Optimized RAPD analysis generates high-quality genomic DNA profiles at high annealing temperature.
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Animals↗
SEARCH · PubMed Health
Results for “Genome quality”
Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.
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High-quality genomic DNA from human whole blood and mononuclear cells.
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Adsorption↗
Genome physical mapping with large-insert bacterial clones by fingerprint analysis: methodologies, source clone genome coverage, and contig map quality.
Genome physical mapping with large-insert clones by fingerprint analysis is becoming an active area of genomics research. Here, we report two new capillary electrophoresis-based fingerprinting methods for genome physical mapping and the effects of different fingerprinting methods and source clone genome coverage on quality physical map construction revealed by computer simulations and laboratory experiments. It was shown that the manual sequencing gel-based two-enzyme fingerprinting method consistently generated larger and more accurate contigs, followed by the new capillary electrophoresis-based three-enzyme method, the new capillary electrophoresis-based five-enzyme (SNaPshot) method, the agarose gel-based one-enzyme method, and the automatic sequencing gel-based four-enzyme method, in descending order, when 1% or fewer questionable clones were allowed. Analysis of clones equivalent to 5x, 8x, 10x, and 15x genomes using the fingerprinting methods revealed that as the number of clones increased from 5x to 10x, the contig length rapidly increased for all methods. However, when the number of clones was increased from 10x to 15x coverage, the contig length at best increased at a lower rate or even decreased. The results will provide useful knowledge and strategies for effective construction of quality genome physical maps for advanced genomics research.
Arabidopsis↗
Genomic instability and the role of radiation quality.
Genomic instability (GI) is a hallmark of tumorigenic progression and is observed as delayed genetic damage in the progeny of irradiated and unirradiated bystander cells. The expression of GI can be influenced by genotype, cell type and radiation quality. While several studies have demonstrated the induction of GI by high and low-linear energy transfer (LET) radiation, our work on human and mouse primary cell systems has shown LET-dependent differences in the induction and expression of GI. These differences might be attributed to differences in radiation track structure, dose rate, contribution of bystander cells and radiation dose. This paper reviews the role of radiation quality in the induction of GI and describe the possible mechanisms underlining the observed differences between radiation types on its induction. The experimental results presented suggest that dose might be the most significant factor in determining induction of GI after low-LET radiation.
Bystander Effect↗
Highly Contiguous Is Not Chromosomally Accurate: Integrated Cytogenetic and Genomic Mapping in Two Turtle Genome.
High-quality genome assemblies are essential for robust research across biological and medical fields. Assembly errors can have far-reaching consequences for downstream analyses, including gene annotation and the inference of synteny. In contrast to the rapid growth of genomic data volume, there is a notable lag in the integration of chromosome-level assemblies with cytogenetic data. We conducted the first direct genome-to-genome comparison, integrating comparative chromosome painting, the alignment of chromosome-specific probes to available genome assemblies, and synteny-based comparison of independent chromosome-level assemblies of the loggerhead sea turtle (Caretta caretta, 2n = 56) and the red-eared slider (Trachemys scripta elegans, 2n = 50). Using two independent sets of flow-sorted chromosome-specific probes in cross-species hybridizations, together with the sequencing and mapping of chromosome-derived DNA libraries, we assigned assembled scaffolds to all physical chromosomes of both species. In C. caretta, chromosomal assignments and genome-wide synteny were fully consistent with the published assembly, except for the reduced sizes of two microchromosome scaffolds, which we attribute to under-representation of repetitive DNA. In contrast, in T. s. elegans, cytogenetic validation of the assemblies revealed a false rearrangement compared to a missed one. Our results show that even highly contiguous vertebrate genome assemblies can misrepresent chromosome structure. When cytogenetic analyses reveal such inaccuracies, updated reference genomes should be generated for widely studied species to enable accurate inference of karyotype evolution and downstream comparative genomic analyses.
FISH↗
[Product quality and genome analysis in pig production--a review].
Product quality in the pig is defined by the choice of lean meat including a reasonable intramuscular fat content and good water binding capacity, which can be produced and marketed at a reasonable price, based on good fattening performance and disease resistance. Traits of product quality are mostly of polygenic character, while some of these genes show larger effects. Genome analysis intends to identify the genetic basis of phenotypic trait variation and to complement conventional phenotypic selection criteria by direct regarding of the nucleotide level, thus marker assisted selection. The present paper describes the most important markers in use to improve product quality in swine, and shows perspectives of genome analysis in this regard, including positional and functional strategies.
Animals↗
Genome Update: annotation quality in sequenced microbial genomes.
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Databases, Genetic↗
Functional genomics of wood quality and properties.
Genomics promises to enrich the investigations of biology and biochemistry. Current advancements in genomics have major implications for genetic improvement in animals, plants, and microorganisms, and for our understanding of cell growth, development, differentiation, and communication. Significant progress has been made in the understanding of plant genomics in recent years, and the area continues to progress rapidly. Functional genomics offers enormous potential to tree improvement and the understanding of gene expression in this area of science worldwide. In this review we focus on functional genomics of wood quality and properties in trees, mainly based on progresses made in genomics study of Pinus and Populus. The aims of this review are to summarize the current status of functional genomics including: (1) Gene discovery; (2) EST and genomic sequencing; (3) From EST to functional genomics; (4) Approaches to functional analysis; (5) Engineering lignin biosynthesis; (6) Modification of cell wall biogenesis; and (7) Molecular modelling. Functional genomics has been greatly invested worldwide and will be important in identifying candidate genes whose function is critical to all aspects of plant growth, development, differentiation, and defense. Forest biotechnology industry will significantly benefit from the advent of functional genomics of wood quality and properties.
Cell Wall↗
Chromosome-Level Reference Genome of the Desert Night Lizard Xantusia vigilis.
We present a reference-quality genome assembly for the desert night lizard (Xantusia vigilis). The night lizards (Xantusiidae) are a family of small-bodied lizards found in North America (Xantusia), Central America (Lepidophyma), and Cuba (Cricosaura). The night lizard family has an independent evolutionary history of at least 80 million years from its sister taxa within Scincoidea. The Xantusiids have several unique ecological, behavioral and evolutionary characteristics. For instance, the family contains the only squamate species that form diploid, unisexual, parthenogenic lineages. In addition, most night lizards are viviparous and form stable kin groups that are maintained over multiple years, an unusual life history strategy among lizards. Combining PacBio long-read sequencing, Hi-C, and RNAseq data we developed a reference-quality genome for the desert night lizard, X. vigilis. We assembled a complete mitochondrion and ~ 2.2 Gb nuclear genome, with 20 scaffolds that correlate in size to the X. vigilis karyotype. In addition, we found that X. vigilis chromosome 1 aligns with gene content of both of macrochromosome 1 and microchromosome 9 from a genome assembly of a species in the sister family Cordylidae (Hemicordylus capensis).
Xantusia↗
Comparative evaluation of three high-molecular-weight DNA extraction kits for Oxford Nanopore sequencing of Clostridioides difficile and Clostridium perfringens.
UNLABELLED: Clostridioides difficile and Clostridium perfringens are Gram-positive, spore-forming anaerobic pathogens affecting humans and animals, for which genomic data have been mainly generated using short-read or hybrid sequencing approaches. In this study, we evaluated three commercial non-bead-beating DNA extraction kits designed for high-molecular-weight DNA recovery for Oxford Nanopore long-read whole-genome sequencing of two C. difficile and two C. perfringens strains, including one reference strain and one clinical or environmental isolate per species. Based on sequencing performance and kit ease of use, one kit was selected for additional sequencing of plasmid-carrying strains of both species. All three kits allowed correct identification of sequence types, toxin-encoding genes, and antimicrobial resistance determinants, confirming their suitability for clinical and epidemiological applications. However, the BT MasterPure Kit provided the highest DNA concentrations, longest fragment sizes, and superior read lengths and N50 values, particularly for C. difficile, achieving >100× coverage and enabling reliable circularization of chromosomes and plasmids, including a C. difficile metronidazole resistance plasmid and C. perfringens plasmids carrying toxin and antibiotic resistance genes. The other kits produced slightly lower DNA yields, resulting in shorter reads and reduced genome coverage for C. difficile, highlighting the challenge of extracting high-quality DNA from Gram-positive, spore-forming bacteria. Overall, this study provides practical guidance for selecting DNA extraction protocols optimized for Oxford Nanopore sequencing of C. difficile and C. perfringens, supporting high-quality genome assemblies and plasmid characterization and facilitating the routine genomic surveillance of clinically relevant spore-forming pathogens. IMPORTANCE: High-quality genomic data are essential for accurate characterization of Clostridioides difficile and Clostridium perfringens, two clinically and epidemiologically important Gram-positive, spore-forming pathogens. However, long-read sequencing performance can be strongly influenced by the choice of DNA extraction method, particularly for organisms with robust cell walls, where commonly used methods can lead to fragmented DNA. In this work, DNA of four strains was extracted using three commercial high-molecular-weight DNA extraction kits and sequenced using Oxford Nanopore Technologies. The best-performing kit was also evaluated using three additional strains known to harbor plasmids in order to assess its plasmid recovery efficiency. The results demonstrated successful plasmid recovery, circularization, and characterization. DNA extraction protocols optimized for Oxford Nanopore sequencing enable the rapid and cost-effective characterization of C. difficile and C. perfringens for genomic surveillance or outbreak investigations.
Clostridioides difficile↗
CoSAG-nf: A Scalable Nextflow Pipeline for Co-assembly, Optimization, and Interactive Visualization of High-Throughput Single-Cell Genomes.
MOTIVATION: Single-cell amplified genomes (SAGs) are crucial for resolving intra-population microbial heterogeneity and accurately understanding the metabolic potential of microbial dark matter populations. However, SAGs generated through multiple displacement amplification (MDA) of genomic DNA from single cells with single-copy chromosomes are highly fragmented and prone to contamination, severely hindering high-quality genome reconstruction and functional analysis, which greatly limits their scientific utility. Co-assembly of related SAGs can substantially improve genome quality, but to our knowledge no automated pipeline exists for high-throughput processing, forcing manual implementation of complex workflows that scale poorly to modern dataset sizes. RESULTS: We present CoSAG-nf, an automated high-throughput co-assembly and optimization pipeline for SAGs, implemented following the nf-core framework standards. The pipeline performs alignment-free clustering using sourmash MinHash signatures, then employs iterative tetranucleotide frequency profiling to identify and exclude outlier SAGs from co-assembly groups. CheckM2 quality assessment guides dynamic selection of optimal SAG combinations to optimize genome completeness and minimize contamination. Fully containerized, CoSAG-nf ensures reproducibility and scalability for the high-throughput processing of large-scale SAG datasets across diverse computing environments, including HPC and cloud platforms. The pipeline generates comprehensive HTML reports with quality metrics and taxonomic annotations, providing an end-to-end solution for automated high-throughput single-cell genome reconstruction. AVAILABILITY: CoSAG-nf is freely available under the MIT License at: https://github.com/linfengxu/CoSAG-nf. Archival code repository snapshots are published at zenodo with doi: https://doi.org/10.5281/zenodo.21525244. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Journal Article↗
Comparative genomics of ESKAPE pathogen species: Integrating pan-genome architecture, antimicrobial resistance, and virulence factor repertoires.
BACKGROUND: ESKAPE pathogens are major causes of hospital-acquired infections and are characterized by extensive antimicrobial resistance (AMR) and diverse virulence mechanisms. Although species-specific pan-genome studies have revealed substantial genomic diversity, the relationships among genome plasticity, resistance burden, and virulence remain incompletely understood across the ESKAPE complex. METHODS: We analyzed 120 high-quality genomes representing six single-species ESKAPE groups (20 genomes per species). Genome quality was assessed using CheckM2. Species-specific pan-genomes were constructed with Roary, AMR genes were identified using AMRFinderPlus, and virulence factors were detected against the VFDB database using DIAMOND. AMR genes were mapped to core and accessory genome compartments through integration of Prokka annotations and Roary outputs. Statistical associations were evaluated using Fisher's exact tests and correlation analyses, with false discovery rate correction applied within each test family. Core-genome maximum-likelihood phylogenies were reconstructed to provide an evolutionary framework. RESULTS: Pan-genome sizes ranged from 4720 to 17,272 genes, with Enterobacter and Pseudomonas possessing the largest accessory genomes. Multidrug resistance (MDR; resistance to ≥3 antimicrobial classes) was detected in 93.3% of strains. After false discovery rate correction, AMR genes remained significantly enriched in the accessory genomes of Enterobacter, Enterococcus, Klebsiella, and Staphylococcus, whereas Acinetobacter and Pseudomonas did not show significant enrichment in either genome compartment. Within-species analyses identified significant positive associations between accessory genome size and AMR class burden in Staphylococcus, Enterococcus, and Enterobacter, whereas the moderate Pearson correlation observed in Pseudomonas was not significant after FDR correction. Virulence factor repertoires varied markedly among species, with Pseudomonas exhibiting the highest burden and Enterococcus the lowest. CONCLUSIONS: ESKAPE pathogens display distinct patterns of resistance and virulence. Accessory genome expansion was associated with higher AMR burden in several species, whereas other species showed no significant association between accessory genome size and AMR burden and no significant enrichment of AMR genes in either genome compartment, highlighting the species-specific nature of AMR evolution.
Virulence Factors↗
Chromosome-level genome assembly of hawthorn spider mite, Amphitetranychus viennensis (Acari: Tetranychidae).
The hawthorn spider mite, Amphitetranychus viennensis, is a major pest of orchards and ornamentals in the Palaearctic region, with adaptability and acaricide resistance. The lack of high-quality genomic resources limits understanding of its detoxification mechanisms and the development of RNAi-based pest control strategies. In this study, we utilized Illumina, Pacific Biosciences (PacBio), and Hi-C sequencing technologies to assemble a chromosome-level reference genome of A. viennensis. The assembled genome spans 141.96 Mb, with a contig N50 of 1.35 Mb. BUSCO analysis confirmed a high level of completeness, covering 91.6% of annotated genes. The assembly includes 50.97 Mb of repetitive sequences, representing 35.93% of the genome, and annotates 13,968 protein-coding genes. Using Hi-C sequencing, we anchored 47 contigs to three chromosomes, accounting for 97.27% of the estimated nuclear genome and achieving a contig N50 of 45.83 Mb. This high-quality genome assembly provides a valuable foundation for evolutionary and genomic research on spider mites, while also serving as a genetic resource to inform molecular control strategies and support sustainable pest management.
Animals↗
A chromosome-level genome assembly and annotation of Cercis chuniana (Fabaceae).
The genus Cercis L., at the base of the subfamily Cercidoideae of Fabaceae, is known for its ecological adaptability and significant medicinal, ornamental, and economic value. However, the lack of a high-quality genome hinders the understanding of the evolution of Cercis and Fabaceae. In this study, we present a chromosome-level genome of Cercis chuniana by combining Illumina short reads, PacBio HiFi long reads, and Hi-C data. The final genome size is 355.53 Mb, consisting of 12 contigs with a N50 of 42.34 Mb. Notably, 344.24 Mb, corresponding to 96.82% of the genome, was anchored to seven chromosomes. The assembly comprises 24.83% repetitive sequences, including 19.32% long terminal repeats. Additionally, a total of 33,837 protein-coding genes were predicted in the genome, with 32,709 (96.67%) genes successfully annotated. The high-quality genome assembly of C. chuniana not only bridges the existing gap in genomic data and offers important resources for molecular studies of this species, but also provides essential insights for future studies on speciation, functional and comparative genomics within the Fabaceae family.
Genome, Plant↗
Chromosome-level genome assembly and annotation of Pterygoplichthys pardalis.
Suckermouth catfishes, with their evolved powerful features, have become notorious invasive species, causing significant damage to aquatic ecosystems. However, the lack of high-quality genomes severely restricts research on this group within the field. In this study, we de novo assembled the chromosome-level genome assembly of Pterygoplichthys pardalis using multiple platforms of sequencing data, including Illumina short reads, Nanopore long reads, and Hi-C sequencing reads, resulting in a 1.51 Gb genome assembly. Multiple evaluations, including read mapping ratio (98.52%), transcript mapping ratio (99.61%), conserved BUSCO gene set (98.8%), and N50 score (49.47 Mb), indicated the high continuity and accuracy of the genome assembly we generated. Genome annotation found that 0.97 Gb of genome sequences are repetitive sequences, accounting for 64.47% of the genome assembly. Further, 23,859 protein-coding genes were successfully predicted, 92.92% of which could be annotated in functional databases. This high-quality genome assembly of P. pardalis provides a valuable resource for understanding the genetic underpinnings of P. pardalis's invasive success and offers critical data for future fisheries research and management.
Animals↗
Diversity of Salmonella enterica isolates from urban river and sewage water in Blantyre, Malawi.
BACKGROUND: Salmonella enterica encompasses over 2,600 serovars, including several commonly associated with severe infection in humans. Salmonella is a major cause of sepsis in Africa; however, diagnosis requires clinical microbiology facilities. Environmental surveillance has the potential to play a role in Salmonella surveillance. METHODS: We undertook water-based environmental surveillance in Blantyre, Malawi, from 2018-2020, taking samples from rivers (87.9%), a sewage plant (8.85%) and other water sources (3.24%), isolating and storing 1,042 non-typhoidal Salmonella (NTS) isolates in this period. Of these, 341 NTS isolates were whole genome sequenced, genome quality was checked, duplicate genomes from any given sample were removed and core genome phylogeny was reconstructed. AMRFinder, PathogenWatch and SISTR were used to further investigate serovar, sequence type and antimicrobial resistance determinants. RESULTS: After quality checks, and removal of duplicate genomes, 270 NTS genomes remained for further analysis. Multiple Salmonella serovars associated with human infection were detected, of which S. Typhimurium (55/270 isolates) was the most common, including 44 of Sequence Type (ST) 313, a serovar commonly associated with severe invasive disease (iNTS). Six lineage 2 ST313 genomes possessed AMR genes predicting multidrug resistance (MDR), while 29 lineage 3 isolates contained no AMR predictive genes. PCR based detection of staG has been proposed as a diagnostic marker of S. Typhi; however, all eight genomes that contained staG identified as Salmonella enterica serovar Orion, raising concerns about the specificity of this marker as a monoplex for environmental surveillance of S. Typhi. DISCUSSION: The study identified diverse Salmonella serovars in the environment, including those reported to cause invasive disease, emphasizing the complex but potentially valuable contribution of implementing environmental surveillance for Salmonella in high burden areas lacking diagnostic microbiology capacity.
Sewage↗
Genomic relations among 31 species of Mammillaria haworth (Cactaceae) using random amplified polymorphic DNA.
Thirty-one species of Mammillaria were selected to study the molecular phylogeny using random amplified polymorphic DNA (RAPD) markers. High amount of mucilage (gelling polysaccharides) present in Mammillaria was a major obstacle in isolating good quality genomic DNA. The CTAB (cetyl trimethyl ammonium bromide) method was modified to obtain good quality genomic DNA. Twenty-two random decamer primers resulted in 621 bands, all of which were polymorphic. The similarity matrix value varied from 0.109 to 0.622 indicating wide variability among the studied species. The dendrogram obtained from the unweighted pair group method using arithmetic averages (UPGMA) analysis revealed that some of the species did not follow the conventional classification. The present work shows the usefulness of RAPD markers for genetic characterization to establish phylogenetic relations among Mammillaria species.
Cactaceae↗
Isolation of genomic DNA from feathers.
The use of feathers in veterinary clinical practice simplifies the sampling of avian genomic DNA, especially when blood extraction is difficult because of the age or the size of the bird. A rapid and accurate protocol was used to isolate high-quality genomic DNA from feathers. The technique includes a lysis step of the feather quill, which differs in temperature and time of incubation depending on the feather size. Purification of genomic DNA is performed with phenol: chloroform: isoamyl alcohol extraction and ethanol precipitation. This protocol consistently provided significant amounts of high-quality genomic DNA from more than 800 birds belonging to 120 different species. Genomic DNA isolated with this method was used for Southern blotting and also in several polymerase chain reaction systems devoted to sex determination and paternity testing.
Animals↗