BMC Genomics最新文献

{"title":"Correction: Transcriptome-wide dynamics of m⁶A methylation in ISKNV and Sinopec chuatsi cells infected with ISKNV.","authors":"Qijin Miao, Jing Jiang, Siyou Huang, Jie Gao, Qingqing Liu, Rui Zheng, Yiling Kang, Changjun Guo, Jianguo He, Junfeng Xie","doi":"10.1186/s12864-026-13214-8","DOIUrl":"10.1186/s12864-026-13214-8","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"27 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13390428/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148560819","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of a pleiotropic QTL and candidate genes underlying ear traits of maize (Zea mays L.) through controlling the activity of inflorescence meristem.","authors":"Xiaomeng Shen, Yifei Wang, Luyuan Wang, Yan Bai, Fenglin Jiang, Luling Jiang, Xiangyin Hou, Jinsheng Lai, Liru Cao, Weibin Song","doi":"10.1186/s12864-026-13186-9","DOIUrl":"https://doi.org/10.1186/s12864-026-13186-9","url":null,"abstract":"<p><strong>Background: </strong>The ear of maize is a highly domesticated organ that has undergone a substantial increase in volume compared to its wild ancestor teosinte, resulting in a significant yield enhancement in modern cultivated maize. Application of quantitative trait loci (QTLs) mapping using the maize-teosinte segregation population facilitated the identification of more potential favorable variations for utilization in cultivation. However, the mature ear traits of the maize-teosinte population are influenced by genetic introgression from teosinte, which poses significant challenges to the investigation of yield-related traits due to abnormal sex differentiation of the inflorescence at the immature ear stage.</p><p><strong>Results: </strong>This study investigated mature ear traits along with the activity of the female inflorescence meristem (IM) using a Teosinte‑Maize introgression (TM) population via measuring the IM size. A total of 32 QTLs were detected across multiple environments over several years, with individual QTLs explaining 5.18% to 21.48% of the phenotypic variation. Notably, a major pleiotropic QTL regulating IM size and many ear traits was identified and narrowed to a 3.64 cM genetic interval on chromosome 3, namely qIM3. One candidate gene encoding ZmEREB147 (Zm00001d043205) was identified with the help of transcriptome data, and Gene Ontology (GO) analysis demonstrated that qIM3 is involved in several hormone-mediated pathways and meristem development.</p><p><strong>Conclusions: </strong>The rapid implementation of these findings in maize molecular breeding holds important potential application value and provides broad prospects for improving maize yield.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148547690","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":"Complete chloroplast genome of Sabia discolor Dunn and comparative analysis with related species from Sabiaceae.","authors":"Quan Lu, Peng Zhang, Xianglan Liang, Song Guo","doi":"10.1186/s12864-026-13209-5","DOIUrl":"https://doi.org/10.1186/s12864-026-13209-5","url":null,"abstract":"<p><strong>Background: </strong>Sabia discolor Dunn is an ethnomedicinally significant plant with underexplored genetic resources. To elucidate its chloroplast genome structure, evolutionary characteristics, and phylogenetic position within the genus Sabia, we sequenced and analyzed its complete chloroplast genome.</p><p><strong>Results: </strong>Using Illumina HiSeq™ platform for sequencing, followed by assembly with GetOrganelle and annotation with CPGAVAS2, we characterized the genome. The results showed that the chloroplast genome of S. discolor is a 161,581 bp circular DNA molecule with a typical quadripartite structure and a GC content of 39.25%. It harbors 129 genes, including 84 protein-coding genes, 8 rRNAs, and 37 tRNAs. We detected 80 simple sequence repeats (SSRs) and 55 long repeats. Codon usage bias analysis revealed a weak preference, with an effective number of codons (ENC) value of 49.01, primarily shaped by natural selection rather than mutation pressure. Comparative analysis identified a significant contraction in the inverted repeat (IR) regions and six highly variable regions (e.g., trnH-psbA, ndhF), which are proposed as potential molecular markers for species identification. Phylogenetic analysis based on complete chloroplast genomes revealed two major clades within Sabia, with S. discolor placed in Clade I, closely clustered with S. parviflora, S. limoniacea, S. fasciculata, and S. swinhoei, while S. dielsii formed a distinct basal lineage.</p><p><strong>Conclusions: </strong>This study provides fundamental genetic resources for future research on the conservation, phylogenetics, and molecular identification of S. discolor and its relatives.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148547729","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":"Two putatively novel loci associated with spike length and their breeding potential in Chinese endemic wheat.","authors":"Puyang Ding, Haopeng Zhang, Chao Wang, Tongzhu Wang, Md Nahibuzzaman Lohani, Jiating Chen, Xia Yang, Hafiz Muhammad Faisal Umer, Muhammad Junaid Jalil, Yunfeng Jiang, Guoyue Chen, Quan Xie, Jian Ma","doi":"10.1186/s12864-026-13201-z","DOIUrl":"https://doi.org/10.1186/s12864-026-13201-z","url":null,"abstract":"<p><p>Spike length (SL) is a key determinant of wheat spike architecture and yield potential. In this study, SL was evaluated across multiple environments in a panel of 182 Chinese endemic wheat accessions. Substantial phenotypic variation and high broad-sense heritability were observed, indicating strong genetic control. Genome-wide association study (GWAS) was performed using 38,490 high-quality SNPs under a mixed linear model incorporating population structure and kinship (Q + K). Four loci significantly associated with SL were identified on chromosomes 2B, 3B, 4A, and 7A, explaining 2.53-8.06% of the phenotypic variation. Two loci on chromosomes 4A and 7A co-localized with previously reported SL QTL within the linkage disequilibrium decay distance, confirming their genetic stability. In contrast, loci on chromosomes 2B (QSL.sau.2B) and 3B (QSL.sau.3B) reside in genomic regions not previously associated with SL, suggesting potentially novel genetic factors. Allelic effect analysis based on BLUP values revealed pleiotropic effects of SL-associated loci on spike density, spikelet number, plant height, and anthesis date. Notably, QSL.sau.3B was consistently associated with SL across environments and further supported through effect analysis in an additional wheat population of 220 accessions, confirming its stability and breeding relevance. These results advance understanding of the genetic architecture of SL and provide valuable resources for wheat improvement.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148535156","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":"Long-read transcriptome sequencing reveals isoform signatures in preeclamptic placentas.","authors":"Yancheng Song, YuTing Guo, Jie Wu, Debang Li, Xiaohua Wang, Yongchun Zuo, Yongqiang Xing","doi":"10.1186/s12864-026-13207-7","DOIUrl":"https://doi.org/10.1186/s12864-026-13207-7","url":null,"abstract":"<p><strong>Background: </strong>Preeclampsia is a major pregnancy-specific multisystem disorder that affects a substantial proportion of pregnancies globally and is a significant contributor to maternal and neonatal mortality. The molecular pathogenesis of this complex disease, however, remains elusive. Long-read sequencing technologies, with their ability to produce long, continuous reads, offer enhanced resolution for genomic studies. This study utilizes this technology to reveal novel insights at the isoform level in preeclamptic placentas.</p><p><strong>Result: </strong>In this study, we enrolled six participants, including three with normotensive pregnancies and three with preeclamptic pregnancies. By integrating Oxford Nanopore Technologies (ONT) long-read sequencing, Illumina short-read RNA-Seq, ATAC-seq, and Whole-Genome Bisulfite Sequencing (WGBS) of placental tissues, we generated an isoform-resolved transcriptome. We identified a total of 48,175 isoforms, encompassing 19,584 previously unannotated splice variants from known genes and 2,744 novel isoforms from the newly identified loci. Furthermore, we found that epigenetic modifications in promoter regions trigger alternative first exon usage, leading to additional novel isoforms of key preeclampsia regulators (e.g., ADARG1).</p><p><strong>Conclusion: </strong>This study expands the known transcriptomic landscape of the human placenta, revealing tens of thousands of previously unannotated isoforms. Integration of cross-platform validation and multi-omics datasets not only confirmed the robustness of these findings but also provided insights into their potential biological functions. The resources generated here establish a valuable foundation for future investigations into placental development and the molecular mechanisms of preeclampsia.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148547708","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":"Identifying candidate genes for trichome traits in grapevine through a genome-wide association study.","authors":"Zhongyi Yang, Yuxuan Zhou, Lingling Hu, Qianqian Zheng, Congling Fang, Shuyi Zhou, Chao Yu, Yangshengkai Xu, Liufei Huang, Tao Jiang, Yueyan Wu","doi":"10.1186/s12864-026-13158-z","DOIUrl":"https://doi.org/10.1186/s12864-026-13158-z","url":null,"abstract":"<p><p>As the primary organ for photosynthesis in plants, the leaf surface trichomes play crucial roles in modulating light energy absorption and defending against biotic and abiotic stresses. The characteristic distribution of trichomes on grape leaves serves as an important diagnostic trait for cultivar identification, yet their genetic regulatory mechanisms remain poorly understood. In this study, we performed the first genome-wide association study (GWAS) on seven leaf trichome-related traits in grapevine. Utilizing resequencing data from 153 grape accessions combined with two-year phenotypic observations, we identified 201 significant single nucleotide polymorphisms (SNPs) consistently detected across both years, and further screened 314 candidate genes. These SNPs were distributed across 16 chromosomes, with chromosome 16 harboring the highest number of associated loci. Functional enrichment analysis revealed that the candidate genes were primarily involved in transcriptional regulation, ubiquitination modification, signal transduction, and cell wall metabolism. RT-qPCR validation confirmed that several candidate genes were highly expressed in young leaves, with significantly higher transcript levels in densely trichomatous cultivars compared to sparse-trichome varieties. Notably, the expression levels of VIT_18s0001g14070, VIT_05s0077g01370, VIT_05s0020g01710, and VIT_15s0046g01010 showed significant positive correlations with trichome density. This study provides new insights into the genetic basis of leaf trichome formation in grapevine and offers valuable references for breeding stress-resistant grape cultivars. Importantly, we highlight a grapevine-specific signal: a significant association interval enriched with multiple stilbene synthase genes (e.g., the VIT_16s0100g00770 cluster), suggesting a potential mechanistic link between trichome architecture and stilbenoid-mediated chemical defense. Collectively, the stable SNPs and candidate genes reported here provide immediate resources for developing breeder-friendly markers and accelerating marker-assisted selection to improve grapevine resilience to biotic stresses.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148547725","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":"Mammalian-evolved strains of the fungal pathogen Cryptococcus neoformans show adaptation via heritable transcript level differences specific to mouse MHC haplotype.","authors":"Carter B Ayers, Matthew J Nalley, Hiten D Madhani, Wayne K Potts, Erin E McClelland, Rebecca L Seipelt-Thiemann","doi":"10.1186/s12864-026-13196-7","DOIUrl":"https://doi.org/10.1186/s12864-026-13196-7","url":null,"abstract":"<p><strong>Background: </strong>Organisms adapt to novel environments using changes to genome, gene expression, and protein functions. This study focused on changes that had occurred when a fungal pathogen previously encountered hosts that differed only at the major histocompatibility complex (MHC) region, loci that control immune recognition during the adaptive immune response. To investigate how this fungal pathogen adapted to the host environment, next generation sequencing data were examined from strains of Cryptococcus neoformans (C. neoformans) that had been previously passaged eight times through congenic mice that specifically differed at the MHC locus, H2. Transcript levels and the genomic sequence for each post-adapted fungal strain were examined to identify molecular adaptation strategies via heritable gene expression changes (epigenetic changes) and mutation (DNA changes).</p><p><strong>Results: </strong>The post-adapted strains displayed repeated changes in transcript levels, as determined by RNA-sequencing. Some of these epigenetically regulated genes (ERGs) only occurred in strains passaged in MHC specific hosts, suggesting possible prior adaptations to specific host MHCs. To our knowledge, this is the first time ERGs have been reported as possible pathogen adaptations to specific host MHC alleles. Additionally, of the total 47 single nucleotide polymorphisms (SNPs) identified, 7 SNPs each were found in 2 or more fungal strains (of the 6 analyzed strains) passaged through different MHC congenic hosts, suggesting much of the fungal mutation-based adaptation was to the mouse host, and not MHC-specific.</p><p><strong>Conclusions: </strong>These data demonstrated that these passaged C. neoformans strains adapted to the MHC haplotype of a novel mammalian host environment primarily via epigenetic rather than mutation-based mechanisms.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148535021","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":"Integrating whole-genome resequencing data reveals adaptive selection signatures under extreme environments of goat populations in China.","authors":"Kaijie Yang, Jie Dong, Wannian Wang, Ke Cai, Jianhua Liu, Liying Qiao, Wenzhong Liu","doi":"10.1186/s12864-026-13176-x","DOIUrl":"https://doi.org/10.1186/s12864-026-13176-x","url":null,"abstract":"<p><p>With the increasing frequency of extreme weather events globally, livestock are facing ever-increasing demands for environmental adaptability. Some goat populations have demonstrated remarkable adaptability under long-term extreme environmental stress, and their genomes retain characteristic genetic imprints formed by adaptive evolution. This study integrated whole-genome resequencing data from 496 individuals from 29 endemic goat populations in China, along with data from 11 environmental factors. Through signal selection analysis and genome-environment association analysis, we identified 262 candidate genes associated with environmental adaptation. Subsequently, we screened Chinese goat populations in extreme environments based on environmental data. We used the FST and θπ methods to scan the genomes of these goat populations. In four extreme environments (high elevation, hot, and arid), 95, 74, and 162 candidate genes were identified, respectively. Based on research related to environmental adaptation, we found that genes such as FGF5, CAMK4, COL4A3BP, and CACNG4 may play important roles in goat adaptation to extreme environments. This study not only deepens our understanding of the evolutionary mechanisms of environmental adaptation in Chinese goats, but also provides important theoretical basis for goat stress resistance breeding and germplasm resource conservation.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148535078","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":"Temporal transcriptomic and lipidomic analysis reveals multi-omics dynamic profiles of B. napus seed germination.","authors":"Bo Zhang, Junyan Wu, Li Ma, Haiqing Liu, Wancang Sun, Jianfeng Duan","doi":"10.1186/s12864-026-13202-y","DOIUrl":"https://doi.org/10.1186/s12864-026-13202-y","url":null,"abstract":"<p><strong>Background: </strong>Lipids represent the major storage reserve in Brassica napus seeds. During germination, lipid mobilization delivers indispensable energy to support seedling establishment, thereby profoundly influencing germination vigor and subsequent seedling growth capacity. Although lipid mobilization is fundamentally required for successful rapeseed germination, the temporal coordination between transcriptional reprogramming and lipid metabolic conversion remains largely elusive, and the underlying molecular regulatory network remains to be systematically deciphered.</p><p><strong>Results: </strong>We conducted an integrated transcriptomic and lipidomic analysis on dry B. napus seeds and germinating seeds at 6, 12, 24, and 48 h after imbibition. The results revealed distinct stage-specific characteristics of gene expression and lipid metabolism during germination. In the early imbibition stage, differentially expressed genes (DEGs) were primarily enriched in biological processes related to water transport, stress response, and signal transduction, whereas significant changes in lipid metabolism were observed to be relatively delayed. During the initiation of germination, triacylglycerols (TGs) underwent rapid degradation, accompanied by a significant up-regulation of genes involved in the β-oxidation and gluconeogenesis pathways. In the late germination stage, genes responsible for membrane lipid synthesis were sharply up-regulated, which induced extensive membrane lipid remodeling.</p><p><strong>Conclusion: </strong>This work represents the first systematic integration of transcriptomic and lipidomic data focusing on dynamic changes during the germination stage in B. napus, systematically illustrating the global molecular and lipid metabolic features of rapeseed seeds across sequential imbibition stages. It further delineates stage-specific expression patterns of key functional genes and lipid metabolites throughout germination. Collectively, these results advance our comprehensive understanding of the regulatory networks controlling rapeseed seed germination, and offer reliable theoretical references and candidate gene resources for breeding high-yield and high-quality B. napus varieties.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148535161","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":"Global profiling of the protein lactylome in porcine liver.","authors":"Shuhao Fan, Shunyao Lu, Jinyu Guan, Yu Li, Wei Li, Yueyun Ding, Xianrui Zheng, Zongjun Yin, Xiaodong Zhang","doi":"10.1186/s12864-026-13200-0","DOIUrl":"https://doi.org/10.1186/s12864-026-13200-0","url":null,"abstract":"<p><p>Given the significant physiological and metabolic similarities between pig liver and human liver, along with the importance of pigs as excellent clinical models (successful xenotransplantation and survival in humans), this study presents for the first time a comprehensive lactylation map of the pig liver, revealing that protein lactylation (Kla) is a widespread and functionally important modification in this metabolically active organ. Through high-resolution mass spectrometry, we conducted a global analysis of lactylated proteins and sites in healthy pig liver, identifying 4,110 Kla sites on 1,486 proteins. Bioinformatics feature analysis indicated that these proteins are mainly located in the cytoplasm, mitochondria, and nucleus, and are significantly enriched in core metabolic pathways including glycolysis, the tricarboxylic acid cycle, and the pentose phosphate pathway. Motif analysis identified specific sequence patterns around lactoylated lysines. Comparative analysis showed that specific histone lactylation sites (such as H3K23, H2AK96, H2BK5) are conserved in pigs, mice, and humans, while also revealing tissue-specific characteristics compared to pig ovarian cells. These findings emphasize the close connection between liver lactylation and cellular energy metabolism, and provide a valuable comparative framework for studying the role of lactylation in human liver physiology and disease.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148534882","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}