BMC genomic data最新文献

{"title":"Single-cell genomic analysis of cancer cells from one treatment-naïve patient with metastatic prostate cancer.","authors":"Juan Jovel, Bernhard Polzer, Jordan Patterson, Hou Yong, Catalina Vasquez, Sandra O'keefe, Desmond Pink, Guibo Li, Adrian Fairey, Benjamin Adam, Jeremy Teitelbaum, Amir Salimi, Stefan Kirsh, Barbara Alberter, Lori Lowes, Eric Carpenter, Michael Kolinsky, Zhongyi Zhu, Qing Zhou, Peter Venner, Christopher Venner, David Williams, Alison Allan, Paul C Boutros, Christoph A Klein, Gane Wong, John D Lewis","doi":"10.1186/s12863-026-01435-5","DOIUrl":"https://doi.org/10.1186/s12863-026-01435-5","url":null,"abstract":"<p><strong>Background: </strong>Prostate cancer is among the most prevalent malignancies in men and a leading cause of cancer mortality worldwide. While localized prostate cancer is often curable, progression to metastatic and castration-resistant disease either in lymph nodes or bone/bone marrow remains the major cause of death. Understanding the genomic events that drive metastasis-particularly in treatment-naïve patients-is critical to improving early detection and individualized therapy. Bulk tumor sequencing has revealed key mutational signatures but cannot resolve the cellular heterogeneity and clonal dynamics underlying metastatic spread. Single-cell genomic approaches now enable high-resolution dissection of tumor evolution, uncovering the diversity of cancer clones across disease sites.</p><p><strong>Results: </strong>We performed whole-genome and whole-exome sequencing on single cancer cells from a treatment-naïve patient with metastatic prostate cancer, isolating cells from the primary tumor, circulating tumor cells (CTCs), disseminated tumor cells (DTCs) in bone marrow, and metastatic bone lesions. Copy number aberrations (CNAs) and single-nucleotide variants (SNVs) were characterized to define genomic heterogeneity and infer clonal relationships. Frequent monoallelic losses in tumor suppressors (PTEN, TP53, FOXO4, STAG2) and gains in oncogenes (MTOR, RAF1, HRAS) and an angiogenic growth factor (VEGFB), were observed. Metastatic cells displayed fewer genomic alterations than CTCs or DTCs. While this observation is consistent with the hypothesis that metastatic competence may be associated with relative genomic stability, normal cell contamination of the metastatic biopsy cannot be excluded, and this interpretation should be considered preliminary. Clonal evolution analysis revealed a complex branching pattern consistent with multidirectional dissemination, suggesting bidirectional seeding between the primary tumor, circulation, and metastatic sites as one possible model of spread, though alternative explanations including phylogenetic reconstruction artefacts cannot be excluded from a single-patient study.</p><p><strong>Conclusions: </strong>This study provides a single-cell genomic map of metastatic prostate cancer from a treatment-naïve patient, highlighting the coexistence of diverse subclones across disease sites and supporting a multidirectional model of cancer spread.These findings raise the hypothesis that metastatic progression can emerge from multiple subclones with distinct CNA and SNV profiles. Single-cell genomic profiling of untreated tumors represents a promising approach to reconstruct clonal evolution and inform precision therapies targeting early metastatic lineages, though validation in larger patient cohorts will be required.</p><p><strong>Clinical trial number: </strong>Not applicable.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147846791","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A draft genome assembly of the planorbid snail Armiger crista (Hygrophila, Planorbiidae).","authors":"Panagiota Kotsakiozi, Marina Karoumpali, Erika Šlachtová, Elena Sarropoulou, Maria Stoumpoudi, Aristeidis Parmakelis","doi":"10.1186/s12863-026-01434-6","DOIUrl":"https://doi.org/10.1186/s12863-026-01434-6","url":null,"abstract":"<p><strong>Objectives: </strong>The draft genome assembly was generated within the framework of a greater study aiming to investigate the differences in genomic features characterizing freshwater gastropod species differing in their threat status according to the IUCN assessments.</p><p><strong>Data description: </strong>Mollusca is among the most species-rich animal groups, yet their genomes are underrepresented in genomic databases. Major drawbacks for this are the complexity of Mollusca genomes as well as the fact that due to the presence of mucopolysaccharides in their tissues, they tend to provide low quality DNA extracts. Therefore, the generation of high-quality Molluscan genome assemblies is a challenging issue. The A. crista draft genome of the present study will serve as an addition to the planorbid genomes assembled today representing three different genera (Anisus, Biomphalaria, Bulinus). Therefore, it will serve as an additional genomic asset in the effort to elucidate the ecology, evolution and taxonomy of the highly diverse taxon of Mollusca.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147857831","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic analysis of Toona sinensis leaves with eight different colors at various developmental stages.","authors":"Lei Wang, Mei Yu, Dan Wu, Zhi-Gang Bao, Lu Lu, Chun-Long Zhai, Kun Liu, Yi-Zeng Lu, Yong-Jun Zhao","doi":"10.1186/s12863-026-01433-7","DOIUrl":"https://doi.org/10.1186/s12863-026-01433-7","url":null,"abstract":"<p><p>Toona sinensis, a medicinal and edible plant, holds economic and ecological significance in Asia. Despite its diverse applications, the genetic basis of leaf color formation remains unclear. This study aimed to investigate the molecular mechanisms underlying color variations across three cultivars (red, brown, green) at different developmental stages. Young tender leaflets from apical tips and fully expanded leaflets from basal positions of the same compound leaf were collected for RNA-Seq analysis. Differential expression analysis revealed significant enrichment of genes involved in flavonoid biosynthesis, phenylpropanoid biosynthesis, and carotenoid metabolism pathways, suggesting their key roles in pigment accumulation. These metabolites are not only critical for coloration but also contribute to disease resistance and antioxidation. This research provides novel insights into the genetic regulatory networks governing leaf color formation in T. sinensis, facilitating molecular breeding for color trait improvement.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147857801","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"TrichoBase: a standardized genomic resource for comparative genomics of Trichoderma species.","authors":"Alsayed Alfiky, Said A Dora","doi":"10.1186/s12863-026-01429-3","DOIUrl":"https://doi.org/10.1186/s12863-026-01429-3","url":null,"abstract":"<p><p>The ecological versatility of the fungal genus Trichoderma spans roles from mycoparasite to saprotroph, presenting a compelling model to investigate how genomic variation underpins niche adaptation. However, comparative genomic studies of Trichoderma are hampered by inconsistent annotation methods across independently sequenced genomes, complicating direct cross-species analysis. To address this, we developed and applied a unified, evidence-based annotation pipeline integrating RNA-seq and homology data to six key species spanning the genus's ecological range (T. asperellum, T. harzianum, T. virens, T. reesei, T. longibrachiatum, and T. citrinoviride). This work presents 'TrichoBase', a consistently annotated genomic resource comprising standardized gene models, functional annotations, and comparative profiles. Using this comparable dataset, we confirm and quantitatively refine the correlation between transposable element (TE) accumulation and genome size expansion. We further demonstrate that TE-rich genomes of mycoparasitic strains are enriched in carbohydrate-active enzymes (CAZymes) and biosynthetic gene clusters (BGCs), while saprotrophic opportunistic lineages show streamlined profiles. Notably, the resource revealed patchy phylogenetic distributions of specific BGC families, such as sorbicillinoid and brefeldin A-like clusters. We provide the complete resource including annotation files, analysis scripts, and a reproducible pipeline to serve as a foundational dataset for future functional genomics and ecological studies in Trichoderma.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147846839","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chromosome-scale, single haploid assembly of achiote (Bixa orellana).","authors":"Meric C Lieberman, Margarita Aguilar-Espinosa, David Chan-Rodriguez, Luca Coma, Renata Rivera-Madrid, Isabelle M Henry","doi":"10.1186/s12863-026-01430-w","DOIUrl":"https://doi.org/10.1186/s12863-026-01430-w","url":null,"abstract":"<p><strong>Objectives: </strong>Bixa orellana, commonly known as achiote, is the domesticated species within the Bixa genus. It is a commercially important plant due to its high bixin content, primarily used as a pigment in the food industry. Achiote is a cross-pollinated, highly heterozygous species with a small genome size. This study aims to generate a de novo genome assembly of Bixa orellana L., which will be crucial for identifying the genes involved in bixin synthesis and its regulation. This assembly will offer valuable insights for future applications related to agronomical traits aimed at increasing bixin yield in achiote or different plant or microorganism systems, as well as for improving the genetic potential of achiote crops.</p><p><strong>Data description: </strong>A de novo assembly of the genome of Bixa orellana L., accession PN4 was generated from ~145 x consensus coverage of PacBio long reads. This Hifiasm assembly included 10 chromosome-scale superscaffolds representing 96.4% of the assembly, for an overall genome size of 270 Mb. Illumina RNA-Seq libraries from different tissues sampled from the same cultivar were used to annotate the genome.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"27 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147846793","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Shotgun metagenomic dataset of leaf endophytic microbiome of the garden sage (Salvia officinalis L.).","authors":"Mouliraj Palanisamy, Olubukola Oluranti Babalola, Sathishkumar Ramalingam","doi":"10.1186/s12863-026-01428-4","DOIUrl":"https://doi.org/10.1186/s12863-026-01428-4","url":null,"abstract":"<p><strong>Objectives: </strong>Garden sage (Salvia officinalis L.) is a traditional medicinal plant known for its rich bioactive secondary metabolites. However, there is limited information about the diversity of endophytic microbial communities, including bacteria, fungi, archaea, and viruses. Therefore, the study employs shotgun metagenomics to generate and make publicly available a dataset representing the leaf endophytic microbiome of Salvia officinalis.</p><p><strong>Data description: </strong>Metagenomic DNA was extracted from leaves of S. officinalis collected as three biological replicates and sequenced using the Illumina NovaSeq X platform. Host-derived and contaminant sequences were removed by mapping reads to the S. officinalis reference genome using BWA-MEM. The resulting high-quality FASTQ files were analyzed to characterize the taxonomic composition of the endophytic microbiome using Kraken2-based classification.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"27 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147846757","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"IMPDH1 is a potential immune evasion-related oncoprotein in endometrial cancer.","authors":"Yongning Chen, Fei Ma, Weichang Chen, Ruibin Jiang, Fei Wu, Shipeng Gong, Yadi Zhang","doi":"10.1186/s12863-026-01427-5","DOIUrl":"https://doi.org/10.1186/s12863-026-01427-5","url":null,"abstract":"<p><p>Endometrial cancer is one of the most common gynecologic malignancies, with increasing evidence suggesting the involvement of immune-related processes rather than direct immune evasion mechanisms in its progression. However, effective immune-related biomarkers for prognostic evaluation and therapeutic targeting remain limited. This study aimed to identify novel immune-associated molecules based on clinical endometrial cancer specimens using integrated proteomic and bioinformatic approaches. Proteomic analysis was performed on tumor and adjacent normal tissues from endometrial cancer patients. Differentially expressed proteins were screened and further analyzed through transcriptomic validation, survival analysis, immune infiltration assessment, and pathway enrichment to explore their clinical relevance and potential functional roles in the tumor immune microenvironment. IMPDH1 was identified as a significantly upregulated protein in endometrial cancer and was associated with unfavorable prognosis. High expression of IMPDH1 was correlated with reduced CD8⁺ T cell infiltration and features of an immunosuppressive tumor microenvironment. Functional enrichment suggested its involvement in purine metabolism and a potential role in immune-related processes. This study identifies IMPDH1 as a novel immune-related biomarker in endometrial cancer, with potential value for prognosis and immunotherapy.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147824236","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Draft genome sequence and annotation of fungal pathogen Cladosporium tenuissimum SHK1100 causing postharvest sooty spot of fig fruit.","authors":"Masahito Nakano","doi":"10.1186/s12863-026-01426-6","DOIUrl":"https://doi.org/10.1186/s12863-026-01426-6","url":null,"abstract":"","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147790541","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Complete genome sequence of Streptococcus periodonticum strain CRC221 isolated from human colorectal tumor tissue.","authors":"Jia-Su Li, Shu-Dan Chen, Jia-Quan Wu, Min-Xin Gao, Zhao-Shen Li, Yi-Qi Du, Wei-Liang Hou","doi":"10.1186/s12863-026-01425-7","DOIUrl":"https://doi.org/10.1186/s12863-026-01425-7","url":null,"abstract":"<p><strong>Objectives: </strong>Streptococcus periodonticum is a facultative anaerobic, Gram-positive coccus originally isolated from human periodontitis lesions and implicated in colorectal cancer pathogenesis. This study aimed to comprehensively characterize the genome of strain CRC221, isolated from human colorectal tumor tissue, to support future research on its potential role in tumorigenesis.</p><p><strong>Data description: </strong>Genomic DNA from strain CRC221 was sequenced using Illumina NovaSeq 6000 and PacBio platforms. The final assembly yielded a complete circular chromosome of 1,851,769 bp with 38.81% GC content. Structural annotation predicted 1,837 genes, comprising 1,707 protein-coding sequences (CDSs), 12 rRNAs, 59 tRNAs, 3 non-coding RNAs, and 56 pseudogenes. Functional annotation associated most CDSs with core bacterial survival pathways, particularly carbohydrate and amino acid metabolism. Notably, 94 genes were annotated as virulence factors, 68 as antibiotic resistance genes, and 319 as pathogen-host interaction factors. Comparative genomics revealed an ANI of 97.51% and a dDDH value of 71.8% against the reference S. periodonticum genome (GCA_003963555.1). Pan-genome analysis indicated an open genome architecture containing 199 conserved core genes. These genomic data provide a foundation for investigating the biological characteristics of intratumoral S. periodonticum and its potential relevance to colorectal cancer.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147730790","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Distinct physiological and transcriptomic responses between tolerant and susceptible rapeseed (Brassica napus) germplasm to flooding stress.","authors":"Ronghao Guo, Yongli Fu, Xing Su, Zhengda Ge, Wenxuan Chai, Yanni Zhao, Jungang Dong, Keqi Li, Weinan Sun, Zhen Huang, Chengyu Yu","doi":"10.1186/s12863-026-01423-9","DOIUrl":"https://doi.org/10.1186/s12863-026-01423-9","url":null,"abstract":"<p><p>Waterlogging and submergence are major abiotic stresses impairing rapeseed development and hence evaluation of submergence tolerance ability is crucial for the development of tolerant lines through breeding approaches. This study investigated submergence impact on the survival rate, physiological responses, and transcriptomic variation of the young seedlings of 706 Brassica napus germplasm. We identified 57 highly tolerant and 109 highly susceptible accessions underwent six days submergence. Most accessions originated from the downstream of Yangtze River region had higher tolerance level. SOD enzymic activity increased both in the five representative tolerant and susceptible genotypes under submergence stress. POD activity also increased in the tolerant genotypes whereas CAT activity decreased, showing a opposite trend compared to the susceptible genotypes. The tolerant genotypes showed less chlorosis and produced less malondialdehyde than that in the susceptible group, while soluble protein content increased more than that in the susceptible genotypes. Transcriptome analysis detected 5,072 and 5,063 up-regulated genes, as well as 3,512 and 3,889 down-regulated genes in the tolerant / susceptible group in comparison to their respective control. Many genes encoding the transcription factors in AP2/ERF, bHLH, MYB, WRKY, and NAC families were also significantly regulated. The differentially expressed genes shared by the two pairs comparison were mainly enriched in such KEGG pathways as circadian rhythm, tryptophan metabolism, and porphyrin and chlorophyll metabolism. The specific pathways in the tolerant group were enriched in carbon metabolism, phenylpropanoid biosynthesis, and biosynthesis of amino acid, while the susceptible group was more distributed in hormone signal transduction, sucrose and starch metabolism, and vitamin B6 metabolism etc. The results uncovered distinct physiological and transcriptomic differences between tolerant and susceptible genotypes.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147663264","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}