BMC genomic data最新文献

{"title":"Profiling the full-length transcriptome of plasma cell mastitis via nanopore sequencing.","authors":"Su Li, Hongyue Chen, Yan Fan, Can Wang, Lijing An, Qifeng Xu, Wenming Cai, Suzhen Zhao, Tian Tian, Baoyong Zhang, Mengmeng Yang, Lulu Zhang","doi":"10.1186/s12863-025-01312-7","DOIUrl":"https://doi.org/10.1186/s12863-025-01312-7","url":null,"abstract":"<p><strong>Introduction: </strong>In this study, we aimed to determine the transcriptomic profile of plasma cell mastitis (PCM) and elucidate its underlying mechanisms using nanopore sequencing technology (ONT).</p><p><strong>Methods and results: </strong>Through comparisons and analyses of redundantly removed transcripts with known reference genome annotations, we identified 39,408 novel transcripts and 20,980 genes. By exploring full-length transcriptome data, we characterized selective splicing, selective polyadenylation events, and simple sequence repeat (SSR) site information, which enhanced our understanding of genome annotation and gene structure in plasma cell mastitis. Additionally, we investigated predicted transcription factors and LncRNAs, screening those with differences for further investigations. The GO and KEGG enrichment analysis of differentially expressed genes (DEGs) and differentially expressed transcripts (DETs) revealed subtle distinctions between them, with primary enrichments being in immune response and intercellular interactions. Our protein-protein interaction (PPI) analysis of hub proteins from DETs indicated up-regulated genes' involvement in immune response and down-regulated genes' role in cell adhesion. Furthermore, we assessed immune cell infiltration in plasma cell mastitis, observing various immune cells, such as B cells, T cells, and DC cells.</p><p><strong>Conclusion: </strong>These preliminary findings offer novel insights into the pathogenesis of plasma cell mastitis and present promising ideas for optimizing personalized treatment approaches, warranting further exploration and follow-up studies.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"29"},"PeriodicalIF":1.9,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12001594/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144042586","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 assembly of the largemouth bass (Micropterus salmoides).","authors":"Tao Zhu, Hongmei Song, Jinxing Du, Caixia Lei, Jing Tian, Chenghui Wang, Chuanju Dong, Shengjie Li","doi":"10.1186/s12863-025-01318-1","DOIUrl":"https://doi.org/10.1186/s12863-025-01318-1","url":null,"abstract":"<p><strong>Objective: </strong>Largemouth bass (Micropterus salmoides, LMB) is an important species in aquaculture, and the annual production is rapidly increasing. Genetic and breeding studies related to LMB have promising applications, and a high-quality genome assembly is essential for interpreting genetic and sequencing data. In this study, we sequenced the genome of a male LMB using the PacBio Sequel platform, high-throughput chromosome conformation capture (Hi-C), and paired-end Illumina sequencing. Additionally, Full-length transcript sequencing was performed using isoform sequencing (Iso-Seq). Following the assembly and annotation, a draft assembly for male LMB was obtained.</p><p><strong>Data description: </strong>This work generated PacBio data of 164.5 Gb, Hi-C data of 113.4 Gb, Illumina data of 54.7 Gb, and Iso-Seq data of 22.8 Gb. The assembly revealed that the LMB genome has a total length of 877.7 Mb, with an N50 of 37.2 Mb, comprising 23 chromosomes and 202 scaffolds. Annotation results indicated that 32.8% of the genome consists of repetitive sequences, containing 23,952 coding genes with an average gene length of 17,328 bp.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"28"},"PeriodicalIF":1.9,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12001621/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144047333","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":"Correlation of rice yield based on RILs population QTL analysis.","authors":"Junrong Liu, Xinyi Lou, Lin Zhang, Tiangang Hou, Xin Xin, Yan Wang, Shu Wang, Yuancai Huang, Chanchan Zhou, Baoyan Jia, Yue Feng","doi":"10.1186/s12863-025-01316-3","DOIUrl":"https://doi.org/10.1186/s12863-025-01316-3","url":null,"abstract":"<p><p>Rice production has been a primary concern in crop quality breeding. In this study, India japonica variety M494 and indica variety Z9B were used as parents. Hybridization and selfing were conducted to obtain recombinant inbred lines (RILs) as the experimental material. The F₃ and F₇ populations were analyzed to determine six yield-related traits, including panicle length, effective panicle number, number of grains per panicle, seed setting rate, yield per plant, and grain density. QTL mapping of rice yield-related traits and tillering angle was performed using the SSR molecular marker linkage map, resulting in the identification of 19 QTLs controlling panicle length, grain number per panicle, effective panicle number, seed setting rate, grain density.Additionally, multiple regression analysis and path analysis were employed to investigate the relationship between different agronomic traits and rice yield in the F₇ population. An optimal regression equation, Y_YPP = -24.515 + 0.694X_PL + 1.273X_PN + 0.007X_PPG + 18.981X_SSR was derived, and it was concluded that SSR was the trait with the greatest impact on YPP, followed by PL.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"27"},"PeriodicalIF":1.9,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11995468/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144042141","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":"Shotgun metagenomics dataset of the core rhizo-microbiome of monoculture and soybean-precedent carrot.","authors":"Olubukola Oluranti Babalola, Alaba Adewole Adebayo, Ben Jesuorsemwen Enagbonma","doi":"10.1186/s12863-025-01320-7","DOIUrl":"https://doi.org/10.1186/s12863-025-01320-7","url":null,"abstract":"<p><strong>Objectives: </strong>Carrot is a significant vegetable crop contributing to agricultural diversity and food security, but less is known about the core microbiome associated with its rhizosphere. More so, the effect of preceding crop and cropping history on the composition and diversity of carrot rhizo-microbiome remains largely unknown. With shotgun metagenomics, the study unveils how cropping systems direct rhizo-microbiome structure and functions, previously limited by other methods.</p><p><strong>Data description: </strong>Metagenomic-DNA molecule was extracted from four replicates each (12 samples) of a distant bulk soil and the rhizosphere soils from monoculture and soybean-precedent carrots, with the Power soil® DNA Isolation kit. The DNA samples were subjected to Next Generation Sequencing using the Illumina Novaseq X Plus (PE 150) platform. Raw sequencing reads were assembled and annotated with MEGAHIT and LCA algorithms in MEGAN software respectively, before a quality control check was done with FASTP. CD-Hit was used to de-replicate the sequences and the removal of host genomic-DNA and contaminant sequences was done with Bowtie2. The clean sequence data, in FastQ files, were analyzed for taxonomic classification and functional diversity of the rhizosphere microbiome using the Micro_NR and KEGG database respectively. The findings provide insights into microbiome dynamics, with potential implications for sustainable agricultural practices.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"26"},"PeriodicalIF":1.9,"publicationDate":"2025-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11993964/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144043824","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":"The chromosome-level genome of water hyacinth (Eichhornia crassipes).","authors":"Zhihao Qian, Jingshan Yang, Zhizhong Li, Jinming Chen","doi":"10.1186/s12863-025-01317-2","DOIUrl":"10.1186/s12863-025-01317-2","url":null,"abstract":"<p><strong>Objectives: </strong>Water hyacinth (Eichhornia crassipes) is one of the most notorious invasive aquatic plants in the world and is known to cause significant ecological and socioeconomic impacts. Here, we reported a high-quality chromosome-level genome for water hyacinth, which will be a valuable reference for future investigations of its invasion.</p><p><strong>Data description: </strong>A chromosome-level genome for water hyacinth was constructed by combing MGI short-reads sequencing, PacBio HiFi (High-fidelity) sequencing, and Hi-C sequencing, which resulted in ca. 1132.2 Mb in size the contig and scaffold N50 length of 18.76 Mb and 69.84 Mb, respectively. A total of 1024.36 Mb (90.47%) of the assembled sequences were anchored to 16 pseudochromosomes, dividing into subgenome A (468.72 Mb in size) and subgenome B (555.64 Mb in size). A total of 57,683 protein-coding genes were predicted, including 25,445 protein-coding genes for subgenome A and 27,992 protein-coding genes for subgenome B. Furthermore, the LAI and QV scores of the water hyacinth genome were 12.32 and 48.91, respectively.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"25"},"PeriodicalIF":1.9,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11980121/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143813193","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":"First fine mapping of a strain of Rhizoctonia Solani AG-3, causing tobacco target spot.","authors":"Pan Ma, Mengjuan Qiu, Rubing Xu, Zhao Wang, Tom Hsiang, Junbin Huang, Lu Zheng, Yanyan Li","doi":"10.1186/s12863-025-01315-4","DOIUrl":"10.1186/s12863-025-01315-4","url":null,"abstract":"<p><strong>Objectives: </strong>Rhizoctonia solani AG-3 is the casual pathogen of tobacco target spot, a serious fungal disease of tobacco that severely decreases yield and quality. To examine the pathogenic mechanisms of this fungus, it is crucial to understand its genetics. The objective of this work was to generate the first fine mapping of a R. solani AG-3 strain from tobacco and to explore potential virulence genes, which will lay the foundation for genetic characterization and its interaction with tobacco. The functional genes involved in this study can be used as the candidates for follow-up experimental analyses.</p><p><strong>Data description: </strong>Rhizoctonia solani AG-3 strain XEMS25-1 was isolated from disease leaves of tobacco target spot in Enshi, Hubei Province, China. The DNA was sequenced using Pacific Biosciences Sequel II (PacBio) and Illumina NovaSeq PE150 (Nova). Data from both sequencing platforms were combined, and the de novo assembly yielded an estimated 39.4 Mb genome. Completeness of the genome examined using Benchmarking Universal SingleCopy Orthologs (BUSCO) showed that the assembly had 93.7% of the 758 genes in fungi_odb10. PHI (Pathogen Host Interactions) database analysis revealed 519 reduced virulence genes, 91 loss of pathogenicity genes, 28 hypervirulence genes and 18 effectors might be the pathogenicity-related genes in R. solani AG-3 strain XEMS25-1. These genes could be selected as the RNA-silencing targets for exploring the molecular mechanisms of R. solani AG-3 pathogenicity on tobacco.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"24"},"PeriodicalIF":1.9,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11963629/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143774753","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":"Haplotype-resolved and gap-free genome of a floating aquatic plant from the Oryzeae tribe, Hygroryza aristata.","authors":"Li-Yao Yang, Li-Kun Huang, Jin-Bin Lin, Cun-Jing Xu, Wei-Qi Tang, Bi-Guang Huang","doi":"10.1186/s12863-025-01314-5","DOIUrl":"10.1186/s12863-025-01314-5","url":null,"abstract":"<p><strong>Objectives: </strong>Hygroryza aristata, an aquatic plant native to Southeast Asia, shows a high degree of adaptability to aquatic environments. H. aristata, which belongs to the Oryzeae tribe and is closely related to rice (Oryza sativa), holds potential for crop improvement, particularly in flood tolerance. This study aimed to sequence and assemble the genome of H. aristata.</p><p><strong>Data description: </strong>We assembled the genome of H. aristata using 31.91 Gb of Pacific Biosciences (PacBio) High-fidelity (HiFi) data and 22.36 Gb of ultra long Oxford Nanopore Technology (ONT) data, resulting in two gap-free haplotype genomes, hap1 (349.74 Mb) and hap2 (347.98 Mb), each with 12 chromosomes and 23 telomeres. The continuity of chromosomes was supported by High-throughput chromosome conformation capture (Hi-C) data. The assemblies demonstrated high completeness, with > 99.8% of coverage rates, 98.4% of Benchmarking Universal Single-Copy Orthologs (BUSCO) scores, and > 11.0 of Long Terminal Repeat Assembly Index (LAI) scores per haplotype. RNA sequencing (RNA-seq) data (176.06 Gb) of six tissues was generated for genome annotation, identifying 39,139 and 38,746 protein-coding genes in hap1 and hap2, respectively.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"23"},"PeriodicalIF":1.9,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11951829/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143733437","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":"The genome assembly of the farmed European whitefish Coregonus lavaretus L. from the Finnish selective breeding programme.","authors":"Kisun Pokharel, Daniel Fischer, Terhi Iso-Touru, Ilma Tapio, Miika Tapio, Tuomas Leinonen, Antti Kause","doi":"10.1186/s12863-025-01313-6","DOIUrl":"10.1186/s12863-025-01313-6","url":null,"abstract":"<p><strong>Objectives: </strong>European whitefish (Coregonus lavaretus L.) is a freshwater salmonid that inhabits cold regions of central and north Europe and Siberia. It is an important aquaculture species in Finland, selectively bred since 1999. The breeding programme has applied genomic selection that uses SNP markers and phenotypic data to improve traits such as growth, product quality, and fish health. Salmonids are known for chromosomal rearrangements, and the current C. lavaretus reference genome that is based on an individual from Switzerland may deviate from the Finnish one. Therefore, we have assembled a genome for the Finnish European whitefish. This allows us to better assess the genetic basis of fish traits and to enhance the accuracy of genomic selection.</p><p><strong>Data description: </strong>The genome of European whitefish was sequenced using a combination of Illumina and PacBio technologies and assembled using wtbg2 and HiRise software. The assembly has a size of 2.94 Gb and comprises 6,706 scaffolds with the scaffold N50 of 1.36 Mb.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"22"},"PeriodicalIF":1.9,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11934727/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143702409","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 high-quality chromosome-level genome assembly of Antiaris toxicaria.","authors":"Weicheng Huang, Jiaxin Xiang, Yamei Ding, Wanzhen Liu, Ni Fang, Yongmei Xiong, Seping Dai, Hui Yu","doi":"10.1186/s12863-025-01309-2","DOIUrl":"10.1186/s12863-025-01309-2","url":null,"abstract":"<p><strong>Objectives: </strong>Antiaris toxicaria is a tall tree belonging to the Moraceae family, known for its medicinal value. Its latex contains various cardiac glycosides, which hold significant research and potential application value. However, the lack of genomic resources for A. toxicaria currently hinders molecular genetic studies on its medicinal components. For its effective conservation and elucidation of the distinctive genetic traits of and medical components, we present its chromosome-level genome assembly.</p><p><strong>Data description: </strong>Here, we assembled two haplotypes of A. toxicaria, including a 671.73-Mb HapA subgenome containing 27,213 genes and a 666.41-Mb HapB subgenome containing 28,840 genes. Their contig N50 sizes were 90.18 and 90.29 Mb, respectively. The transposable elements represented 61.15% and 64.13% of the total assembled genome in HapA and HapB subgenome, respectively. A total of 27,213 and 28,840 genes were predicted in the two haplotypes. Hopefully, this chromosome-level genome of A. toxicaria will provide a valuable resource to enhance understanding of the biosynthesis of medicinal compounds.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"21"},"PeriodicalIF":1.9,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11934813/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143702407","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":"Genome-wide identification and characterization of stress-responsive genes in Chlorella vulgaris.","authors":"Yasmeen Khizar, Umer Farooq, Kotb A Attia, Obaid Ur Rehman, Asmaa M Abushady, Sajid Fiaz, Umar Zeb, Rashid Iqbal, Muhammad Uzair","doi":"10.1186/s12863-025-01307-4","DOIUrl":"10.1186/s12863-025-01307-4","url":null,"abstract":"<p><strong>Background: </strong>Chlorella vulgaris is a significant green alga that has a role in the bioremediation of environmental pollutants, especially heavy metals. Therefore, to meet the emerging needs of sustainable bioremediation, it is the need of the hour to improve the bioremediation potential of Chlorella vulgaris. Stress-related genes play significant roles in homeostasis and stress management in algal species, including C. vulgaris. It deals with varying pH and temperature, toxic heavy metals, oxidative stress, and many others. While certain stress-responsive proteins such as Heat Shock Proteins (HSPs) and Antioxidant Enzymes have been previously reported in C. vulgaris, this study aims to expand the scope by identifying and characterizing a diverse range of genes from various gene families, many of which have not been studied before in C. vulgaris.</p><p><strong>Method: </strong>A comprehensive analysis of the stress-related genes was conducted in which comparative phylogenetic analysis; conserved motif detection, determination of gene structure, and their subcellular localization were performed.</p><p><strong>Results: </strong>As a result of this study, 15 stress-related genes in C. vulgaris were annotated and characterized. The phylogenetic analysis represented that these genes evolved independently in C. vulgaris. Twenty highly conserved motifs amino acid structures have been exhibited. These motifs have a potential role in stress management. The proteins are localized at different locations in the cells. In parallel to genome-wide analysis, an experiment was conducted in a wet lab to evaluate the growth curve of C. vulgaris under Cd and pH stress.</p><p><strong>Conclusions: </strong>The results revealed a probability that C. vulgaris has some mechanisms and genes that act as key players for survival. Moreover, this study not only provides identification and characterization of stress-related genes but also lays the foundation for further identification, annotation, and confirmation by expression profiling under different stress conditions such as toxic heavy metals and pH.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"20"},"PeriodicalIF":1.9,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11927275/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143677443","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}