126,820 results match your criteria comparative genome


Whole genome sequencing and comparative genomic analyses of Planococcus alpniumensis MSAK28401, a new species isolated from Antarctic krill.

BMC Microbiol 2021 Oct 22;21(1):288. Epub 2021 Oct 22.

State Key Laboratory for Biocontrol / Southern Laboratory of Ocean Science and Engineering (Guangdong, Zhuhai), School of Marine Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou, 510275, People's Republic of China.

Background: Extremophiles have attracted much attention in the last few decades, as they possess different properties by producing certain useful metabolites. However, the secondary metabolism of the extremophiles of Antarctic krill has received little attention.

Results: In this study, a new bacterial strain MSAK28401 from Antarctic krill was isolated and identified. Read More

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October 2021

DNA Fingerprint Analysis of Raman Spectra Captures Global Genomic Alterations in Imatinib-Resistant Chronic Myeloid Leukemia: A Potential Single Assay for Screening Imatinib Resistance.

Cells 2021 Sep 22;10(10). Epub 2021 Sep 22.

Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai 410210, India.

Monitoring the development of resistance to the tyrosine kinase inhibitor (TKI) imatinib in chronic myeloid leukemia (CML) patients in the initial chronic phase (CP) is crucial for limiting the progression of unresponsive patients to terminal phase of blast crisis (BC). This study for the first time demonstrates the potential of Raman spectroscopy to sense the resistant phenotype. Currently recommended resistance screening strategy include detection of BCR-ABL1 transcripts, kinase domain mutations, complex chromosomal abnormalities and BCR-ABL1 gene amplification. Read More

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September 2021

The Effect of Impaired Polyamine Transport on Pneumococcal Transcriptome.

Pathogens 2021 Oct 14;10(10). Epub 2021 Oct 14.

Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, MS 39762, USA.

Infections due to , a commensal in the nasopharynx, still claim a significant number of lives worldwide. Genome plasticity, antibiotic resistance, and limited serotype coverage of the available polysaccharide-based conjugate vaccines confounds therapeutic interventions to limit the spread of this pathogen. Pathogenic mechanisms that allow successful adaption and persistence in the host could be potential innovative therapeutic targets. Read More

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October 2021

Genome Analysis of Nicotinamide Adenine Dinucleotide-Independent Isolates From Korea.

Pathogens 2021 Sep 23;10(10). Epub 2021 Sep 23.

College of Veterinary Medicine, Konkuk University, Seoul 05029, Korea.

(MS) is an avian pathogen that causes respiratory disease, infectious synovitis, and eggshell apex abnormalities in chickens. Nicotinamide adenine dinucleotide (NAD)-independent MS was first reported in 1975. Despite the atypical traits of NAD-independent MS, its independence from NAD has not been studied. Read More

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September 2021

Whole Genome Sequencing Analysis of Serovar Typhi: History and Current Approaches.

Microorganisms 2021 Oct 15;9(10). Epub 2021 Oct 15.

Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia.

In recent years, the advance in whole-genome sequencing technology has changed the study of infectious diseases. The emergence of genome sequencing has improved the understanding of infectious diseases, which has revamped many fields, such as molecular microbiology, epidemiology, infection control, and vaccine production. In this review we discuss the findings of serovar Typhi genomes, publicly accessible from the initial complete genome to the recent update of serovar Typhi genomes, which has greatly improved serovar Typhi and other pathogen genomic research. Read More

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October 2021

Myxobacterial Genomics and Post-Genomics: A Review of Genome Biology, Genome Sequences and Related 'Omics Studies.

Microorganisms 2021 Oct 13;9(10). Epub 2021 Oct 13.

Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3DD, UK.

Myxobacteria are fascinating and complex microbes. They prey upon other members of the soil microbiome by secreting antimicrobial proteins and metabolites, and will undergo multicellular development if starved. The genome sequence of the model myxobacterium DK1622 was published in 2006 and 15 years later, 163 myxobacterial genome sequences have now been made public. Read More

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October 2021

Characterization of Inducible HSP70 Genes in an Antarctic Yeast, PI12, in Response to Thermal Stress.

Microorganisms 2021 Sep 30;9(10). Epub 2021 Sep 30.

Malaysia Genome Institute, Jalan Bangi, Kajang 43000, Selangor, Malaysia.

The induction of highly conserved heat shock protein 70 (HSP70) is often related to a cellular response due to harmful stress or adverse life conditions. In this study, we determined the expression of genes in the Antarctic yeast, , under different several thermal treatments for several exposure periods. The main aims of the present study were (1) to determine if stress-induced could be used to monitor the exposure of the yeast species to various types of thermal stress; (2) to analyze the structures of the HSP70 proteins using comparative modeling; and (3) to evaluate the relationship between the function and structure of HSP70 in . Read More

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September 2021

Pan-Genome Analysis of Effectors in Korean Strains of the Soybean Pathogen pv. .

Microorganisms 2021 Sep 30;9(10). Epub 2021 Sep 30.

Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea.

pv. is a major pathogen of soybean in Korea. Here, we analyzed pathogenicity genes based on a comparative genome analysis of five Korean strains and one strain from the United States, 8ra. Read More

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September 2021

The Characterization of a Novel Phage, pPa_SNUABM_DT01, Infecting .

Microorganisms 2021 Sep 27;9(10). Epub 2021 Sep 27.

Laboratory of Aquatic Biomedicine, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.

The bacterial genus is a common causative agent of infections in veterinary medicine. In this study, we focused on canine otitis externa isolates. Due to prolonged antibiotic treatment of otitis externa, antibiotic resistance is common and has become a major complication. Read More

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September 2021

Genome Comparisons of the Fission Yeasts Reveal Ancient Collinear Loci Maintained by Natural Selection.

J Fungi (Basel) 2021 Oct 14;7(10). Epub 2021 Oct 14.

Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary.

Fission yeasts have a unique life history and exhibit distinct evolutionary patterns from other yeasts. Besides, the species demonstrate stable genome structures despite the relatively fast evolution of their genomic sequences. To reveal what could be the reason for that, comparative genomic analyses were carried out. Read More

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October 2021

Genomic Analysis of ATCC 23271, a Potential Probiotic Strain with Anti- Activity.

J Fungi (Basel) 2021 Sep 24;7(10). Epub 2021 Sep 24.

Rede de Biodiversidade e Biotecnologia da Amazônia Legal, BIONORTE, São Luís 65055-310, MA, Brazil.

(ATCC 23271) was originally isolated from the human intestine and has displayed antimicrobial activity, primarily against species. Complete genome sequencing and comparative analyses were performed to elucidate the genetic basis underlying its probiotic potential. The ATCC 23271 genome was found to contain 2,193,335 bp, with 2123 protein-coding sequences. Read More

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September 2021

The First Whole Genome Sequencing of Provides Insights into Its Medicinal Application and Evolution.

J Fungi (Basel) 2021 Sep 22;7(10). Epub 2021 Sep 22.

State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.

is a medicinal macrofungal genus typified by , the very species utilized in traditional Chinese medicines by Chinese ancient people. To facilitate the medicinal application of , we, for the first time, perform its genome sequencing and analyses from a monokaryon strain. A 33. Read More

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September 2021

Genome Study of a Novel Virulent Phage vB_SspS_KASIA and Mu-like Prophages of sp. M16 Provides Insights into the Genetic Diversity of the Virome.

Int J Mol Sci 2021 Oct 14;22(20). Epub 2021 Oct 14.

Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.

is a ubiquitous bacterial genus of aquatic ecosystems, and its bacteriophages are also isolated from aquatic environments (oceans, lakes, ice, and wastewater). In this study, the isolation and characterization of a novel virulent phage vB_SspS_KASIA and the identification of three prophages of its host, sp. M16, including a mitomycin-inducible Mu-like siphovirus, vB_SspS_MuM16-1, became the starting point for comparative analyses of phages infecting spp. Read More

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October 2021

Telomeric-Like Repeats Flanked by Sequences Retrotranscribed from the Telomerase RNA Inserted at DNA Double-Strand Break Sites during Vertebrate Genome Evolution.

Int J Mol Sci 2021 Oct 13;22(20). Epub 2021 Oct 13.

Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy.

Interstitial telomeric sequences (ITSs) are stretches of telomeric-like repeats located at internal chromosomal sites. We previously demonstrated that ITSs have been inserted during the repair of DNA double-strand breaks in the course of evolution and that some rodent ITSs, called TERC-ITSs, are flanked by fragments retrotranscribed from the telomerase RNA component (TERC). In this work, we carried out an extensive search of TERC-ITSs in 30 vertebrate genomes and identified 41 such loci in 22 species, including in humans and other primates. Read More

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October 2021

Targeting SARS-CoV-2 Variants with Nucleic Acid Therapeutic Nanoparticle Conjugates.

Pharmaceuticals (Basel) 2021 Oct 1;14(10). Epub 2021 Oct 1.

Nanotechnology Innovation Center, Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.

The emergence of SARS-CoV-2 variants is cause for concern, because these may become resistant to current vaccines and antiviral drugs in development. Current drugs target viral proteins, resulting in a critical need for RNA-targeted nanomedicines. To address this, a comparative analysis of SARS-CoV-2 variants was performed. Read More

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October 2021

Genomic Features and Molecular Function of a Novel Stress-Tolerant Strain Isolated from an Extreme Environment.

Biology (Basel) 2021 Oct 12;10(10). Epub 2021 Oct 12.

Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China.

Due to its topographical position and climatic conditions, the Qinghai-Tibet Plateau possesses abundant microorganism resources. The extremophilic strain KKD1 isolated from Hoh Xil possesses strong stress tolerance, enabling it to propagate under high salinity (13%) and alkalinity (pH 10.0) conditions. Read More

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October 2021

Comparative Genomic Analysis of Strains Isolated from Different Niches.

Genes (Basel) 2021 Sep 25;12(10). Epub 2021 Sep 25.

State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.

The potential probiotic benefits of have received increasing attention recently. We used comparative genomic analysis to explore the differences in the genome and the physiological characteristics of isolated from the fecal samples of Chinese adults and infants. The relationships between genotypes and phenotypes were analyzed to assess the effects of isolation sources on the genetic variation of . Read More

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September 2021

Splice Site Variant in Dogo Argentino Dogs with Disproportionate Dwarfism.

Genes (Basel) 2021 Sep 24;12(10). Epub 2021 Sep 24.

Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland.

Dwarfism phenotypes occur in many species and may be caused by genetic or environmental factors. In this study, we investigated a family of nine Dogo Argentino dogs, in which two dogs were affected by disproportionate dwarfism. Radiographs of an affected dog revealed a decreased level of endochondral ossification in its growth plates, and a premature closure of the distal ulnar physes. Read More

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September 2021

Comparative Analysis of Eight Mitogenomes of Bark Beetles and Their Phylogenetic Implications.

Insects 2021 Oct 18;12(10). Epub 2021 Oct 18.

Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China.

Many bark beetles of the subfamily Scolytinae are the most economically important insect pests of coniferous forests worldwide. In this study, we sequenced the mitochondrial genomes of eight bark beetle species, including , , , , , , , and , to examine their structural characteristics and determine their phylogenetic relationships. We also used previously published mitochondrial genome sequence data from other Scolytinae species to identify and localize the eight species studied within the bark beetle phylogeny. Read More

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October 2021

OmniSARS2: A Highly Sensitive and Specific RT-qPCR-Based COVID-19 Diagnostic Method Designed to Withstand SARS-CoV-2 Lineage Evolution.

Biomedicines 2021 Sep 26;9(10). Epub 2021 Sep 26.

Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal.

Extensive transmission of SARS-CoV-2 during the COVID-19 pandemic allowed the generation of thousands of mutations within its genome. While several of these become rare, others largely increase in prevalence, potentially jeopardizing the sensitivity of PCR-based diagnostics. Taking advantage of SARS-CoV-2 genomic knowledge, we designed a one-step probe-based multiplex RT-qPCR (OmniSARS2) to simultaneously detect short fragments of the SARS-CoV-2 genome in ORF1ab, E gene and S gene. Read More

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September 2021

Liquid Biopsy as a Diagnostic and Prognostic Tool for Women and Female Dogs with Breast Cancer.

Cancers (Basel) 2021 Oct 19;13(20). Epub 2021 Oct 19.

Laboratory of Molecular Investigation in Cancer (LIMC), Department of Molecular Biology, Faculdade de Medicina de São José, São José do Rio Preto 15090-000, Brazil.

Introduction: Breast cancer (BC) is the malignant neoplasm with the highest mortality rate in women and female dogs are good models to study BC.

Objective: We investigated the efficacy of liquid biopsy to detect gene mutations in the diagnosis and follow-up of women and female dogs with BC.

Materials And Methods: In this study, 57 and 37 BC samples were collected from women and female dogs, respectively. Read More

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October 2021

Application of CRISPR/Cas9 Tools for Genome Editing in the White-Rot Fungus .

Biomolecules 2021 Oct 15;11(10). Epub 2021 Oct 15.

Department of Microbiology, University of Helsinki, Viikinkaari 9, 00790 Helsinki, Finland.

is an emerging reference species that can be used to investigate white-rot fungal plant biomass degradation, as it has flexible physiology to utilize different types of biomass as sources of carbon and energy. Recent comparative (post-) genomic studies on resulted in an increasingly detailed knowledge of the genes and enzymes involved in the lignocellulose breakdown in this fungus and showed a complex transcriptional response in the presence of lignocellulose-derived compounds. To fully utilize this increasing amount of data, efficient and reliable genetic manipulation tools are needed, e. Read More

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October 2021

Depside and Depsidone Synthesis in Lichenized Fungi Comes into Focus through a Genome-Wide Comparison of the Olivetoric Acid and Physodic Acid Chemotypes of .

Biomolecules 2021 Oct 2;11(10). Epub 2021 Oct 2.

Senckenberg Biodiversity and Climate Research Centre (SBiK-F), 60325 Frankfurt am Main, Germany.

Primary biosynthetic enzymes involved in the synthesis of lichen polyphenolic compounds depsides and depsidones are non-reducing polyketide synthases (NR-PKSs), and cytochrome P450s. However, for most depsides and depsidones the corresponding PKSs are unknown. Additionally, in non-lichenized fungi specific fatty acid synthases (FASs) provide starters to the PKSs. Read More

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October 2021

Whole-Genome Sequencing Analysis of a -Negative   O63:H6 Isolate Associated with Hemolytic Uremic Syndrome.

Diagnostics (Basel) 2021 Oct 2;11(10). Epub 2021 Oct 2.

Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea.

Shiga toxin-encoding genes () of enterohemorrhagic   (EHEC) can be lost during infection or in vitro cultivation, and in clinical practice, it is difficult to distinguish EHEC that have lost (EHEC-LST) from enteropathogenic . (EPEC), as both are -negative and -positive. In this study, we performed whole-genome sequencing (WGS) of a -negative, -positive . Read More

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October 2021

Major Reorganization of Chromosome Conformation During Muscle Development in Pig.

Front Genet 2021 5;12:748239. Epub 2021 Oct 5.

GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France.

The spatial organization of the genome in the nucleus plays a crucial role in eukaryotic cell functions, yet little is known about chromatin structure variations during late fetal development in mammals. We performed high-throughput chromosome conformation capture (Hi-C) sequencing of DNA from muscle samples of pig fetuses at two late stages of gestation. Comparative analysis of the resulting Hi-C interaction matrices between both groups showed widespread differences of different types. Read More

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October 2021

Whole-Genome Sequencing of Reveals Phylogenetic Evolution and Immunological Variances in Various Fishes.

Front Genet 2021 5;12:736500. Epub 2021 Oct 5.

College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.

An adult , a surface-dwelling golden-line barbel fish, was collected from Maitian river (Kunming City, Yunnan Province, China) for whole-genome sequencing, assembly, and annotation. We obtained a genome assembly of 1.7 Gb with a scaffold N50 of 1. Read More

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October 2021

Brussowvirus SW13 requires a cell surface-associated polysaccharide to recognise its host.

Appl Environ Microbiol 2021 Oct 20:AEM0172321. Epub 2021 Oct 20.

School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, Cork T12 YT20.

Four acteriophage nsensitive utants (BIMs) of the dairy starter bacterium UCCSt50 were isolated following a challenge with the SW13. The BIMs displayed an altered, sedimentation phenotype. Whole genome sequencing and comparative genomic analysis of the BIMs uncovered mutations within a family-2-glycosyltransferase-encoding gene (06955) located within the variable region of the cell wall-associated hamnose-lucose olymer (Rgp) biosynthesis locus (designated here as the gene cluster). Read More

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October 2021

Genome mosaicism in field strains of as footprints of in-host horizontal chromosomal transfer.

Appl Environ Microbiol 2021 Oct 20:AEM0166121. Epub 2021 Oct 20.

IHAP, ENVT, INRAE, Université de Toulouse, 31300 Toulouse, France.

Horizontal gene transfer was long thought to be marginal in , but the capacity of some of these wall-less bacteria to exchange large chromosomal regions has been recently documented. Mycoplasma chromosomal transfer (MCT) is an unconventional mechanism that relies on the presence of a functional integrative conjugative element (ICE) in at least one partner and involves the horizontal acquisition of small and large chromosomal fragments from any part of the donor genome, which results in progenies composed of an infinitive variety of mosaic genomes. The present study focuses on , an important pathogen of cattle responsible for major economic losses worldwide. Read More

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October 2021

Genomic Characterization of Two Novel RCA Phages Reveals New Insights into the Diversity and Evolution of Marine Viruses.

Microbiol Spectr 2021 Oct 20:e0123921. Epub 2021 Oct 20.

Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.

Viruses are the most abundant living entities in marine ecosystems, playing critical roles in altering the structure and function of microbial communities and driving ocean biogeochemistry. Phages that infect clade-affiliated (RCA) cluster strains are an important component of marine viral communities. Here, we characterize the genome sequences of two new RCA phages, CRP-9 and CRP-13, which infect RCA strain FZCC0023. Read More

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October 2021

Characterization of the First Cultured Psychrotolerant Representative of from Antarctica Reveals Its Unique Genome Structure.

Microbiol Spectr 2021 Oct 20:e0042421. Epub 2021 Oct 20.

Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan.

Culture-independent analysis shows that spp. inhabit a wide range of low-temperature environments, but to date, no psychrotolerant or psychrophilic strains have been reported. Here, we characterized the first cultivated psychrotolerant representative, designated strain TUM19329, isolated from an Antarctic lake using a polyphasic approach and comparative genomic analysis. Read More

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October 2021