BMC genomic data最新文献

{"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}

{"title":"Transcriptomic analysis of maize leaves under different irrigation treatments in field conditions.","authors":"Yuan-Xin Li, Ru-Zhi Li, Jing Yang, Zhi-Wei Wang, Xiao-Guang Li, Hou-Zhen Yi, Xin-Ping Guo, Hang Zhou, Kai-Hua Jia, Peng-Fei Chu","doi":"10.1186/s12863-025-01302-9","DOIUrl":"10.1186/s12863-025-01302-9","url":null,"abstract":"<p><strong>Objectives: </strong>As one of the most widely cultivated agricultural crops in the world, maize (Zea mays L.) yield is often affected by water stress. In this study, we designed eight different irrigation levels in a field environment, covering a wide range of gradients, and conducted a comprehensive transcriptomic analysis of maize leaves under these eight treatments. The results revealed the molecular mechanisms by which maize responds to drought, optimal irrigation, and excessive irrigation in field conditions. This not only deepens our understanding of maize's response to water stress but also provides valuable genetic resources and theoretical insights for future genetic improvement.</p><p><strong>Data description: </strong>This study designed eight different irrigation levels under field conditions and conducted comprehensive transcriptome sequencing of maize ear leaf tissues. Analysis of the transcriptome data identified differentially expressed genes (DEGs), and principal component analysis (PCA) revealed a clear separation trend among samples under varying water conditions. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses highlighted functional categories associated with water response, cellular metabolism, and growth regulation. These findings provide valuable insights into the molecular mechanisms of maize under drought, optimal irrigation, and over-irrigation conditions, laying a foundation for future genetic improvement efforts.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"19"},"PeriodicalIF":1.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921481/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143665555","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":"Unveiling the complete genome sequence of Paenibacillus taichungensis: genomic features and biocontrol potential.","authors":"Shanwen Ding, Zijun Ma, Yafei Tang, Lin Yu, Zifu He, Xiaoman She","doi":"10.1186/s12863-025-01310-9","DOIUrl":"10.1186/s12863-025-01310-9","url":null,"abstract":"<p><strong>Objectives: </strong>The genus Paenibacillus encompasses a diverse group of Gram-positive bacteria with significant biotechnological potential. However, the research data and application cases of Paenibacillus taichungensis were still poorly understood. In this study, we isolated a P. taichungensis strain BB507, which demonstrated antibacterial effect on Ralstonia solanacearum species complex, and provided data and analysis of its complete genome.</p><p><strong>Data description: </strong>Strain BB507 was isolated from a pine rhizosphere in Meizhou city, Guangdong province of China, and showed antibacterial activity against Ralstonia solanacearum species complex. Complete genome was sequenced using Illumina NovaSeq (second-generation) and Oxford Nanopore (third-generation) platforms. The genome of BB507 comprised of a 6,974,531 bp circular chromosome and a 352,197 bp circular plasmid, encoding a total of 6,649 gene with an average gene length of 950 bp, 103 transfer RNAs, 2 sRNAs, and 36 rRNAs. Three candidate CRISPRs, 6 genomic islands and 14 prophages were predicted. The bacterial orthologous average nucleotide identity (OAT) and the type genome server (TYGS) analysis highlighted the strain BB507 was clustered into a subgroup with P. taichungensis. antiSMASH v7.0 predicted the presence of 10 secondary metabolite gene clusters in the genome. These findings will serve as a useful resource for further research in industrial and agricultural biotechnology.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"18"},"PeriodicalIF":1.9,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11912702/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143652416","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 sequencing highlights the fungal sclerotium formation of medicinal fungi Polyporus umbellatus.","authors":"Li Chi, Tianrui Liu, Zhongyi Hua, Pengjie Han, Honghong Jiao, Yuan Yuan","doi":"10.1186/s12863-025-01311-8","DOIUrl":"10.1186/s12863-025-01311-8","url":null,"abstract":"<p><strong>Objectives: </strong>Polyporus umbellatus is a well-known medicinal fungus in Asia. Due to its long growth cycle, wild resources of P. umbellatus are rapidly declining. Research on P. umbellatus growth is scarce, thereby impeding the investigation into the mechanism of sclerotium formation. In this study, the whole genome sequence of P. umbellatus was assembled and annotated.</p><p><strong>Data description: </strong>The generated genome was 79.74 Mb with an N50 of 969.73 Kbp, a GC content of 50.63%, encoding 10,864 protein-coding genes. Additionally, 82 ribosomal RNAs, 488 transfer RNAs, 25 small nuclear RNAs (snRNAs) and 741 micro RNA (miRNAs) were identified. This genomic resource will unveil molecular mechanisms of sclerotium formation and provides insight into the underlying molecular processes in medicinal fungi.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"17"},"PeriodicalIF":1.9,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11912782/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143652398","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 dataset of single-cell transcriptomic atlas of Bama pig and potential marker genes across seven tissues.","authors":"Long Chen, Xingyan Tong, Yujie Wu, Can Liu, Chuang Tang, Xu Qi, Fanli Kong, Mingzhou Li, Long Jin, Bo Zeng","doi":"10.1186/s12863-025-01308-3","DOIUrl":"10.1186/s12863-025-01308-3","url":null,"abstract":"<p><p>The use of single-cell sequencing technology for single-cell transcriptomics studies in pigs is expanding progressively. However, the comprehensive classification of cell types across different anatomical tissues and organs of pig in multiple datasets remains relatively limited. This study employs single-cell and single-nucleus sequencing technologies in Bama pig to identify unique marker genes and their corresponding transcriptomic profiles across diverse cell types in various anatomical tissues and organs, including subcutaneous fat, visceral fat, psoas major muscle, liver, spleen, lung, and kidney. Through detailed data analyses, we observed widespread cellular diversity across various anatomical tissues and organs of Bama pig. This work contributes a comprehensive dataset that supports physiological studies and aids in the identification and prediction of potential marker genes through single-cell transcriptomics of these tissues. The methodologies and data employed in this study are designed to improve the accuracy of cell type identification and ensure consistent cell type allocation.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"16"},"PeriodicalIF":1.9,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11899051/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143617683","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":"217 closed Salmonella reference genomes using PacBio sequencing.","authors":"Yan Luo, Jae Hee Jang, Maria Balkey, Maria Hoffmann","doi":"10.1186/s12863-025-01304-7","DOIUrl":"10.1186/s12863-025-01304-7","url":null,"abstract":"<p><strong>Objectives: </strong>Whole Genome Sequencing (WGS) is widely used in food safety for the detection, investigation, and control of foodborne bacterial pathogens. However, the WGS data in most public databases, such as the National Center for Biotechnology Information (NCBI), primarily consist of Illumina short reads which lack some important information for repetitive regions, structural variations, and mobile genetic elements, and the genomic location of certain important genes like antimicrobial resistance genes (AMR) and virulence genes. To address this limitation, we have contributed 217 closed circular Salmonella enterica genomes that were generated using PacBio sequencing to the NCBI Pathogen Detection (PD) database and GenBank. This dataset provides a higher level of accuracy to genome representations in the database.</p><p><strong>Data description: </strong>High-quality complete reference genomes generated from PacBio long reads can provide essential details that are not available in draft genomes from short reads. A complete reference genome allows for more accurate data analysis and researchers to establish connections between genome variations and known genes, regulatory elements, and other genomic features. The addition of 217 complete genomes from 78 different Salmonella serovars, each representing either a distinct SNP cluster within the NCBI PD database or a unique strain, significantly enriches the diversity of the reference genome database.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"15"},"PeriodicalIF":1.9,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11871702/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143531473","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 of the fungal pathogen Penicillium expansum (PPRI25879) isolated in South Africa.","authors":"Molemi Rauwane, Sandiswa Figlan, Wai Yin Chan, Khayalethu Ntushelo","doi":"10.1186/s12863-025-01299-1","DOIUrl":"10.1186/s12863-025-01299-1","url":null,"abstract":"<p><strong>Objectives: </strong>Penicillium expansum, a necrotrophic plant pathogen with a wide range of fruit hosts, is an important causal agent of blue mold rot. The fruit business suffers significant financial losses because of blue mold rot that occurs during fruit storage, transportation, and sale. The objective of this work was to generate a high-quality draft genome assembly of P. expansum, which will contribute to enhancing the management of blue mold, especially in stone and pome fruits, including grapes, by improving our understanding of the epidemiology of the pathogen and its interactions with the host.</p><p><strong>Data description: </strong>Here, we describe the genome sequence of Penicillium expansum isolate PPRI25879, one of the most virulent strains isolated from grapes in South Africa. Sequencing reads from P. expansum produced approximately 3.5 Gb. The assembly generated a draft genome of size 32.1 Mb, consisting of 1648 contigs, with an N50 of 508 KB. Examination of the genome completeness with Benchmarking Universal Single-Copy Orthologs (BUSCO) showed the draft genome carries 97.9% of the 746 genes in the Eurotiomycetes_odb10 database. The draft genome sequence will allow improved genomic comparisons among the most important pathogens belonging to the Penicillium genus, with the aim of improving our knowledge of their plant-pathogen interactions, population biology, and control.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"14"},"PeriodicalIF":1.9,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11846280/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143473366","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":"Transcriptome profiling across 11 different tissues in Pisum sativum.","authors":"Ru-Zhi Li, Guan Li, Xiao-Yan Zhang, Lei-Lei Li, Zhi-Wei Wang, Feng-Jing Song, Kai-Hua Jia, Na-Na Li, Peng-Fei Chu","doi":"10.1186/s12863-024-01287-x","DOIUrl":"10.1186/s12863-024-01287-x","url":null,"abstract":"<p><strong>Objectives: </strong>Peas (Pisum sativum) are vital for human nutrition and have significantly contributed to the understanding of Mendelian inheritance laws. In this study, we performed transcriptome sequencing on 11 distinct pea tissues, offering an extensive gene expression dataset. This study not only provides valuable insights into the gene expression patterns across various pea tissues but also lays the foundation for future research aimed at understanding the molecular mechanisms underlying pea growth, development, and response to environmental stimuli.</p><p><strong>Data description: </strong>In this study, we conducted transcriptome sequencing on tissue samples from 11 distinct pea plants, each with three biological replicates. This approach yielded a comprehensive RNA-seq dataset, abundant in transcriptomic information. Through principal component analysis (PCA) and gene ontology (GO) enrichment analysis, we identified significant variations in gene expression across different samples. This valuable transcriptomic resource enhances our understanding of gene expression in diverse pea tissues and provides new strategies, along with potential candidate genes, for the genetic improvement of peas.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"13"},"PeriodicalIF":1.9,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11841238/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143469249","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}