BMC genomic data最新文献

Objectives: 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.

Data description: 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.

Objectives: 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.

Data description: 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.

Objectives: 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.

Data description: 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.

Objective: Staphylococcus capitis is part of the human microbiome and an opportunistic pathogen known to cause catheter-associated bacteraemia, prosthetic joint infections, skin and wound infections, among others. Detection of S. capitis in normally sterile body sites saw an increase over the last decade in England, where a multidrug-resistant clone, NRCS-A, was widely identified in blood samples from infants in neonatal intensive care units. To address a lack of complete genomes and antibiograms of S. capitis in public databases, we performed long- and short-read whole-genome sequencing, hybrid genome assembly, and antimicrobial susceptibility testing of 22 diverse isolates.

Data description: We present complete genome assemblies of two S. capitis type strains (subspecies capitis: DSM 20326; subspecies urealyticus: DSM 6717) and 20 clinical isolates (NRCS-A: 10) from England. Each genome is accompanied by minimum inhibitory concentrations of 13 antimicrobials including vancomycin, teicoplanin, daptomycin, linezolid, and clindamycin. These 22 genomes were 2.4-2.7 Mbp in length and had a GC content of 33%. Plasmids were identified in 20 isolates. Resistance to teicoplanin, daptomycin, gentamicin, fusidic acid, rifampicin, ciprofloxacin, clindamycin, and erythromycin was seen in 1-10 isolates. Our data are a resource for future studies on genomics, evolution, and antimicrobial resistance of S. capitis.

Objectives: Coffea liberica is one of the species within the Coffea genus known for its distinctive flavor and resistance to leaf rust disease. Through breeding approaches, two superior varieties of C. liberica, designated as Liberoid Meranti 1 (Lim 1) and Liberoid Meranti 2 (Lim 2), were introduced in 2015. These varieties are known for their high adaptability in peatlands. The genetic basis of plant adaptability to peatlands remains largely unknown. It is therefore essential to identify genome-wide DNA polymorphisms in Lim 1 and 2 in order to gain insights into its capacity for adaptation in peatlands.

Data description: Whole genome sequencing was performed on three plants from each variety (Lim 1 and 2), resulting in 430 million sequencing reads. The mean depth of sequencing for each sample was 36.90x. The reads were mapped to the Coffea canephora genome, with an average mapping rate of 96.34%. The sequencing data revealed the presence of 3,766,805 single-nucleotide polymorphisms (SNPs) and 1,123,683 insertion-deletions (indels) in all six plants. Among the SNPs, there was a notable prevalence of transitions, with a ratio of approximately twofold compared to transversions. The generated data offers invaluable genomic resources for marker development, with significant implications for understanding peatlands adaptability.

High intraocular pressure (IOP) is an important risk factor for glaucoma, which is influenced by genetic and environmental factors. However, the etiology of high IOP remains uncertain. Metabolites are compounds involved in metabolism which provide a link between the internal (genetic) and external environments. O-methylascorbate has been reported to be associated with IOP. In addition, researchers have identified several genetic variants which are associated with metabolite concentrations, including O-methylascorbate and another vitamin C related metabolite, ascorbic acid 2-sulfate. We aimed to understand how O-methylascorbate and ascorbic acid 2-sulfate, or genetic variants associated with these metabolites, modify the associations between dietary environmental variables and IOP. We used data from 8060 participants of the Canadian Longitudinal Study on Aging. Using linear models adjusted for relevant covariates, we tested for interactions between six genetic variants previously found to be associated with O-methylascorbate and ascorbic acid 2-sulfate and four environmental variables related to diet (alcohol consumption frequency, smoking status, fruit consumption, and vegetable consumption). We also tested for interactions between serum concentrations of O-methylascorbate and ascorbic acid 2-sulfate and these environmental factors. We used a False Discovery Rate approach to correct for the 32 interaction tests performed. One interaction was suggestively significant after multiple testing correction (adjusted P-value < 0.1): rs8050812 and alcohol consumption frequency. Understanding how genetic variants and metabolites interact with the environment could shed light on biological pathways controlling IOP and lead to improved prevention and treatment of glaucoma.

Objective: 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.

Objective: 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.

Data description: 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.

Objectives: 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.

Data description: 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.

Objective: 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.

Data description: 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.