186/s12864-026-12757-0","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"27 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13134140/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147810738","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 sequence of the ornamental plant Digitalis purpurea reveals the molecular basis of flower color and morphology variation.","authors":"Jakob Maximilian Horz, Katharina Wolff, Ronja Friedhoff, Boas Pucker","doi":"10.1186/s12864-026-12889-3","DOIUrl":"https://doi.org/10.1186/s12864-026-12889-3","url":null,"abstract":"<p><p>Digitalis purpurea (foxglove) is a widely distributed ornamental plant. Here, we present a long read sequencing-based genome sequence of a magenta flowering D. purpurea plant and a corresponding prediction of gene models. The high assembly continuity is indicated by the N50 of 4.3 Mbp and the completeness is supported by discovery of about 96% complete BUSCO genes. This genomic resource paves the way for an in-depth investigation of the flower pigmentation of D. purpurea. Structural genes of the anthocyanin biosynthesis and the corresponding transcriptional regulators were identified. The comparison of magenta and white flowering plants revealed a large insertion in the anthocyanidin synthase gene in white flowering plants that most likely renders this gene non-functional and could explain the loss of anthocyanin pigmentation. Furthermore, we found a large insertion in the DpTFL1/CEN gene to be likely responsible for the development of large terminal flowers.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"27 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13134276/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147810787","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 sequencing of MDR K. pneumoniae circulating in Moroccan river ecosystems: a comprehensive genomic analysis of environmental isolates.","authors":"Amine Aiddi, Ilham Zerdani, Aboubakr Khazaz, Hafsa Mguild, Adil El Hamouchi, Kaotar Nayme","doi":"10.1186/s12864-026-12903-8","DOIUrl":"https://doi.org/10.1186/s12864-026-12903-8","url":null,"abstract":"<p><strong>Background: </strong>Klebsiella pneumoniae is a major opportunistic pathogen and a recognized contributor to the global burden of antimicrobial resistance (AMR). Although traditionally associated with healthcare settings, it is increasingly detected in environmental compartments influenced by anthropogenic activities. Aquatic ecosystems may act as reservoirs and dissemination hubs for multidrug-resistant (MDR) lineages and resistance genes. However, genomic data on environmental K. pneumoniae in Morocco remain scarce. This pilot study aimed to characterize a targeted subset of MDR K. pneumoniae isolates recovered from Moroccan rivers using whole-genome sequencing (WGS), with a focus on resistance determinants, virulence-associated loci, plasmid content, and phylogenetic relationships.</p><p><strong>Results: </strong>The main findings revealed marked genetic heterogeneity among the environmental K. pneumoniae isolates. Of the 44 isolates recovered from six Moroccan rivers, 11 MDR isolates were selected for WGS and belonged to nine distinct sequence types, including the high-risk clones ST147 and ST307. Resistance to extended-spectrum β-lactams was mainly associated with ESBL genes, particularly bla_CTX-M-15, whereas carbapenem resistance was linked to bla_OXA-48 and bla_NDM-14 in a subset of isolates. The genomes also carried multiple determinants associated with resistance to other major antimicrobial classes. In addition, the isolates showed diverse plasmid backgrounds, heterogeneous virulence-associated loci, and substantial capsular diversity. Phylogenetic and pangenome analyses further indicated high intraspecific variability and extensive genome plasticity across the collection.</p><p><strong>Conclusions: </strong>This pilot study provides the first whole-genome-based characterization of river-derived MDR K. pneumoniae in Morocco. It demonstrates that aquatic ecosystems harbor genetically diverse lineages carrying clinically relevant resistance and virulence determinants. These findings underscore the imperative of integrating environmental surveillance into national AMR monitoring strategies within a One Health framework.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147810449","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":"Identification of a robust QTL hotspot across environments governing drought tolerance in lentil (Lens culinaris Medikus).","authors":"Dharmendra Singh, Ankita Tripathi, Jyoti Taunk, Kishore Gaikwad, Madan Pal","doi":"10.1186/s12864-026-12711-0","DOIUrl":"https://doi.org/10.1186/s12864-026-12711-0","url":null,"abstract":"<p><strong>Background: </strong>Drought stress significantly hinders the growth and productivity of many crops, including lentil. Hence, improving our understanding of the genetic and molecular bases underlying drought response is essential for mitigating yield losses under water-limited conditions. The primary objective of this study was to identify quantitative trait loci (QTLs) associated with various morpho-physiological traits using genotyping-by-sequencing (GBS) and to identify putative candidate genes contributing to drought tolerance in lentil.</p><p><strong>Result: </strong>A F₇ recombinant inbred line (RIL) population was developed to map QTLs for morpho-physiological traits including root and shoot length, fresh and dry weight of roots and shoots, drought score, seedling survivability, relative water content, proline, superoxide dismutase (SOD), glutathione peroxidase (GPX) enzyme activities and seed yield/plant under controlled (hydroponic) and rainout shelter conditions over multiple drought environments during 2021-2024. A 'hotspot QTL' cluster consisting of six QTLs was detected for drought tolerance related traits viz. seed yield/plant, fresh weight of roots and shoots and chlorophyll content on linkage group 7. These QTLs detected under four environments were found to be strongly linked with drought tolerance and explained 48.83% phenotypic variance on a cumulative basis. Furthermore, the hotspot harboured several drought responsive functionally annotated genes.</p><p><strong>Conclusion: </strong>The present study provides valuable insights into QTLs and SNPs associated with drought tolerance in lentil. The identification of a robust QTL hotspot region, together with key candidate genes, offers promising targets for fine mapping and development of marker assisted breeding strategies aimed at improving drought tolerance in lentil.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147810891","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":"Divided-and-combined association test for pleiotropic effects with GWAS summary statistics.","authors":"Boheng Hu, Yaoyao Chen, Xueqin Zheng, Hongping Guo","doi":"10.1186/s12864-026-12883-9","DOIUrl":"https://doi.org/10.1186/s12864-026-12883-9","url":null,"abstract":"<p><p>Many genome-wide association studies (GWAS) conducted over the past two decades have focused on testing the one-to-one association between genetic variants and complex diseases or phenotypes. Despite their considerable success, such one-to-one testing approaches are underpowered because they do not utilize information on pleiotropic effects. Currently available public GWAS summary statistics provide resources for multi-trait association testing. Quadratic statistics are widely used to detect pleiotropic effects, as they follow a chi-square or weighted chi-square distribution under the null hypothesis. Nevertheless, such methods often fail to achieve superior power. To address this limitation, this study proposes a divided-and-combined association test (DCAT) for detecting pleiotropic effects using GWAS summary statistics. DCAT constructs the covariance matrix of Z-scores by combining phenotype correlation and genotype partial correlation via the Kronecker product. It consists of a family of quadratic statistics with different covariance matrix weights and leverages the respective advantages of each statistic. The distribution of each statistic is then approximated using a location-shifted generalized gamma distribution for p-value calculation, with the resulting p-values integrated via the Cauchy combination test. Simulation results demonstrate that DCAT controls the type I error at a reasonable level and achieves the highest statistical power in most scenarios. In the real-data analysis of four cardiovascular diseases, DCAT identifies more significant genes compared with the other four representative methods.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147810729","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":"Transcriptomic and proteomic profiling of piroplasmosis resistance in Yunnan humped cattle.","authors":"Yuming Chen, Xiaona Chen, Rong Liu, Chunqing Li, Heng Xiao, Shanyuan Chen","doi":"10.1186/s12864-026-12897-3","DOIUrl":"https://doi.org/10.1186/s12864-026-12897-3","url":null,"abstract":"<p><strong>Background: </strong>Piroplasmosis, including Theileriosis and Babesiosis, poses a threat to livestock health and productivity worldwide. However, the molecular mechanisms underlying breed-specific differences in resistance to piroplasmosis remain poorly understood. Compared to Bos taurus, Bos indicus generally exhibits greater resistance to diseases such as piroplasmosis and trypanosomiasis, as well as enhanced adaptability to hot and humid environments. Yunnan humped cattle, an indigenous B. indicus breed, are well adapted to coarse feed and harsh environments, yet the molecular basis of their disease resistance has not been systematically investigated.</p><p><strong>Results: </strong>By integrating transcriptomic and proteomic analyses, we demonstrated that genetic background is the primary determinant shaping distinct immune response strategies between cattle breeds. Mucosal immunity and innate immunity emerged as key contributors to differential resistance to piroplasmosis. We identified several candidate genes and protein biomarkers highly expressed in Yunnan humped cattle, including CCL4, CCL5, IL1R2, IL5RA, BOLA, BOLA-DRB3, IFNB1, and the protein HPX. These candidates are likely to be directly or indirectly involved in host resistance to piroplasmosis and may have potential utility as molecular markers.</p><p><strong>Conclusions: </strong>This study improves our understanding of disease resistance in Yunnan humped cattle. The identified candidate genes and proteins may serve as molecular markers for marker-assisted breeding, offering a theoretical basis for developing cattle populations resistant to piroplasmosis.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147810503","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}