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33 publications found.

Reference genome and comparative genome analysis for the WHO reference strain for Mycobacterium bovis BCG Danish, the present tuberculosis vaccine.
Published: July, 2019

Abstract: BACKGROUND: Mycobacterium bovis bacillus Calmette-Guérin (M. bovis BCG) is the only vaccine available against tuberculosis (TB). In an effort to standardize the vaccine production, three substrains, i.e. BCG Danish 1331, Tokyo 172-1 and Rus...
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Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system.
Published: June, 2019

Abstract: BACKGROUND: Complete and contiguous genome assemblies greatly improve the quality of subsequent systems-wide functional profiling studies and the ability to gain novel biological insights. While a de novo genome assembly of an isolated bacterial s...
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A chromosome-scale genome assembly of cucumber (Cucumis sativus L.).
Published: June, 2019

Abstract: BACKGROUND: Accurate and complete reference genome assemblies are fundamental for biological research. Cucumber is an important vegetable crop and model system for sex determination and vascular biology. Low-coverage Sanger sequences and high-cove...
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Genome Sequence and Methylation Patterns of sp. Strain BOL3-1, the First Haloarchaeon Isolated and Cultured from Salar de Uyuni, Bolivia.
Published: May, 2019

Abstract: sp. strain BOL3-1 was isolated from Salar de Uyuni, Bolivia, and sequenced using single-molecule real-time sequencing. Its 3.7-Mbp genome was analyzed for gene content and methylation patterns and incorporated into the Haloarchaeal Genomes Databas...
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The Reference Genome Sequence of Scutellaria baicalensis Provides Insights into the Evolution of Wogonin Biosynthesis.
Published: April, 2019

Abstract: Scutellaria baicalensis Georgi is important in Chinese traditional medicine where preparations of dried roots, "Huang Qin," are used for liver and lung complaints and as complementary cancer treatments. We report a high-quality reference genome se...
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Biocompatible N-acetyl cysteine reduces graphene oxide and persists at the surface as a green radical scavenger.
Published: March, 2019

Abstract: We demonstrate that N-acetyl cysteine (NAC) reduces graphene oxide (GO) at room temperature. This represents a new green method to produce reduced GO (rGO). NAC adheres to the rGO surface as demonstrated by several spectroscopy techniques and avoi...
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The alternative reality of plant mitochondrial DNA
Published: March, 2019

Abstract: Plant mitochondrial genomes are usually assembled and displayed as circular maps based on the widely-held assumption that circular genome molecules are the primary form of mitochondrial DNA, despite evidence to the contrary. Many plant mitochondri...
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Characterizing the Major Structural Variant Alleles of the Human Genome.
Published: January, 2019

Abstract: In order to provide a comprehensive resource for human structural variants (SVs), we generated long-read sequence data and analyzed SVs for fifteen human genomes. We sequence resolved 99,604 insertions, deletions, and inversions including 2,238 (1...
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Complete Genome Sequence and Methylome Analysis of Micrococcus luteus SA211, a Halophilic, Lithium-Tolerant Actinobacterium from Argentina.
Published: January, 2019

Abstract: Micrococcus luteus has been found in a wide range of habitats. We report the complete genome sequence and methylome analysis of strain SA211 isolated from a hypersaline, lithium-rich, high-altitude salt flat in Argentina with single-molecule real-...
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Reference genome for the WHO reference strain for Mycobacterium bovis BCG Danish, the present tuberculosis vaccine
Published: December, 2018

Abstract: Mycobacterium bovis bacillus Calmette-Guérin (M. bovis BCG) is the only vaccine available against tuberculosis (TB). This study reports on an integrated genome analysis workflow for BCG, resulting in the completely assembled genome sequence...
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SMRT long reads and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (Hirundo rustica rustica).
Published: November, 2018

Abstract: Background: The barn swallow (Hirundo rustica) is a migratory bird that has been the focus of a large number of ecological, behavioural and genetic studies. To facilitate further population genetics and genomic studies, here we present a reference...
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Improved reference genome of Aedes aegypti informs arbovirus vector control.
Published: November, 2018

Abstract: Female Aedes aegypti mosquitoes infect more than 400 million people each year with dangerous viral pathogens including dengue, yellow fever, Zika and chikungunya. Progress in understanding the biology of mosquitoes and developing the tools to...
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Whole-genome landscape of Medicago truncatula symbiotic genes.
Published: November, 2018

Abstract: Advances in deciphering the functional architecture of eukaryotic genomes have been facilitated by recent breakthroughs in sequencing technologies, enabling a more comprehensive representation of genes and repeat elements in genome sequence assemb...
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Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps.
Published: November, 2018

Abstract: Plant genomes are often characterized by a high level of repetitiveness and polyploid nature. Consequently, creating genome assemblies for plant genomes is challenging. The introduction of short-read technologies 10 years ago substantially increas...
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The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird.
Published: October, 2018

Abstract: Many animal species comprise discrete phenotypic forms. A common example in natural populations of insects is the occurrence of different color patterns, which has motivated a rich body of ecological and genetic research [1-6]. The occurrence of d...
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Long-read sequence capture of the hemoglobin gene clusters across gadid species.
Published: October, 2018

Abstract: Combining high-throughput sequencing with targeted sequence capture has become an attractive tool to study specific genomic regions of interest. Most studies have so far focused on the exome using short-read technology. These approaches are not de...
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Genomic Structural Variations Within Five Continental Populations of .
Published: October, 2018

Abstract: Chromosomal structural variations (SV) including insertions, deletions, inversions, and translocations occur within the genome and can have a significant effect on organismal phenotype. Some of these effects are caused by structural variations con...
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Long-read sequencing identified a causal structural variant in an exome-negative case and enabled preimplantation genetic diagnosis.
Published: September, 2018

Abstract: Background: For a proportion of individuals judged clinically to have a recessive Mendelian disease, only one heterozygous pathogenic variant can be found from clinical whole exome sequencing (WES), posing a challenge to genetic diagnosis and gene...
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Long-read sequencing across the C9orf72 'GGGGCC' repeat expansion: implications for clinical use and genetic discovery efforts in human disease.
Published: August, 2018

Abstract: BACKGROUND: Many neurodegenerative diseases are caused by nucleotide repeat expansions, but most expansions, like the C9orf72 'GGGGCC' (GC) repeat that causes approximately 5-7% of all amyotrophic lateral sclerosis (ALS) and frontotemporal dementi...
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The complete methylome of an entomopathogenic bacterium reveals the existence of loci with unmethylated Adenines.
Published: August, 2018

Abstract: DNA methylation can serve to control diverse phenomena in eukaryotes and prokaryotes, including gene regulation leading to cell differentiation. In bacteria, DNA methylomes (i.e., methylation state of each base of the whole genome) have been descr...
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Long-read sequence capture of the haemoglobin gene clusters across codfish species.
Published: August, 2018

Abstract: Combining high-throughput sequencing with targeted sequence capture has become an attractive tool to study specific genomic regions of interest. Most studies have so far focused on the exome using short-read technology. These approaches are not de...
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A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits.
Published: June, 2018

Abstract: Rose is the world's most important ornamental plant, with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Roses are outbred and can have various ploidy levels. Our obje...
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Draft genome of the Peruvian scallop Argopecten purpuratus.
Published: April, 2018

Abstract: Background: The Peruvian scallop, Argopecten purpuratus, is mainly cultured in southern Chile and Peru was introduced into China in the last century. Unlike other Argopecten scallops, the Peruvian scallop normally has a long life span of up to 7 t...
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Overview of Next-Generation Sequencing Technologies.
Published: April, 2018

Abstract: High throughput DNA sequencing methodology (next generation sequencing; NGS) has rapidly evolved over the past 15 years and new methods are continually being commercialized. As the technology develops, so do increases in the number of correspondin...
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Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains.
Published: January, 2018

Abstract: BACKGROUND: Without knowledge of their genomic sequences, it is impossible to make functional models of the bacteria that make up human and animal microbiota. Unfortunately, the vast majority of publicly available genomes are only working drafts, ...
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Single-Molecule Sequencing Reveals the Chromosome-Scale Genomic Architecture of the Nematode Model Organism Pristionchus pacificus.
Published: October, 2017

Abstract: The nematode Pristionchus pacificus is an established model for integrative evolutionary biology and comparative studies with Caenorhabditis elegans. While an existing genome draft facilitated the identification of several genes controlling variou...
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De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads
Published: October, 2017

Abstract: Reference-quality genomes are expected to provide a resource for studying gene structure, function, and evolution. However, often genes of interest are not completely or accurately assembled, leading to unknown errors in analyses or additional clo...
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Comparative Analysis of Ralstonia solanacearum Methylomes
Published: April, 2017

Abstract: Ralstonia solanacearum is an important soil-borne plant pathogen with broad geographical distribution and the ability to cause wilt disease in many agriculturally important crops. Genome sequencing of multiple R. solanacearum strains has identifie...
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Condition-dependent co-regulation of genomic clusters of virulence factors in the grapevine trunk pathogen Neofusicoccum parvum
Published: September, 2016

Abstract: The ascomycete Neofusicoccum parvum, one of the causal agents of Botryosphaeria dieback, is a destructive wood-infecting fungus and a serious threat to grape production worldwide. The capability of colonizing woody tissue combined with the secreti...
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Complete genome of Staphylococcus aureus Tager 104 provides evidence of its relation to modern systemic hospital-acquired strains
Published: March, 2016

Abstract: Background Staphylococcus aureus (S. aureus) infections range in severity due to expression of certain virulence factors encoded on mobile genetic elements (MGE). As such, characterization of these MGE, as well as single nucleotide pol...
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Diversification of bacterial genome content through distinct mechanisms over different timescales.
Published: November, 2014

Abstract: Bacterial populations often consist of multiple co-circulating lineages. Determining how such population structures arise requires understanding what drives bacterial diversification. Using 616 systematically sampled genomes, we show that Streptoc...
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Emergence of scarlet fever Streptococcus pyogenes emm12 clones in Hong Kong is associated with toxin acquisition and multidrug resistance
Published: November, 2014

Abstract: A scarlet fever outbreak began in mainland China and Hong Kong in 2011 (refs. 1–6). Macrolide- and tetracycline-resistant Streptococcus pyogenes emm12 isolates represent the majority of clinical cases. Recently, we identified two m...
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Microevolution of Burkholderia pseudomallei during an acute infection.
Published: September, 2014

Abstract: We used whole-genome sequencing to evaluate 69 independent colonies of Burkholderia pseudomallei isolated from seven body sites of a patient with acute disseminated melioidosis. Fourteen closely related genotypes were found, providing evidence for...
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