BMC genomic data最新文献

{"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":"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":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13154648/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147846757","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","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":"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":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13276951/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147824236","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","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":"10.1186/s12863-026-01426-6","url":null,"abstract":"<p><p>OBJECTIVES: Cladosporium tenuissimum, a widespread filamentous fungus belonging to the C. cladosporioides species complex, has been identified as a causal agent of sooty spot disease on postharvest fig fruits. Despite its ecological and agricultural importance, genomic resources for this species remain limited. Here, I report a draft genome sequence of C. tenuissimum strain SHK1100, isolated from symptomatic fig fruits in Japan, to facilitate comparative and functional genomic studies. DATA DESCRIPTION: The draft genome was assembled using long-read sequencing data, resulting in a total assembly length of 32.8 Mb, composed of 58 contigs with an N50 of 1.92 Mb and L50 of 8. The genome completeness of the assembly reached 98.0% in Benchmarking Universal Single-Copy Orthologs analysis with no contamination. In total, 12,016 protein-coding genes were predicted in the assembled genome. Functional annotation assigned putative functions to a large proportion of predicted genes, including annotations for 77.1% of genes into Clusters of Orthologous Groups, 33.7% of genes using Gene Ontology, and 21.6% of genes as putative effectors. This draft genome provides a foundation for understanding the pathogenic mechanisms and secondary metabolite biosynthesis of Cladosporium species associated with plant diseases.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13235164/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147790541","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","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":"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":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13231736/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147730790","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","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":"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":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13202964/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147663264","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bacterial community profiling of Malaysian drinking water reservoirs using metagenomic amplicon sequencing.","authors":"Muhammad Farhan Roslan, Mohd Faiz Mat Saad, Suriyanti Su Nyun Pau, Syazwani Basir, Habsah Aziz, Muhamad Afiq Akbar, Hamidun Bunawan","doi":"10.1186/s12863-026-01422-w","DOIUrl":"10.1186/s12863-026-01422-w","url":null,"abstract":"<p><p>OBJECTIVES: Microbial communities in freshwater are pivotal for driving nutrient transformation, bioremediation, and maintaining the health balance of these ecosystems. However, microbial communities in freshwater ecosystems may undergo rapid shifts in composition in response to environmental changes. In some cases, these shifts may signal ecological imbalance. In the tropics like Malaysia, high humidity coupled with high temperatures and seasonal rainfalls creates an even hotter and highly variable environmental conditions that promote microbial proliferation and increase the risk of introducing potentially pathogenic microorganisms from surrounding anthropogenic sources via surface runoff. The current study offers a comprehensive characterisation of bacterial community composition in Malaysian freshwater drinking reservoirs using high throughput 16 S rRNA gene amplicon sequencing. This approach enables bacterial community profiling and supports initial microbial risk assessment in these vital freshwater ecosystems. DATA DESCRIPTION: State Authorities permitted the collection of water samples from eight freshwater reservoirs within Peninsular Malaysia’s protective zones. The 16 S rRNA gene’s V3-V4 hypervariable region was amplified for next generation sequencing. Raw DNA sequence data in FASTQ format were quality-filtered, adapter-trimmed and processed using a QIIME v1.9.1 based pipeline that integrated standard bioinformatics tools for OTU clustering and taxonomic assignment. Utilising R v3.3.1, statistical analyses and data visualisations were performed on this dataset. Characterising the community structure of bacteria in these important freshwater ecosystems is the first step to working with this dataset.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13202894/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147655483","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A curated database of rumen ciliate protozoal 18S rRNA gene sequences for metataxonomic applications.","authors":"Katie Lawther, Ilma Tapio, Arturo Vera-Ponce de León, Velma T E Aho, Sharon A Huws, Nicholas J Dimonaco","doi":"10.1186/s12863-026-01420-y","DOIUrl":"10.1186/s12863-026-01420-y","url":null,"abstract":"<p><strong>Objectives: </strong>Protozoa are key members of the rumen microbiome playing significant roles in nutrient cycling and methane production, yet are understudied. As rumen metataxonomic studies increasingly incorporate protozoal primers, the lack of curated dedicated reference databases limits accurate classification. This dataset was developed to address that gap and support future protozoa-focused rumen microbial analyses.</p><p><strong>Data description: </strong>The curated dataset comprises 228 rumen ciliate protozoal 18S rRNA gene sequences sourced from publicly available datasets. Sequences were processed to remove redundancy and standardise naming. The final database spans 23 families, 53 genera, and 100 species, and is suitable for use in metataxonomic pipelines, including QIIME2. It provides a valuable resource for researchers aiming to improve taxonomic resolution of protozoal communities in rumen environments.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13088586/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147617217","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A pilot study revealed the gut microbiota based on 16S rRNA metagenomics in gestational diabetes.","authors":"Rizwana Kousar, Sadia Latif, Mahrukh Zahoor, Sidra Tabassum","doi":"10.1186/s12863-026-01413-x","DOIUrl":"10.1186/s12863-026-01413-x","url":null,"abstract":"<p><p>OBJECTIVE: Microbiome being a potential biomarker holds the future hope for insight into GD pathogenesis, diagnosis and cure. Many factors such as diet, lifestyle, environment, host genetics shape the diversity and composition of human microbiome. Although recent studies have indicated that gut microbiome dysbiosis was significantly associated with the onset of gestational diabetes mellitus (GDM). Information on the alteration of gut microbiota composition in Pakistani women is limited. Therefore, present study was designed to elucidate gut microbiota taxonomic composition and relative abundance of taxa in local GD women. DATA DESCRIPTION: 16S Metagenomics data revealed variation in bacterial community structure in gestational diabetic (GD), pregnant non-diabetic (PND), non-pregnant diabetic (NPD) and non-pregnant non-diabetic (NPND) women. Predominant bacterial phyla residing faecal sample of GD, NPD, PND included Firmicutes, Bacteriodota, Proteobacteria accounting for 95.07%, 97.1% and 97.04%, of relative abundance respectively. While Predominant phyla inhabiting faecal sample of NPND included firmicutes, Bacteriodota, and Actinobacteriodota accounting for 98.4%. Simpson’s Reciprocal Index showed great variability, the value ranged between 11.655 and 16.17. The distance matrix depicted dissimilarity between samples with dissimilarity coefficient values ranging between 0.381 and 0.588. These findings would pave the way for future studies, which will aid in early diagnosis, management and treatment. CLINICAL TRIAL NUMBER: Not applicable.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13151273/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147576673","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole-genome resequencing datasets of four Alternaria isolates obtained from carrot seeds.","authors":"Yuhan Ma, Feiyun Zhuang, Zhiwei Zhao, Zeyang Liu, Xiangping Yan, Xing Liu, Chenggang Ou","doi":"10.1186/s12863-026-01415-9","DOIUrl":"10.1186/s12863-026-01415-9","url":null,"abstract":"<p><p>OBJECTIVE: Carrot (Daucus carota) is a widely cultivated vegetable crop with high nutritional value. Alternaria is one of the most damaging fungal pathogens to carrots, responsible for diseases such as leaf blight and root rot. However, public genomic resources for carrot-associated Alternaria remain limited, and no genomic data have been reported for seed-transmitted pathogens of this genus to date. This Data Note presents resequencing datasets of four Alternaria isolates obtained from carrot seeds, which will support future research on pathogen diversity and population genetics. DATA DESCRIPTION: We isolated > 20 Alternaria-like isolates from carrot seeds collected from commercial seed production fields in Suzhou District of Jiuquan City and Jinta County of Jiayuguan City, Gansu Province, China (2023–2025; ~7–8 per year), delineated four species based on phenotypic characterization and multilocus sequencing of the ITS rDNA region (primers ITS1/ITS4) and the EF-1α gene (primers EF1-F/EF1-R), and resequenced one representative per species—A. tenuissima (AtD1), A. dauci (AdD3), A. carotiincultae (AcD3), and A. alternata (AaD2)—using paired-end 150-bp sequencing on an Illumina HiSeq/NovaSeq platform. Datasets are available in the NCBI SRA under BioProject PRJNA1344466 ( https://identifiers.org/ncbi/bioproject:PRJNA1344466 ) as four SRA Runs: SRR35781711, SRR35781712, SRR35781713, and SRR35781714.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13126878/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147488564","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Complete genome sequence of Streptococcus shenyangsis isolated from buccal mucosa.","authors":"Seok Bin Yang, Doyun Ku, Kyu Hwan Kwack, Ji-Hoi Moon, Jae-Hyung Lee","doi":"10.1186/s12863-026-01418-6","DOIUrl":"10.1186/s12863-026-01418-6","url":null,"abstract":"<p><p>OBJECTIVE: Streptococcus shenyangsis is a recently reported member of the genus Streptococcus, rarely detected in the human oral cavity and for which genomic information remains limited. To broaden our understanding of its genomic diversity and ecological relevance, we sequenced an oral isolate of S. shenyangsis obtained from a healthy Korean adult. DATA DESCRIPTION: Whole-genome sequencing was performed using the PacBio Sequel II platform. The genome of strain KHUD_015 consists of a single circular chromosome of 2,153,473 bp with a G + C content of 40.0% and 99.8% completeness. The strain encodes 1,906 protein-coding genes, four rRNA operons (5 S, 16 S, and 23 S), and 59 tRNAs. Comparative genomic analysis with the type strain D19ᵀ identified 1,506 core and a total of 586 strain-specific clusters across the two genomes. Of these, strain KHUD_015 harbors 349 unique gene clusters comprising 353 genes, mainly assigned to COG categories L (replication, recombination, and repair), K (transcription), and M (cell wall/membrane biogenesis), with additional genes related to V (defense mechanisms) and P (inorganic ion transport and metabolism). This complete genome represents the first oral isolate of S. shenyangsis and provides a valuable reference for future comparative and functional genomic studies investigating the population structure, metabolic potential, and ecological roles of this underexplored streptococcal species.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13123132/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147488596","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}