BMC genomic data最新文献

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A resource of longitudinal RNA-seq data of Holstein cow rumen, duodenum, and colon epithelial cells during the lactation cycle. 荷斯坦奶牛泌乳周期瘤胃、十二指肠和结肠上皮细胞纵向RNA-seq数据资源。
IF 1.9
BMC genomic data Pub Date : 2025-01-27 DOI: 10.1186/s12863-025-01295-5
Yahui Gao, George E Liu, Li Ma, Cong-Jun Li, Ransom L Baldwin
{"title":"A resource of longitudinal RNA-seq data of Holstein cow rumen, duodenum, and colon epithelial cells during the lactation cycle.","authors":"Yahui Gao, George E Liu, Li Ma, Cong-Jun Li, Ransom L Baldwin","doi":"10.1186/s12863-025-01295-5","DOIUrl":"10.1186/s12863-025-01295-5","url":null,"abstract":"<p><strong>Objective: </strong>As one of the most important ruminant breeds, Holstein cattle supply a significant portion of milk and dairy for human consumption, playing a crucial role in agribusiness. The goal of our study was to examine the molecular adaptation of gastrointestinal tissues that facilitate milk synthesis in dairy cattle. DATA DESCRIPTION: We performed RNA-seq analysis on epithelial cells from the rumen, duodenum, and colon at eight different time points: Days 3, 14, 28, 45, 120, 220, and 305 in milk, as well as the dry period. Samples were taken from five multiparous dairy cows as biological replicates per tissue per stage, except for Days 14 and 28, for which the sample size was three. These tissues each serve critical and distinct roles in the digestion and absorption of nutrients and are all vital for providing the necessary substrates required for milk production. Understanding the intricate connections between the tissues involved in providing nutrients necessary to support milk synthesis and their role in digestion can deepen the understanding of lactation physiology. This resource aims to deliver in-depth insights into cattle lactation, highlighting the distinct traits of gastrointestinal tissues and illuminating the intricate transcriptomic dynamics throughout the lactation period.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"9"},"PeriodicalIF":1.9,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11773790/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143054409","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}
引用次数: 0
Genome sequence resources for three strains of the genus Clonostachys. 龙葵属三株基因组序列资源。
IF 1.9
BMC genomic data Pub Date : 2025-01-24 DOI: 10.1186/s12863-025-01297-3
Zongping Sun, Fan Zhang, Nana Zhong, Kang Zhou, Jun Tang
{"title":"Genome sequence resources for three strains of the genus Clonostachys.","authors":"Zongping Sun, Fan Zhang, Nana Zhong, Kang Zhou, Jun Tang","doi":"10.1186/s12863-025-01297-3","DOIUrl":"10.1186/s12863-025-01297-3","url":null,"abstract":"<p><strong>Objective: </strong>Clonostachys, a genus with rich morphological and ecological diversity in Bionectriaceae, has a wide distribution among diverse habitats. Several studies have reported Clonostachys fungi as effective biological agents against multiple fungal plant pathogens. To clarify the diversity and biocontrol mechanisms of the Clonostachys fungi, this study was undertaken to sequence and assemble the genomes of two C. chloroleuca and one C. rhizophaga.</p><p><strong>Data description: </strong>Here, we performed genomic sequencing of three strains of genus Clonostachys collected from the China General Microbiological Culture Collection Center (CGMCC) using Illumina HiSeq 2500 sequencing technology. Whole genome analysis indicated that their genomes consist of 58,484,224 bp with a GC content of 48.58%, 58,114,960 bp with a GC content of 47.74% and 58,450,453 bp with a GC content of 48.58%, respectively. BUSCO analysis of the genome assembly indicated that the completeness of these genomes was at least 98%. In summary, these datasets provide a valuable resource for ongoing studies that include further exploration of biological function, marker development, enhanced biological control ability of Clonostachys fungi, and population diversity.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"8"},"PeriodicalIF":1.9,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11758714/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143043828","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}
引用次数: 0
Complete genome sequence of Pseudomonas aeruginosa YK01, a sequence type 16 isolated from a patient with keratitis. 从角膜炎患者分离的16型铜绿假单胞菌YK01的全基因组序列。
IF 1.9
BMC genomic data Pub Date : 2025-01-22 DOI: 10.1186/s12863-025-01298-2
Shuo Jiang, Mengmin Ye, Ke Liu, Huiluo Cao, Xiaoshan Lin
{"title":"Complete genome sequence of Pseudomonas aeruginosa YK01, a sequence type 16 isolated from a patient with keratitis.","authors":"Shuo Jiang, Mengmin Ye, Ke Liu, Huiluo Cao, Xiaoshan Lin","doi":"10.1186/s12863-025-01298-2","DOIUrl":"10.1186/s12863-025-01298-2","url":null,"abstract":"<p><strong>Objectives: </strong>Pseudomonas aeruginosa, a Gram-negative opportunistic pathogen, is frequently associated with multidrug resistance and global epidemic outbreaks, contributing significantly to morbidity and mortality in hospitalized patients. However, P. aeruginosa belonging to the sequence type (ST) 16 was rarely reported. Here, this report presents the complete genome sequence of YK01, a ST16 P. aeruginosa isolate from a patient with keratitis. The complete reference genome of P. aeruginosa YK01 is expected to provide valuable data for investigating its genomic population, enhancing understanding of genetic basis of P. aeruginosa species complex.</p><p><strong>Data description: </strong>A complete genome of 6.3 Mb was obtained for P. aeruginosa YK01 by combining Illumina 150-bp short reads and Nanopore long reads. The assembly is fully complete with chromosomal genome size of 6,183,266 bp, presenting a GC content of 66.7%, and a plasmid with the size of 46,067 bp, presenting GC content of 59.0%. Predicted chromosomal genomic features include 5,709 CDS, 12 rRNAs, 63 tRNAs, 4 ncRNAs, and 5,788 genes. To our knowledge, this genome data represents the first complete genome of P. aeruginosa ST16, providing crucial information for further comparative genome analysis.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"7"},"PeriodicalIF":1.9,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11753164/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143026070","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}
引用次数: 0
Assembly and characterization of the complete mitogenome of Bauhinia purpurea (Leguminosae). 紫荆(豆科)有丝分裂全基因组的组装与鉴定。
IF 1.9
BMC genomic data Pub Date : 2025-01-20 DOI: 10.1186/s12863-025-01296-4
Siqi Xie, Yong Chen, Danjing Zheng, Shukai Luo, Shiyuan Meng, Yan Zhong
{"title":"Assembly and characterization of the complete mitogenome of Bauhinia purpurea (Leguminosae).","authors":"Siqi Xie, Yong Chen, Danjing Zheng, Shukai Luo, Shiyuan Meng, Yan Zhong","doi":"10.1186/s12863-025-01296-4","DOIUrl":"10.1186/s12863-025-01296-4","url":null,"abstract":"<p><strong>Objective: </strong>Mitochondrial genome sequences are very useful for understanding the mitogenome evolution itself and reconstructing phylogeny of different plant lineages. Bauhinia purpurea, a species from the legume family Leguminosae, is widely distributed in South China and has high ornamental value. Here, we sequenced and assembled the mitogenome of B. purpurea to provide a useful genetic resource for further evolutionary studies.</p><p><strong>Data description: </strong>We assembled and characterized the complete mitogenome of B. purpurea based on Illumina sequence data. The mitogenome size was 525,727 bp, and its GC content was 45.38%. A total of 35 protein-coding genes, 16 tRNA genes, and 3 rRNA genes were identified in the mitogenome. We also identified 124 pairs of repeats and 6 mitogenome sequences of plastid origin (MTPTs). These MTPTs range from 108 bp to 751 bp, covering 0.65% of the mitogenome.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"6"},"PeriodicalIF":1.9,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11744893/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143017246","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}
引用次数: 0
Complete genome sequence of Pseudarthrobacter sp. NIBRBAC000502770 from coal mine of Hongcheon on Republic of Korea. 韩国洪川煤矿产假节杆菌sp. NIBRBAC000502770全基因组序列。
IF 1.9
BMC genomic data Pub Date : 2025-01-17 DOI: 10.1186/s12863-025-01300-x
Min-Kyu Park, Yeong-Jun Park, Myung-Suk Kang, Min-Ha Kim, Soo-Young Kim, Jae-Ho Shin
{"title":"Complete genome sequence of Pseudarthrobacter sp. NIBRBAC000502770 from coal mine of Hongcheon on Republic of Korea.","authors":"Min-Kyu Park, Yeong-Jun Park, Myung-Suk Kang, Min-Ha Kim, Soo-Young Kim, Jae-Ho Shin","doi":"10.1186/s12863-025-01300-x","DOIUrl":"10.1186/s12863-025-01300-x","url":null,"abstract":"<p><strong>Objectives: </strong>The data were collected to obtain the complete genome sequence of Pseudarthrobacter sp. NIBRBAC000502770, isolated from the rhizosphere of Sasamorpha in a heavy metal-contaminated coal mine in Hongcheon, Republic of Korea. The objective was to explore the strain's genetic potential for plant growth promotion and heavy metal resistance, particularly arsenate and copper. The aim focused on identifying microbes that enhance plant growth in metal-tolerant environments and evaluating the strain's bioremediation and agricultural uses. This study sought key genes for bioremediation and agricultural applications in contaminated soils, aiding sustainable management and biotechnology.</p><p><strong>Data description: </strong>We report the complete genome sequence of Pseudarthrobacter sp. NIBRBAC000502770, isolated from a coal mine in Hongcheon, Republic of Korea. The genome contains a chromosome (4,403,796 bp) and a plasmid (74,326 bp, named pMK-1) with 286-fold coverage. Genome annotation identified 4,209 genes, including 3,926 protein-coding genes, 51 tRNA genes, and 15 rRNA genes, with a G + C content of 66.1%. Functional analysis revealed genes related to plant growth promotion and heavy metal resistance, such as arsenate (arsR, arsC) and copper (copC, copD) resistance genes. Genes involved in auxin biosynthesis suggest potential agricultural applications. The genome and plasmid are available in GenBank (CP041198.1, CP014497.1), offering insights into bioremediation and plant growth in metal-contaminated environments.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"5"},"PeriodicalIF":1.9,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11740416/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143017272","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}
引用次数: 0
Establishing a GRU-GCN coordination-based prediction model for miRNA-disease associations. 建立基于GRU-GCN协调的mirna -疾病关联预测模型。
IF 1.9
BMC genomic data Pub Date : 2025-01-14 DOI: 10.1186/s12863-024-01293-z
Kai-Cheng Chuang, Ping-Sung Cheng, Yu-Hung Tsai, Meng-Hsiun Tsai
{"title":"Establishing a GRU-GCN coordination-based prediction model for miRNA-disease associations.","authors":"Kai-Cheng Chuang, Ping-Sung Cheng, Yu-Hung Tsai, Meng-Hsiun Tsai","doi":"10.1186/s12863-024-01293-z","DOIUrl":"10.1186/s12863-024-01293-z","url":null,"abstract":"<p><strong>Background: </strong>miRNAs (microRNAs) are endogenous RNAs with lengths of 18 to 24 nucleotides and play critical roles in gene regulation and disease progression. Although traditional wet-lab experiments provide direct evidence for miRNA-disease associations, they are often time-consuming and complicated to analyze by current bioinformatics tools. In recent years, machine learning (ML) and deep learning (DL) techniques are powerful tools to analyze large-scale biological data. Hence, developing a model to predict, identify, and rank connections in miRNAs and diseases can significantly enhance the precision and efficiency in investigating the relationships between miRNAs and diseases.</p><p><strong>Results: </strong>In this study, we utilized miRNA-disease association data obtained by biotechnological experiments to develop a DL model for miRNA-disease associations. To improve the accuracy of prediction in this model, we introduced two labeling strategies, weight-based and majority-based definitions, to classify miRNA-disease associations. After preprocessing, data was trained with a novel model combining gated recurrent units (GRU) and graph convolutional network (GCN) to predict the level of miRNA-disease associations. The miRNA-disease association datasets were from HMDD (the Human miRNA Disease Database) and categorized by two distinct labeling approaches, weight-based definitions and majority-based definitions. We classified the miRNA-disease associations into three groups, \"upregulated\", \"downregulated\" and \"nonspecific\", by regression analysis and multiclass classification. This GRU-GCN coordinated model achieved a robust area under the curve (AUC) score of 0.8 in all datasets, demonstrating the efficacy in predicting potential miRNA-disease relationships.</p><p><strong>Conclusions: </strong>By introducing innovative label-preprocessing methods, this study addressed the relationships between miRNAs and diseases, and improved the ambiguity of the results in different experiments. Based on these refined label definitions, we developed a DL-based model to refine and predict the results of associations between miRNAs and diseases. This model offers a valuable tool for complementing traditional experimental methods and enhancing our understanding of miRNA-related disease mechanisms.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"4"},"PeriodicalIF":1.9,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11734345/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142985591","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}
引用次数: 0
Integrated metabolomic and transcriptomic analysis of anthocyanin metabolism in wheat pericarp. 小麦果皮花青素代谢的综合代谢组学和转录组学分析。
IF 1.9
BMC genomic data Pub Date : 2025-01-13 DOI: 10.1186/s12863-024-01294-y
Jiao Wang, Lei Sun, Bo Jiao, Pu Zhao, Tianyun Xu, Sa Gu, Chenmin Huo, Jianzhou Pang, Shuo Zhou
{"title":"Integrated metabolomic and transcriptomic analysis of anthocyanin metabolism in wheat pericarp.","authors":"Jiao Wang, Lei Sun, Bo Jiao, Pu Zhao, Tianyun Xu, Sa Gu, Chenmin Huo, Jianzhou Pang, Shuo Zhou","doi":"10.1186/s12863-024-01294-y","DOIUrl":"10.1186/s12863-024-01294-y","url":null,"abstract":"<p><strong>Background: </strong>Wheat seeds display different colors due to the types and contents of anthocyanins, which is closely related to anthocyanin metabolism. In this study, a transcriptomic and metabolomic analysis between white and purple color wheat pericarp aimed to explore some key genes and metabolites involved in anthocyanin metabolism.</p><p><strong>Results: </strong>Two wheat cultivars, a white seed cultivar Shiluan02-1 and purple seed cultivar Hengzi151 were used to identify the variations in differentially expressed genes (DEGs) and differentially accumulated flavonoids (DAFs). Based on metabolomic data, 314 metabolites and 191 DAFs were identified. Chalcone, flavonol, pro-anthocyanidin and anthocyanidin were the most differentially accumulated flavonoid compounds in Hengzi151. 2610 up-regulated and 2668 down-regulated DEGs were identified according to transcriptomic data. The results showed that some structural genes in anthocyanin synthesis pathway were prominently activated in Hengzi151, such as PAL, CAD, CHS and so on. Transcription factors (TFs) of MYB, bHLH, WD40 and some other TFs probably involved in regulating anthocyanin biosynthesis were identified. Some genes from hormone synthetic and signaling pathways that may participate in regulating anthocyanin biosynthesis also have been identified.</p><p><strong>Conclusions: </strong>Our results provide valuable information on the candidate genes and metabolites involved in the anthocyanin metabolism in wheat pericarp.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"3"},"PeriodicalIF":1.9,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11727400/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142980939","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}
引用次数: 0
ERBB3-related gene PBX1 is associated with prognosis in patients with HER2-positive breast cancer. erbb3相关基因PBX1与her2阳性乳腺癌患者的预后相关
IF 1.9
BMC genomic data Pub Date : 2025-01-10 DOI: 10.1186/s12863-024-01292-0
Shufen Mo, Haiming Zhong, Weiping Dai, Yuanyuan Li, Bin Qi, Taidong Li, Yongguang Cai
{"title":"ERBB3-related gene PBX1 is associated with prognosis in patients with HER2-positive breast cancer.","authors":"Shufen Mo, Haiming Zhong, Weiping Dai, Yuanyuan Li, Bin Qi, Taidong Li, Yongguang Cai","doi":"10.1186/s12863-024-01292-0","DOIUrl":"10.1186/s12863-024-01292-0","url":null,"abstract":"<p><strong>Background: </strong>HER2-positive breast cancer (BC) is a subtype of breast cancer. Increased ERBB3 expression has been implicated as a potential cause of resistance to other HER-targeted therapies. Our study aimed to screen and validate prognostic markers associated with ERBB3 expression by bioinformatics and affecting the prognosis of HER2 staging.</p><p><strong>Methods: </strong>Analyzing differences in ERBB3-related groups. ERBB3 expression-related differentially expressed genes (DEGs) were identified and intersected with survival status-related DEGs to obtain intersected genes. Three algorithms, LASSO, RandomForest and XGBoost were combined to identify the signature genes. we construct risk models and generate ROC curves for prediction. Furthermore, we delve into the immunological traits, correlations, and expression patterns of signature genes by conducting a comprehensive analysis that encompasses immune infiltration analysis, correlation analysis, and differential expression analysis.</p><p><strong>Results: </strong>Significant variability in ERBB3 expression and prognosis in high and low ERBB3 expression groups. Twenty-five candidate DEGs were identified by intersecting ERBB3-related DEGs with survival-related DEGs. Utilizing three distinct machine learning algorithms, we identified three signature genes-PBX1, IGHM, and CXCL13-that exhibited significant diagnostic value within the diagnostic model. In addition, the risk model had better prognostic and predictive effects, and the immune infiltration analysis showed that IGHM, CXCL13 might affect the proliferation of BC cells through immune cells. Functional studies demonstrated that interference with PBX1 inhibited the proliferation, migration, and epithelial-mesenchymal transition process of HER2-positive BC cells.</p><p><strong>Conclusion: </strong>PBX1, IGHM and CXCL13 are associated with the expression level of the ERBB3 and are prognostic markers for HER2-positive in BC, which may play an important role in the development and progression of BC.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"2"},"PeriodicalIF":1.9,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11720925/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142967585","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}
引用次数: 0
Population structure and genetic diversity of Toona sinensis revealed by whole-genome resequencing. 香椿全基因组重测序揭示的种群结构和遗传多样性。
IF 1.9
BMC genomic data Pub Date : 2025-01-03 DOI: 10.1186/s12863-024-01288-w
Lei Wang, Chang Lu, Zhi-Gang Bao, Meng Li, Fusheng Wu, Yi-Zeng Lu, Bo-Qiang Tong, Mei Yu, Yong-Jun Zhao
{"title":"Population structure and genetic diversity of Toona sinensis revealed by whole-genome resequencing.","authors":"Lei Wang, Chang Lu, Zhi-Gang Bao, Meng Li, Fusheng Wu, Yi-Zeng Lu, Bo-Qiang Tong, Mei Yu, Yong-Jun Zhao","doi":"10.1186/s12863-024-01288-w","DOIUrl":"https://doi.org/10.1186/s12863-024-01288-w","url":null,"abstract":"<p><strong>Objectives: </strong>Toona sinensis, commonly known as Chinese toon, is a perennial woody plant with significant economic and ecological importance. This study employed whole-genome resequencing of 180 T. sinensis samples collected from Shandong to analyze genetic variation and diversity, ultimately identifying 18,231 high-quality SNPs after rigorous quality control and linkage disequilibrium pruning. This comprehensive genomic resource provides novel insights into the genetic architecture of T. sinensis, facilitating the elucidation of population structure and supporting future breeding programs.</p><p><strong>Data description: </strong>We performed whole-genome resequencing on 180 Toona sinensis samples, generating 1170.26 Gbp of clean data with a Q30 percentage of 93.69%. The average alignment rate to the reference genome was 96.72%, with an average coverage depth of 8 × and a genome coverage of 88.71%. Following data quality control and alignment, we performed SNP calling and filtering to identify high-quality SNPs across all samples. Population structure analyses were then conducted using the identified SNPs, including principal component analysis (PCA), structure analysis, and phylogenetic tree construction. These comprehensive analyses provide a foundation for understanding the genetic diversity and evolutionary dynamics of T. sinensis.</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"26 1","pages":"1"},"PeriodicalIF":1.9,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11697678/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142928691","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}
引用次数: 0
Whole-genome sequence of Pseudomonas sp. strain HOU2 isolated from dangshen (Codonopsis javanica) roots. 党参根中假单胞菌HOU2的全基因组序列分析。
IF 1.9
BMC genomic data Pub Date : 2024-12-26 DOI: 10.1186/s12863-024-01291-1
Van Hong Thi Dao, Loan To Nguyen, Khanh Phuong Do, Vinh The Nguyen, Hieu Van Nguyen, Khanh Ngoc Pham, Truong Xuan Nguyen, Son Truong Dinh
{"title":"Whole-genome sequence of Pseudomonas sp. strain HOU2 isolated from dangshen (Codonopsis javanica) roots.","authors":"Van Hong Thi Dao, Loan To Nguyen, Khanh Phuong Do, Vinh The Nguyen, Hieu Van Nguyen, Khanh Ngoc Pham, Truong Xuan Nguyen, Son Truong Dinh","doi":"10.1186/s12863-024-01291-1","DOIUrl":"10.1186/s12863-024-01291-1","url":null,"abstract":"<p><strong>Objectives: </strong>This study aims to generate a de novo complete whole-genome assembly of Pseudomonas sp. strain HOU2, which is an endophytic bacterium isolated from dangshen roots that shows to improve the growth of in vitro dangshen plants. Further investigation of the whole genome of Pseudomonas sp. strain HOU2 will help identify potential genes or pathways that could be involved in the plant growth-promoting effects on in vitro dangshen plants, providing valuable information for future applications.</p><p><strong>Data description: </strong>The genomic DNA of Pseudomonas sp. strain HOU2 was sequenced using Oxford Nanopore's PromethION sequencer with an R10.4.1 flow cell (Table 1, Data file 1). The assembly of the Pseudomonas sp. strain HOU2 genome was conducted using Flye version 2.9, resulting in a single circular chromosome of 6,047,544 bp with a mean coverage of 488 (Table 1, Data file 2). The annotation of genes, proteins, and features of the HOU2 genome were performed by the RAST server (Rapid Annotation using Subsystem Technology) ( https://rast.nmpdr.org/ ) (Table 1, Data file 3, 4, 5) [6, 7]. The Pseudomonas sp. strain HOU2 genome was determined to be most similar to that of Pseudomonas koreensis using the Type Strain Genome Server ( https://tygs.dsmz.de/ , version v391) [8].</p>","PeriodicalId":72427,"journal":{"name":"BMC genomic data","volume":"25 1","pages":"107"},"PeriodicalIF":1.9,"publicationDate":"2024-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11670358/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142900739","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}
引用次数: 0
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