scholarly journals Distinct genetic spectrums and evolution patterns of SARS-CoV-2

2020 ◽  
Author(s):  
Sheng Liu ◽  
Jikui Shen ◽  
Lei Yang ◽  
Chang-Deng Hu ◽  
Jun Wan
Keyword(s):  
Complete Genome ◽  
Clustering Method ◽  
Single Nucleotide Variants ◽  
Genome Sequences ◽  
Nucleotide Substitutions ◽  
High Quality ◽  
High Coverage ◽  
Single Nucleotide ◽  
Multiple Groups ◽  
Over Time

AbstractFour signature groups of single-nucleotide variants (SNVs) were identified using two-way clustering method in about twenty thousand high quality and high coverage SARS-CoV-2 complete genome sequences. Some frequently occurred SNVs predominate but are mutually exclusively presented in patients from different countries and areas. These major SNV signatures exhibited distinguished evolution patterns over time. Although it was rare, our data indicated possible cross-infections with multiple groups of SNVs existed simultaneously in some patients, suggesting infections from different SARS-CoV-2 clades or potential re-combination of SARS-CoV-2 sequences. Interestingly nucleotide substitutions among SARS-CoV-2 genomes tend to occur at the sites where one bat RaTG13 coronavirus sequences differ from Wuhan-Hu-1 genome, indicating the tolerance of mutations on those sites or suggesting that major viral strains might exist between Wuhan-Hu-1 and RaTG13 coronavirus.

scholarly journals Whole-Genome Sequences of Two Closely Related Bacteria, Actinomyces sp. Strain Chiba101 and Actinomyces denticolens DSM 20671T

2017 ◽  
Vol 5 (14) ◽  
Author(s):  
Yu Kanesaki ◽  
Taichiro Ishige ◽  
Yuriko Sekigawa ◽  
Tomoko Kobayashi ◽  
Yasushi Torii ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Whole Genome ◽  
Genome Sequences ◽  
High Quality ◽  
Content Type

ABSTRACT Actinomyces sp. strain Chiba101, isolated from an arthritic leg joint of a pig raised in Japan, is a bacterium closely related to Actinomyces denticolens. Here, we deciphered the complete genome sequence of Actinomyces sp. Chiba101 and the high-quality draft genome sequence of A. denticolens DSM 20671T.

scholarly journals Genome aging: somatic mutation in the brain links age-related decline with disease and nominates pathogenic mechanisms

2019 ◽  
Vol 28 (R2) ◽  
pp. R197-R206 ◽  
Author(s):  
Michael A Lodato ◽  
Christopher A Walsh
Keyword(s):  
Human Brain ◽  
Somatic Mutation ◽  
Somatic Mutations ◽  
Late Onset ◽  
Whole Genome ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Age Related ◽  
The Brain ◽  
Over Time

AbstractAging is a mysterious process, not only controlled genetically but also subject to random damage that can accumulate over time. While DNA damage and subsequent mutation in somatic cells were first proposed as drivers of aging more than 60 years ago, whether and to what degree these processes shape the neuronal genome in the human brain could not be tested until recent technological breakthroughs related to single-cell whole-genome sequencing. Indeed, somatic single-nucleotide variants (SNVs) increase with age in the human brain, in a somewhat stochastic process that may nonetheless be controlled by underlying genetic programs. Evidence from the literature suggests that in addition to demonstrated increases in somatic SNVs during aging in normal brains, somatic mutation may also play a role in late-onset, sporadic neurodegenerative diseases, such as Alzheimer’s disease and Parkinson’s disease. In this review, we will discuss somatic mutation in the human brain, mechanisms by which somatic mutations occur and can be controlled, and how this process can impact human health.

scholarly journals MethylExtract: High-Quality methylation maps and SNV calling from whole genome bisulfite sequencing data

F1000Research ◽  
2014 ◽  
Vol 2 ◽  
pp. 217 ◽  
Author(s):  
Guillermo Barturen ◽  
Antonio Rueda ◽  
José L. Oliver ◽  
Michael Hackenberg
Keyword(s):  
High Throughput ◽  
Sequence Variation ◽  
High Throughput Sequencing ◽  
Whole Genome ◽  
Single Nucleotide Variants ◽  
High Quality ◽  
Single Nucleotide ◽  
Error Sources ◽  
Link Type ◽  
Genome Methylation

Whole genome methylation profiling at a single cytosine resolution is now feasible due to the advent of high-throughput sequencing techniques together with bisulfite treatment of the DNA. To obtain the methylation value of each individual cytosine, the bisulfite-treated sequence reads are first aligned to a reference genome, and then the profiling of the methylation levels is done from the alignments. A huge effort has been made to quickly and correctly align the reads and many different algorithms and programs to do this have been created. However, the second step is just as crucial and non-trivial, but much less attention has been paid to the final inference of the methylation states. Important error sources do exist, such as sequencing errors, bisulfite failure, clonal reads, and single nucleotide variants.We developed MethylExtract, a user friendly tool to: i) generate high quality, whole genome methylation maps and ii) detect sequence variation within the same sample preparation. The program is implemented into a single script and takes into account all major error sources. MethylExtract detects variation (SNVs – Single Nucleotide Variants) in a similar way to VarScan, a very sensitive method extensively used in SNV and genotype calling based on non-bisulfite-treated reads. The usefulness of MethylExtract is shown by means of extensive benchmarking based on artificial bisulfite-treated reads and a comparison to a recently published method, called Bis-SNP.MethylExtract is able to detect SNVs within High-Throughput Sequencing experiments of bisulfite treated DNA at the same time as it generates high quality methylation maps. This simultaneous detection of DNA methylation and sequence variation is crucial for many downstream analyses, for example when deciphering the impact of SNVs on differential methylation. An exclusive feature of MethylExtract, in comparison with existing software, is the possibility to assess the bisulfite failure in a statistical way. The source code, tutorial and artificial bisulfite datasets are available at http://bioinfo2.ugr.es/MethylExtract/ and http://sourceforge.net/projects/methylextract/, and also permanently accessible from 10.5281/zenodo.7144.

scholarly journals GESS: a database of global evaluation of SARS-CoV-2/hCoV-19 sequences

2020 ◽  
Vol 49 (D1) ◽  
pp. D706-D714 ◽  
Author(s):  
Shuyi Fang ◽  
Kailing Li ◽  
Jikui Shen ◽  
Sheng Liu ◽  
Juli Liu ◽  
...  
Keyword(s):  
Genomic Region ◽  
Comprehensive Analysis ◽  
Mutation Rates ◽  
Global Evaluation ◽  
Single Nucleotide Variants ◽  
High Coverage ◽  
Single Nucleotide ◽  
Genomic Variations ◽  
Area Of Interest ◽  
The World

Abstract The COVID-19 outbreak has become a global emergency since December 2019. Analysis of SARS-CoV-2 sequences can uncover single nucleotide variants (SNVs) and corresponding evolution patterns. The Global Evaluation of SARS-CoV-2/hCoV-19 Sequences (GESS, https://wan-bioinfo.shinyapps.io/GESS/) is a resource to provide comprehensive analysis results based on tens of thousands of high-coverage and high-quality SARS-CoV-2 complete genomes. The database allows user to browse, search and download SNVs at any individual or multiple SARS-CoV-2 genomic positions, or within a chosen genomic region or protein, or in certain country/area of interest. GESS reveals geographical distributions of SNVs around the world and across the states of USA, while exhibiting time-dependent patterns for SNV occurrences which reflect development of SARS-CoV-2 genomes. For each month, the top 100 SNVs that were firstly identified world-widely can be retrieved. GESS also explores SNVs occurring simultaneously with specific SNVs of user's interests. Furthermore, the database can be of great help to calibrate mutation rates and identify conserved genome regions. Taken together, GESS is a powerful resource and tool to monitor SARS-CoV-2 migration and evolution according to featured genomic variations. It provides potential directive information for prevalence prediction, related public health policy making, and vaccine designs.

scholarly journals Complete Genome Sequences of Two Methicillin-Sensitive Staphylococcus aureus Isolates Representing a Population Subset Highly Prevalent in Human Colonization

2016 ◽  
Vol 4 (4) ◽  
Author(s):  
Robert E. Weber ◽  
Franziska Layer ◽  
Stephan Fuchs ◽  
Jennifer K. Bender ◽  
Stefan Fiedler ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Complete Genome ◽  
Draft Genome ◽  
Sequence Type ◽  
Genome Sequences ◽  
High Quality ◽  
Human Colonization

Here, we report the high-quality draft genome sequences of two methicillin-susceptible Staphylococcus aureus isolates, 08-02119 and 08-02300. Belonging to sequence type 582 (ST582) and ST7, both isolates are representatives of clonal lineages often associated with asymptomatic colonization of humans.

scholarly journals Are sites with multiple single nucleotide variants in cancer genomes a consequence of drivers, hypermutable sites or sequencing errors?

2016 ◽  
Author(s):  
Thomas C A Smith ◽  
Antony M Carr ◽  
Adam C Eyre-Walker
Keyword(s):  
Mutation Rate ◽  
Cancer Genome ◽  
Rate Variation ◽  
Single Nucleotide Variants ◽  
Genome Sequences ◽  
Single Nucleotide ◽  
Sequencing Errors ◽  
Cancer Genomes ◽  
Mutation Rate Variation

Across indepedent cancer genomes it has been observed that some sites have been recurrently hit by single nucleotide variants (SNVs). Such recurrently hit sites might be either i) drivers of cancer that are postively selected during oncogenesis, ii) due to mutation rate variation, or iii) due to sequencing and assembly errors. We have investigated the cause of recurrently hit sites in a dataset of >3 million SNVs from 507 complete cancer genome sequences. We find evidence that many sites have been hit significantly more often than one would expect by chance, even taking into account the effect of the adjacent nucleotides on the rate of mutation. We find that the density of these recurrently hit sites is higher in non-coding than coding DNA and hence conclude that most of them are unlikely to be drivers. We also find that most of them are found in parts of the genome that are not uniquely mappable and hence are likly to be due to mapping errors. In support of the error hypothesis, we find that recurently hit sites are not randomly distributed across sequences from different laboratories. We fit a model to the data in which the rate of mutation is constant across sites but the rate of error varies. This model suggests that ~4% of all SNVs are error in this dataset, but that the rate of error varies by thousands-of-fold.

scholarly journals Comparative genomic analysis of the principal Cryptosporidium species that infect humans

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10478
Author(s):  
Laura M. Arias-Agudelo ◽  
Gisela Garcia-Montoya ◽  
Felipe Cabarcas ◽  
Ana L. Galvan-Diaz ◽  
Juan F. Alzate
Keyword(s):  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Single Nucleotide Variants ◽  
Nucleotide Substitutions ◽  
Genomic Comparison ◽  
Single Nucleotide ◽  
Associated Proteins ◽  
Species Specific ◽  
Ngs Data

Cryptosporidium parasites are ubiquitous and can infect a broad range of vertebrates and are considered the most frequent protozoa associated with waterborne parasitic outbreaks. The intestine is the target of three of the species most frequently found in humans: C. hominis, C. parvum, and. C. meleagridis. Despite the recent advance in genome sequencing projects for this apicomplexan, a broad genomic comparison including the three species most prevalent in humans have not been published so far. In this work, we downloaded raw NGS data, assembled it under normalized conditions, and compared 23 publicly available genomes of C. hominis, C. parvum, and C. meleagridis. Although few genomes showed highly fragmented assemblies, most of them had less than 500 scaffolds and mean coverage that ranged between 35X and 511X. Synonymous single nucleotide variants were the most common in C. hominis and C. meleagridis, while in C. parvum, they accounted for around 50% of the SNV observed. Furthermore, deleterious nucleotide substitutions common to all three species were more common in genes associated with DNA repair, recombination, and chromosome-associated proteins. Indel events were observed in the 23 studied isolates that spanned up to 500 bases. The highest number of deletions was observed in C. meleagridis, followed by C. hominis, with more than 60 species-specific deletions found in some isolates of these two species. Although several genes with indel events have been partially annotated, most of them remain to encode uncharacterized proteins.

scholarly journals A rapid, super-selective method for detection of single nucleotide variants in C. elegans

2020 ◽  
Author(s):  
Denis Touroutine ◽  
Jessica E. Tanis
Keyword(s):  
Low Cost ◽  
Primer Design ◽  
Site Directed Mutagenesis ◽  
Amplification Efficiency ◽  
Single Nucleotide Variants ◽  
Nucleotide Substitutions ◽  
Single Nucleotide ◽  
Colony Pcr ◽  
Sequence Composition ◽  
C Elegans

ABSTRACTWith the widespread use of single nucleotide variants generated through mutagenesis screens, the million mutation project, and genome editing technologies, there is pressing need for an efficient and low-cost strategy to genotype single nucleotide substitutions. We have developed a rapid and inexpensive method for detection of point mutants through optimization of SuperSelective (SS) primers for end point PCR in Caenorhabditis elegans. Each SS primer consists of a 5’ “anchor” that hybridizes to the template, followed by a non-complementary “bridge,” and a “foot” corresponding to the target allele. The foot sequence is short, such that a single mismatch at the terminal 3’ nucleotide destabilizes primer binding and prevents extension, enabling discrimination of different alleles. We explored how length, stability, and sequence composition of each SS primer segment affected selectivity and efficiency in order to develop simple rules for primer design that allow for distinction between any mismatches in various genetic contexts over a broad range of annealing temperatures. Manipulating bridge length affects amplification efficiency, while modifying the foot sequence can increase discriminatory power. Flexibility in the positioning of the anchor enables SS primers to be used for genotyping in regions with sequences that are challenging for standard primer design. In summary, we have demonstrated flexibility in design of SS primers and their utility for genotyping in C. elegans. Since SS primers reliably detect single nucleotide variants, we propose that this method could have broad application for SNP mapping, screening of CRISPR mutants, and colony PCR to identify successful site-directed mutagenesis constructs.

scholarly journals Complete Genome Sequences of Priestia megaterium Type and Clinical Strains Feature Complex Plasmid Arrays

2021 ◽  
Vol 10 (27) ◽  
Author(s):  
Philip S. Shwed ◽  
J. Crosthwait ◽  
K. Weedmark ◽  
E. Hoover ◽  
F. Dussault
Keyword(s):  
United States ◽  
Complete Genome ◽  
The United States ◽  
Genome Sequences ◽  
High Quality ◽  
Content Type ◽  
Clinical Strains ◽  
Human Samples

Here, we report the high-quality complete genome sequences and plasmid arrays of Priestia megaterium ATCC 14581 T and of two clinical strains (2008724129 and 2008724142) isolated from human samples in the United States.

scholarly journals Complete Genome Sequences of Eight Rhizobium Symbionts Associated with Common Bean (Phaseolus vulgaris)

2017 ◽  
Vol 5 (30) ◽  
Author(s):  
Rosa Isela Santamaría ◽  
Patricia Bustos ◽  
Olga María Pérez-Carrascal ◽  
Fabiola Miranda-Sánchez ◽  
Pablo Vinuesa ◽  
...  
Keyword(s):  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Complete Genome ◽  
Genome Sequences ◽  
High Quality ◽  
Content Type ◽  
Comparative Analyses ◽  
Content Specificity ◽  
Symbiotic Properties ◽  
Evolutionary Lineages

ABSTRACT We present here the high-quality complete genome sequences of eight strains of Rhizobium-nodulating Phaseolus vulgaris. Comparative analyses showed that some of them belonged to different genomic and evolutionary lineages with common symbiotic properties. Two novel symbiotic plasmids (pSyms) with P. vulgaris specificity are reported here.

Sign in / Sign up

Export Citation Format

Share Document