Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “genome composition”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 775 records · Page 43Linked to original sources
PubMed2026

Complete genome sequence of Streptomyces californicus ADR1, an anti-infective, anti-biofilm and anti-oxidant producing endophyte isolated from the medicinal plant Datura metel.

OBJECTIVE: Streptomyces californicus strain ADR1 is an endophytic actinobacterium isolated from Datura metel that produces secondary metabolites with potent antibacterial and anti-biofilm activities against WHO-listed high-priority Gram-positive pathogens. While anti-bacterial and antioxidant potential of the strain ADR1 has been extensively characterized, its complete genome sequence remains to be investigated for further insights into its biosynthetic potential. This study presents the complete genome sequence analysis of the strain ADR1 to provide a robust genomic foundation for understanding its metabolic versatility and biosynthesis of compounds with therapeutic significance. DATA DESCRIPTION: The ADR1 genome was sequenced using Illumina HiSeq. The assembly comprised 262 scaffolds with a total genome size of 8.4 Mb and G + C content of 72.5%, containing 7427 protein-coding genes. AntiSMASH and IIT-Hyderabad novelBGC analysis revealed 39 biosynthetic gene clusters, including non-ribosomal peptide synthetases, type I polyketide synthases, terpene and melanin clusters, correlating with the diverse therapeutic compounds previously identified through GC-MS analysis. This high-quality genome provides crucial insights into the biosynthetic potential underlying potent antimicrobial and antioxidant activities of the strain ADR1.

Streptomyces↗
PubMed2005

Target practice: aiming at satellite repeats with DNA minor groove binders.

Much progress has been made in recent years in developing small molecules that target the minor groove of DNA. Striking advances have led to the design of synthetic molecules that recognize specific DNA sequences with affinities comparable to those of eukaryotic transcription factors. This makes it feasible to modulate or inhibit DNA/protein interactions in vivo, a major step towards the development of general strategies of anti-gene therapy. Examples from anti-parasitic drugs also suggest that synthetic molecules can affect a variety of cellular functions crucial to cell viability by more generally targeting vast portions of genomes based on their biased base composition. This provides a rationale for developing approaches based on selective interactions with broad genomic targets such as satellite repeats that are associated with structural or architectural components of chromatin essential for cellular proliferation. Using examples drawn from the Drosophila melanogaster model system, we review here the use of synthetic polyamides or diamidines that bind the DNA minor groove and can be used as highly selective agents capable of interfering with specific protein/DNA interactions that occur in A+T-rich repeated sequences that constitute a significant portion of eukaryotic genomes. The satellite localization of cellular proteins that bind the minor groove of DNA via domains such as the AT hook motif is highly sensitive to these molecules. A major consequence of the competition between these proteins and their synthetic mimics is an alteration of the nuclear localization and function of proteins such as topoisomerase II, a major target of anti-cancer drugs.

Animals↗
PubMed2002

Plant genome evolution: lessons from comparative genomics at the DNA level.

Angiosperm genomes show tremendous variability in genome size and chromosome number. Nevertheless, comparative genetic mapping has revealed genome collinearity of closely related species. Sequence-based comparisons were used to assess the conservation of gene arrangements. Numerous small rearrangements, insertions/deletions, duplications, inversions and translocations have been detected. Importantly, comparative sequence analyses have unambiguously shown micro-collinearity of distantly related plant species. Duplications and subsequent gene loss have been identified as a particular important factor in the evolution of plant genomes.

Base Composition↗
PubMed2006

Genome-wide linkage analysis to identify chromosomal regions affecting phenotypic traits in the chicken. II. Body composition.

Two informative chicken F(2) populations based on crosses between a broiler breeder male line and dams from genetically distinct, highly inbred (>99%) chicken lines, the Leghorn G-B2 and Fayoumi M15.2, have been used for genome-wide linkage and QTL analysis. Phenotypic data on 12 body composition traits (breast muscle weight, breast muscle weight percentage, abdominal fat weight, abdominal fat weight percentage, heart weight, heart weight percentage, liver weight, liver weight percentage, spleen weight, spleen weight percentage, and drumstick weight, and drumstick weight percentage) were collected. Birds were genotyped for 269 microsatellite markers across the genome. The QTL Express program was used to detect QTL for body composition traits. Significant levels were obtained using the permutation test. For the twelve traits, a total of 61 (Gga 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 15, 18, 24, and Z) and 45 (Gga 1, 2, 3, 4, 6, 7, 8, 9, 10, 12, 15, 17, and E46) significant QTL were detected at the 5% chromosome-wise significance level, of which 19 and 11 were significant at the 5% genome-wise level for the broiler-Leghorn cross and broiler-Fayoumi cross, respectively. Phenotypic variation for each trait explained by all QTL across the genome ranged from 3.22 to 33.31% in the broiler-Leghorn cross and 4.83 to 47.12% in broiler-Fayoumi cross. Distinct QTL profiles between the 2 crosses were observed for most traits. Cryptic alleles were detected for each trait. Potential candidate genes within the QTL region for body composition traits at the 1% chromosome-wise significance level were identified from databases for future association study. The results of the current study will increase the knowledge of genetic markers associated with body composition traits and aid the process of identifying causative genes. Knowledge of beneficial genetic variation can be incorporated in breeding programs to enhance genetic improvement through marker-assisted selection in chickens.

Animals↗
PubMed2026

From bacterial to microbiome-derived vesicles: genome-informed identity, source qualification, and translational quality for skin-directed cosmetics.

Bacterial extracellular vesicles (BEVs) are increasingly proposed as materials for skin-directed cosmetics, yet rapid adoption of "exosome" terminology has outpaced clarity on their origin, composition, and manufacturing quality. This review argues that the value of BEVs depends on scientific discipline rather than marketing appeal, and that they are promising because they are biologically potent, not because they are intrinsically benign. We retain BEVs as the scientific umbrella term for vesicles released by bacteria and we propose the term microbiome-derived vesicles (MDVs) as the consumer-facing designation for qualified commensal BEVs - a surface term that avoids the difficulty of "bacterial" while its definition preserves bacterial provenance. We develop a three-axis framework for BEV identity that integrates compositional analysis, producer-strain genomics, and functional or safety profiling, and we position whole-genome sequencing (WGS) as decisive for source qualification and mechanistic interpretation but insufficient to prove the efficacy of a purified preparation. Building on this framework, we summarize isolation, purification, and analytical characterization requirements; interpret current skin-efficacy evidence in light of its methodological limits; and discuss formulation, cosmetic application, regulatory positioning, and manufacturable quality. We conclude that transparent bacterial provenance, reproducible preparation, and evidence proportionate to the claims made are prerequisites for evaluating commensal BEVs, described for skin applications as MDVs, as a scientifically defined cosmetic platform.

Bacterial extracellular vesicles↗
PubMed2002

QTLs involved in the restriction of cucumber mosaic virus (CMV) long-distance movement in pepper.

Partial restriction of cucumber mosaic virus (CMV) long-distance movement originating from the Capsicum annuum inbred line 'Vania' was assessed in a doubled-haploid progeny using two screening methods: the first allowed one to assess the resistance of adult plants decapitated above the fourth leaf and inoculated on the third leaf using a common CMV strain, and the second allowed one to assess CMV resistance to long-distance movement on seedlings inoculated using an atypical CMV strain. For both resistance tests, the behavior of the F(1) hybrid between 'Vania' and the susceptible line 'H3' indicated that partial resistance is inherited as a dominant trait. Phenotypic data from the two screening methods were correlated but the one performed on seedlings was much more severe. A subset of 184 molecular markers well-distributed over the pepper genome was selected for QTL mapping using the composite interval mapping (CIM) method. A total of seven genomic regions, including one major effect and several minor effect QTLs, were shown to be associated with partial restriction of CMV long-distance movement. These results are compared with those already obtained in pepper and also in other solanaceous crops, potato and tomato.

Journal Article↗
PubMed2002

Base composition bias might result from competition for metabolic resources.

The GC content of bacterial genomes varies from 25 to 75%, but the reason for this variation is unclear. Here, we show that genomes of bacteria that rely on their host for survival (obligatory pathogens or symbionts) tend to be AT rich. Furthermore, we have analysed bacterial phages, plasmids and insertion sequences, which might also be regarded as 'intracellular pathogens', and show that they too are significantly richer in AT than their hosts. We suggest that the higher energy cost and limited availability of G and C over A and T/U could be a basis for the understanding of these differences.

AT Rich Sequence↗
PubMed1991

Plastid genomes of the Rhodophyta and Chromophyta constitute a distinct lineage which differs from that of the Chlorophyta and have a composite phylogenetic origin, perhaps like that of the Euglenophyta.

A phylogenetic tree has been constructed from comparisons of entire 16S rRNA gene sequences from different prokaryotes and from several algal plastids. According to this study, and to previous work on the ribulose-1,5-bisphosphate carboxylase oxygenase (Rubisco) large and small subunit genes, we postulate that: (1) rhodophyte and chromophyte plastid genomes have a common, composite phylogenetic origin which implies at least two different ancestors, a cyanobacterial and a beta-proteobacterial ancestor; (2) chlorophyte (green algae and land plants) plastids have a cyanobacterial ancestor which probably differs from that of rhodophyte and chromophyte plastids, and in any case constitute a different lineage; (3) euglenophyte plastid genomes also seem to have a composite phylogenetic origin which involves two different lineages.

Base Sequence↗
PubMed1972

Occurrence and properties of lactic dehydrogenases of fermentative mycoplasmas.

Eight fermentative mycoplasmas differing in genome size, deoxyribonucleic acid (DNA) base composition, or sterol dependence were examined for lactic dehydrogenase composition by spectrophotometric assay and polyacrylamide gel electrophoresis. Three completely different patterns of lactic dehydrogenase composition were found. (i) A nicotinamide adenine dinucleotide (NAD)-dependent l(+)-lactic dehydrogenase was found in Mycoplasma pneumoniae, M. gallisepticum, M. mycoides var. mycoides, mycoplasma UM 30847, M. neurolyticum, and Acholeplasma axanthum. Electrophoresis of cell-free extracts of each of these mycoplasmas produced, with the exception of M. mycoides var. mycoides and UM 30847, single, different enzyme bands. M. mycoides var. mycoides and UM 30847 were similar and formed multiple bands of enzyme activity. We were unable to establish whether these multiple bands were due to lactic dehydrogenase isoenzymes or artifacts. (ii) An NAD-dependent d(-)-lactic dehydrogenase which could not be reversed to oxidize lactate was found in M. fermentans. (iii) A. laidlawii A possessed an NAD-independent d(-)-lactic dehydrogenase capable of reducing dichlorophenol-indophenol, and an NAD-dependent l(+)-lactic dehydrogenase which is specifically activated by fructose-1,6-diphosphate. Heretofore, this enzyme regulatory mechanism was known to occur only among the Lactobacillaceae. No yeast-type lactic dehydrogenase activity was found in any of the mycoplasmas examined. The stereoisomer of lactic acid accumulated during growth correlated perfectly with the type of NAD-dependent lactic dehydrogenase found in each mycoplasma. The types of lactic dehydrogenase activity found in these mycoplasmas were not related to genome size, DNA base composition, or sterol dependence.

Cell-Free System↗
PubMed2004

Genomes of the parapoxviruses ORF virus and bovine papular stomatitis virus.

Bovine papular stomatitis virus (BPSV) and orf virus (ORFV), members of the genus Parapoxvirus of the Poxviridae, are etiologic agents of worldwide diseases affecting cattle and small ruminants, respectively. Here we report the genomic sequences and comparative analysis of BPSV strain BV-AR02 and ORFV strains OV-SA00, isolated from a goat, and OV-IA82, isolated from a sheep. Parapoxvirus (PPV) BV-AR02, OV-SA00, and OV-IA82 genomes range in size from 134 to 139 kbp, with an average nucleotide composition of 64% G+C. BPSV and ORFV genomes contain 131 and 130 putative genes, respectively, and share colinearity over 127 genes, 88 of which are conserved in all characterized chordopoxviruses. BPSV and ORFV contain 15 and 16 open reading frames (ORFs), respectively, which lack similarity to other poxvirus or cellular proteins. All genes with putative roles in pathogenesis, including a vascular endothelial growth factor (VEGF)-like gene, are present in both viruses; however, BPSV contains two extra ankyrin repeat genes absent in ORFV. Interspecies sequence variability is observed in all functional classes of genes but is highest in putative virulence/host range genes, including genes unique to PPV. At the amino acid level, OV-SA00 is 94% identical to OV-IA82 and 71% identical to BV-AR02. Notably, ORFV 006/132, 103, 109, 110, and 116 genes (VEGF, homologues of vaccinia virus A26L, A33R, and A34R, and a novel PPV ORF) show an unusual degree of intraspecies variability. These genomic differences are consistent with the classification of BPSV and ORFV as two PPV species. Compared to other mammalian chordopoxviruses, PPV shares unique genomic features with molluscum contagiosum virus, including a G+C-rich nucleotide composition, three orthologous genes, and a paucity of nucleotide metabolism genes. Together, these data provide a comparative view of PPV genomics.

Animals↗
PubMed2025

CoverM: read alignment statistics for metagenomics.

SUMMARY: Genome-centric analysis of metagenomic samples is a powerful method for understanding the function of microbial communities. Calculating read coverage is a central part of analysis, enabling differential coverage binning for recovery of genomes and estimation of microbial community composition. Coverage is determined by processing read alignments to reference sequences of either contigs or genomes. Per-reference coverage is typically calculated in an ad-hoc manner, with each software package providing its own implementation and specific definition of coverage. Here we present a unified software package CoverM which calculates several coverage statistics for contigs and genomes in an ergonomic and flexible manner. It uses "Mosdepth arrays" for computational efficiency and avoids unnecessary I/O overhead by calculating coverage statistics from streamed read alignment results. AVAILABILITY AND IMPLEMENTATION: CoverM is free software available at https://github.com/wwood/coverm. CoverM is implemented in Rust, with Python (https://github.com/apcamargo/pycoverm) and Julia (https://github.com/JuliaBinaryWrappers/CoverM_jll.jl) interfaces.

Metabolomics↗
PubMed1994

Physical map and set of overlapping cosmid clones representing the genome of the archaeon Halobacterium sp. GRB.

We have constructed a complete, five-enzyme restriction map of the genome of the archaeon Halobacterium sp. GRB, based on a set of 84 overlapping cosmid clones. Fewer than 30 kbp, in three gaps, remain uncloned. The genome consists of five replicons: a chromosome (2038 kbp) and four plasmids (305, 90, 37, and 1.8 kbp). The genome of Halobacterium sp. GRB is similar in style to other halobacterial genomes by being partitioned among multiple replicons and by being mosaic in terms of nucleotide composition. It is unlike other halobacterial genomes, however, in lacking multicopy families of insertion sequences.

Chromosome Mapping↗
PubMed1976

Studies on the organisation of the chicken genome and its expression during myogenesis in vitro.

DNA from the chicken genome was analysed both by isopycnic centrifugation in cesium salt density gradients and by reassociation analysis using hydroxyapatite (HAP) chromatography. Centrifugation in neutral CsCl revealed a single non-Gaussian band skewed toward the heavy side, but no discrete satellite components. In heavy metal (Ag+ or Hg++)-Cs2SO4 gradients, 4-8 satellite bands were revealed, comprising 5-9% of the total DNA. Purification of the satellites and recentrifugation in neutral CsCl demonstrated that 80-90% of this DNA would band in the shoulder, with the remainder in the main band. These satellites can account at most for 30% of the heavy shoulder DNA, thus most of the heavy shoulder DNA must be of lower repetition frequencies. Reassociation analyses of chicken DNA demonstrated that the complexity of the non-repetitive DNA is 9.49 X 10(8) nucleotide pairs, equivalent to about 90% of the haploid genome. Repetitive DNA comprises only 8-10% of the genome and has the following composition, relative to total DNA: 3.7% intermediate repetitive, 1.9% highly repetitive, and 3.9% "zero-time binding" DNA. This unusually low repetitive DNA content may be related to the small genome size of chickens, relative to other vertebrates, and to the presence of many microchromosomes in the chicken karyotype. Total cell RNA extracted from perfusion myoblasts, post-fusion myotubes, and myoblasts grown in BrdU was incubated in large excess with 3H-TdR labelled non-repetitive DNA and the resulting hybrids assayed by HAP chromatography. The amount of non-repetitive DNA represented in the RNA was found to increase from 7-8% in the myoblast stage to 10-11% in myotubes. An even smaller proportion, about 5%, is represented in the RNA of myoblasts prevented from differentiating by growth in BrdU.

Animals↗
PubMed1998

Identification of quantitative trait loci affecting carcass composition in swine: II. Muscling and wholesale product yield traits.

A genomic scan was conducted on 540 reciprocal backcross Meishan x White composite pigs for hot carcass weight (HCWT); loin eye area (LOIN); carcass length (CRCL); belly weight (BELLY); and weight of trimmed ham, loin, picnic, and Boston butt adjusted to a constant live (TWPLWT) or carcass (TWPCWT) weight. Genetic markers spanned the entire porcine linkage map and were spaced at approximately 20-cM intervals. Grandparental breed of origin for all chromosomal segments was determined using multipoint linkage procedures, and a least squares regression analysis was conducted. Nominal P-values were converted to a genome-wide level of significance to adjust for the number of tests actually conducted. Seven associations were significant at the genome-wide level relating to chromosomes 1 (SSC 1), 7 (SSC 7), and X (SSC X). The SSC 1 region affected LOIN, TWPLWT, and TWPCWT; SSC 7 affected HWCT and CRCL; and SSC X affected TWPLWT and TWPCWT. Twelve associations relating to seven chromosomal regions (including SSC 1 and X) presented suggestive evidence for quantitative trait loci (QTL), and many of these regions are likely to contain QTL. Chromosomes 8 and 14 had two and three traits with suggestive evidence for QTL, respectively. Many pleiotropic effects were detected for regions on SSC 1, 7, 14, and X in this study and a companion study looking for fat deposition QTL in the same population. In addition, SSC 4 was nearly significant for CRCL in the same region identified as affecting backfat in a wild boar x Large White population. These results expand our knowledge of the inheritance of quantitative traits and are directly relevant to composite populations containing Meishan germplasm.

Alleles↗
PubMed2004

Genome of bacteriophage P1.

P1 is a bacteriophage of Escherichia coli and other enteric bacteria. It lysogenizes its hosts as a circular, low-copy-number plasmid. We have determined the complete nucleotide sequences of two strains of a P1 thermoinducible mutant, P1 c1-100. The P1 genome (93,601 bp) contains at least 117 genes, of which almost two-thirds had not been sequenced previously and 49 have no homologs in other organisms. Protein-coding genes occupy 92% of the genome and are organized in 45 operons, of which four are decisive for the choice between lysis and lysogeny. Four others ensure plasmid maintenance. The majority of the remaining 37 operons are involved in lytic development. Seventeen operons are transcribed from sigma(70) promoters directly controlled by the master phage repressor C1. Late operons are transcribed from promoters recognized by the E. coli RNA polymerase holoenzyme in the presence of the Lpa protein, the product of a C1-controlled P1 gene. Three species of P1-encoded tRNAs provide differential controls of translation, and a P1-encoded DNA methyltransferase with putative bifunctionality influences transcription, replication, and DNA packaging. The genome is particularly rich in Chi recombinogenic sites. The base content and distribution in P1 DNA indicate that replication of P1 from its plasmid origin had more impact on the base compositional asymmetries of the P1 genome than replication from the lytic origin of replication.

Amino Acid Sequence↗
PubMed2006

Genomic analysis of a 1 Mb region near the telomere of Hessian fly chromosome X2 and avirulence gene vH13.

BACKGROUND: To have an insight into the Mayetiola destructor (Hessian fly) genome, we performed an in silico comparative genomic analysis utilizing genetic mapping, genomic sequence and EST sequence data along with data available from public databases. RESULTS: Chromosome walking and FISH were utilized to identify a contig of 50 BAC clones near the telomere of the short arm of Hessian fly chromosome X2 and near the avirulence gene vH13. These clones enabled us to correlate physical and genetic distance in this region of the Hessian fly genome. Sequence data from these BAC ends encompassing a 760 kb region, and a fully sequenced and assembled 42.6 kb BAC clone, was utilized to perform a comparative genomic study. In silico gene prediction combined with BLAST analyses was used to determine putative orthology to the sequenced dipteran genomes of the fruit fly, Drosophila melanogaster, and the malaria mosquito, Anopheles gambiae, and to infer evolutionary relationships. CONCLUSION: This initial effort enables us to advance our understanding of the structure, composition and evolution of the genome of this important agricultural pest and is an invaluable tool for a whole genome sequencing effort.

Animals↗
PubMed2007

Comparison of ovine herpesvirus 2 genomes isolated from domestic sheep (Ovis aries) and a clinically affected cow (Bos bovis).

The rhadinovirus Ovine herpesvirus 2 (OvHV-2) is the causative agent of sheep-associated malignant catarrhal fever. OvHV-2 primarily affects ruminants and has a worldwide distribution. In this study, a composite sequence of OvHV-2 genomic DNA isolated from nasal secretions of sheep experiencing virus-shedding episodes was determined and compared with the sequence of OvHV-2 DNA isolated from a lymphoblastoid cell line derived from a clinically affected cow. The study confirmed the OvHV-2 sequence information determined for the cell line-isolated DNA and showed no apparently significant changes in the OvHV-2 genome during passage through a clinically susceptible species with subsequent maintenance in vitro. Amino acid identity between the predicted open reading frames (ORFs) of the two genomes was 94-100%, except for ORF73, which had an identity of 83%. Polymorphism in ORF73 was due primarily to variability in the G/E-rich repetitive central region of the ORF.

Amino Acid Sequence↗