scholarly journals The Adenine/Thymine Deleterious Selection Model for GC Content Evolution at the Third Codon Position of the Histone Genes in Drosophila

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 721
Author(s):  
Yoshinori Matsuo
Keyword(s):  
Size Effect ◽  
Deleterious Effect ◽  
Codon Position ◽  
Gc Content ◽  
Selection Model ◽  
Drosophila Species ◽  
Whole Genome ◽  
Histone Genes ◽  
The Third ◽  
Adenine Thymine

The evolution of the GC (guanine cytosine) content at the third codon position of the histone genes (H1, H2A, H2B, H3, H4, H2AvD, H3.3A, H3.3B, and H4r) in 12 or more Drosophila species is reviewed. For explaining the evolution of the GC content at the third codon position of the genes, a model assuming selection with a deleterious effect for adenine/thymine and a size effect is presented. The applicability of the model to whole-genome genes is also discussed.

scholarly journals SATELLITE DNAs IN THE EMBRYOS OF VARIOUS SPECIES OF THE GENUS DROSOPHILA

Genetics ◽  
1972 ◽  
Vol 72 (3) ◽  
pp. 431-439
Author(s):  
E C Travaglini ◽  
J Petrovic ◽  
J Schultz
Keyword(s):  
Buoyant Density ◽  
Gc Content ◽  
Drosophila Species ◽  
Class I ◽  
Evolutionary Divergence ◽  
Dna Molecules ◽  
Class Iii ◽  
Satellite Dnas ◽  
Evolutionary Pattern ◽  
Gc Composition

ABSTRACT A tentative evolutionary pattern has been found for two classes of the multiple satellite DNA's found in the genus Drosophila. The satellite DNA's from five Drosophila species (D. melanogaster, D. simulans, D. nasuta, D. virilis and D. hydei) were analyzed and found to fall into three arbitrary CsCl buoyant density classes: Class I, ρ = 1.661-1.669 g cm-3, DNA molecules composed of primarily dA and dT moieties; Class II, ρ = 1.685 and ρ = 1.692, DNA molecules of low GC content; and Class III, ρ = 1.711, a DNA of high GC composition. The dAT satellite DNA's appear in all the species studied except D. hydei, the species of most recent evolutionary divergence, whereas the heavy satellite appears only in the two species of most recent divergence, D. virilis and D. hydei.

scholarly journals Rapid Spread of the SARS-CoV-2 Variant of Concern 202012/01 in Southern Italy (December 2020–March 2021)

2021 ◽  
Vol 18 (9) ◽  
pp. 4766
Author(s):  
Daniela Loconsole ◽  
Francesca Centrone ◽  
Caterina Morcavallo ◽  
Silvia Campanella ◽  
Anna Sallustio ◽  
...  
Keyword(s):  
Clinical Characteristics ◽  
Large Scale ◽  
Southern Italy ◽  
Whole Genome ◽  
Third Wave ◽  
Gene Target ◽  
The Third ◽  
Rapid Spread ◽  
Pharmaceutical Interventions ◽  
Over Time

Epidemiological and virological studies have revealed that SARS-CoV-2 variants of concern (VOCs) are emerging globally, including in Europe. The aim of this study was to evaluate the spread of B.1.1.7-lineage SARS-CoV-2 in southern Italy from December 2020–March 2021 through the detection of the S gene target failure (SGTF), which could be considered a robust proxy of VOC B.1.1.7. SGTF was assessed on 3075 samples from week 52/2020 to week 10/2021. A subset of positive samples identified in the Apulia region during the study period was subjected to whole-genome sequencing (WGS). A descriptive and statistical analysis of the demographic and clinical characteristics of cases according to SGTF status was performed. Overall, 20.2% of samples showed SGTF; 155 strains were confirmed as VOC 202012/01 by WGS. The proportion of SGTF-positive samples rapidly increased over time, reaching 69.2% in week 10/2021. SGTF-positive cases were more likely to be symptomatic and to result in hospitalization (p < 0.0001). Despite the implementation of large-scale non-pharmaceutical interventions (NPIs), such as the closure of schools and local lockdowns, a rapid spread of VOC 202012/01 was observed in southern Italy. Strengthened NPIs and rapid vaccine deployment, first among priority groups and then among the general population, are crucial both to contain the spread of VOC 202012/01 and to flatten the curve of the third wave.

scholarly journals Evaluating coverage bias in next-generation sequencing of Escherichia coli

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0253440
Author(s):  
Samantha Gunasekera ◽  
Sam Abraham ◽  
Marc Stegger ◽  
Stanley Pang ◽  
Penghao Wang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
De Novo ◽  
Fragment Size ◽  
Gc Content ◽  
Main Concern ◽  
Whole Genome ◽  
Assembly Quality ◽  
Coverage Bias

Whole-genome sequencing is essential to many facets of infectious disease research. However, technical limitations such as bias in coverage and tagmentation, and difficulties characterising genomic regions with extreme GC content have created significant obstacles in its use. Illumina has claimed that the recently released DNA Prep library preparation kit, formerly known as Nextera Flex, overcomes some of these limitations. This study aimed to assess bias in coverage, tagmentation, GC content, average fragment size distribution, and de novo assembly quality using both the Nextera XT and DNA Prep kits from Illumina. When performing whole-genome sequencing on Escherichia coli and where coverage bias is the main concern, the DNA Prep kit may provide higher quality results; though de novo assembly quality, tagmentation bias and GC content related bias are unlikely to improve. Based on these results, laboratories with existing workflows based on Nextera XT would see minor benefits in transitioning to the DNA Prep kit if they were primarily studying organisms with neutral GC content.

scholarly journals The Whole-Genome Sequence of the Novel Yeast Species Metschnikowia persimmonesis Isolated from Medicinal Plant Diospyros kaki Thunb

2021 ◽  
Author(s):  
Endang Rahmat ◽  
Inkyu Park ◽  
Youngmin Kang
Keyword(s):  
Gc Content ◽  
Whole Genome Sequence ◽  
Diospyros Kaki ◽  
Whole Genome ◽  
The Novel ◽  
Data Set ◽  
Draft Assembly ◽  
Future Possibility ◽  
Complete Set ◽  
New Yeast

Abstract The new yeast Metschnikowia persimmonesis KCTC 12991BP (KIOM G15050 strain) exhibits strong antimicrobial activity against some pathogens. This activity may be related to the medicinal profile of secondary metabolites that could be found in the genome of this species. Therefore, to explore its future possibility of producing some beneficial activities, including medicinal ability, we report high quality whole-genome assembly of M. persimmonesis produced by PacBio RSII sequencer. The final draft assembly consisted of 16 scaffolds with GC content of 45.90% and comprised a fairly complete set (82.8%) of BUSCO result using Saccharomycetales lineage data set. The total length of the genome was 16.473 Mb, with a scaffold N50 of 1.982 Mb. Annotation of the M. persimmonesis genome revealed presence of 7,029 genes and 6,939 functionally annotated proteins. Based on the analysis of phylogenetic relationship and the average nucleotide identities (ANI), M. persimmonesis was proved to a novel species within the Metschnikowia genus. This finding is expected to significantly contribute to the discovery of high-value natural products from M. persimmonesis as well as for genome biology and evolution comparative analysis within Metschnikowia species.

scholarly journals Comparative Genomics Reveals the Core Gene Toolbox for the Fungus-Insect Symbiosis

mBio ◽  
2018 ◽  
Vol 9 (3) ◽  
Author(s):  
Yan Wang ◽  
Matt Stata ◽  
Wei Wang ◽  
Jason E. Stajich ◽  
Merlin M. White ◽  
...  
Keyword(s):  
Entomopathogenic Fungi ◽  
Gc Content ◽  
Core Gene ◽  
Whole Genome ◽  
Black Flies ◽  
Genome Sequences ◽  
Free Living ◽  
Genomic Features ◽  
Insect Pathogens ◽  
Insect Gut

ABSTRACTModern genomics has shed light on many entomopathogenic fungi and expanded our knowledge widely; however, little is known about the genomic features of the insect-commensal fungi. Harpellales are obligate commensals living in the digestive tracts of disease-bearing insects (black flies, midges, and mosquitoes). In this study, we produced and annotated whole-genome sequences of nine Harpellales taxa and conducted the first comparative analyses to infer the genomic diversity within the members of the Harpellales. The genomes of the insect gut fungi feature low (26% to 37%) GC content and large genome size variations (25 to 102 Mb). Further comparisons with insect-pathogenic fungi (from both Ascomycota and Zoopagomycota), as well as with free-living relatives (as negative controls), helped to identify a gene toolbox that is essential to the fungus-insect symbiosis. The results not only narrow the genomic scope of fungus-insect interactions from several thousands to eight core players but also distinguish host invasion strategies employed by insect pathogens and commensals. The genomic content suggests that insect commensal fungi rely mostly on adhesion protein anchors that target digestive system, while entomopathogenic fungi have higher numbers of transmembrane helices, signal peptides, and pathogen-host interaction (PHI) genes across the whole genome and enrich genes as well as functional domains to inactivate the host inflammation system and suppress the host defense. Phylogenomic analyses have revealed that genome sizes of Harpellales fungi vary among lineages with an integer-multiple pattern, which implies that ancient genome duplications may have occurred within the gut of insects.IMPORTANCEInsect guts harbor various microbes that are important for host digestion, immune response, and disease dispersal in certain cases. Bacteria, which are among the primary endosymbionts, have been studied extensively. However, fungi, which are also frequently encountered, are poorly known with respect to their biology within the insect guts. To understand the genomic features and related biology, we produced the whole-genome sequences of nine gut commensal fungi from disease-bearing insects (black flies, midges, and mosquitoes). The results show that insect gut fungi tend to have low GC content across their genomes. By comparing these commensals with entomopathogenic and free-living fungi that have available genome sequences, we found a universal core gene toolbox that is unique and thus potentially important for the insect-fungus symbiosis. This comparative work also uncovered different host invasion strategies employed by insect pathogens and commensals, as well as a model system to study ancient fungal genome duplication within the gut of insects.

scholarly journals Whole-Genome Sequence of Fish-Pathogenic Enterococcus faecalis Strain BFFF11

2020 ◽  
Vol 9 (7) ◽  
Author(s):  
Tasmina Akter ◽  
M. Mahbubur Rahman ◽  
Alfred Chin Yen Tay ◽  
Rakib Ehsan ◽  
M. Tofazzal Islam
Keyword(s):  
Enterococcus Faecalis ◽  
Genome Sequence ◽  
Gc Content ◽  
Fish Farm ◽  
Pathogenic Bacterium ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type

A fish-pathogenic bacterium, Enterococcus faecalis strain BFFF11, was isolated from a tilapia suffering from streptococcosis in a fish farm in the Gazipur district of Bangladesh. The whole genome of this strain, BFFF11, was 3,067,042 bp, with a GC content of 37.4%.

scholarly journals Whole-Genome Sequencing of Mycobacterium tilburgii Strain MEPHI

2019 ◽  
Vol 8 (40) ◽  
Author(s):  
Jamal Saad ◽  
Michel Drancourt ◽  
Margaret M. Hannan ◽  
Patrick J. Stapleton ◽  
Simon Grandjean Lapierre
Keyword(s):  
Whole Genome Sequencing ◽  
Clinical Isolate ◽  
Genome Sequencing ◽  
Gc Content ◽  
Whole Genome ◽  
Content Type ◽  
Phylogenetic Placement ◽  
Mycobacterium Simiae

Mycobacterium tilburgii is a fastidious mycobacterium which has previously been reported to cause severe disseminated infections. Genome sequencing of the M. tilburgii MEPHI clinical isolate yielded 3.14 Mb, with 66.3% GC content, and confirmed phylogenetic placement within the Mycobacterium simiae complex.

scholarly journals Efficient and accurate determination of genome-wide DNA methylation patterns in Arabidopsis thaliana with enzymatic methyl sequencing

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Suhua Feng ◽  
Zhenhui Zhong ◽  
Ming Wang ◽  
Steven E. Jacobsen
Keyword(s):  
Dna Methylation ◽  
Bisulfite Sequencing ◽  
Accurate Determination ◽  
Gc Content ◽  
Epigenetic Mark ◽  
Whole Genome ◽  
Whole Genome Bisulfite Sequencing ◽  
Genome Wide ◽  
A Genome ◽  
Genome Bisulfite Sequencing

Abstract Background 5′ methylation of cytosines in DNA molecules is an important epigenetic mark in eukaryotes. Bisulfite sequencing is the gold standard of DNA methylation detection, and whole-genome bisulfite sequencing (WGBS) has been widely used to detect methylation at single-nucleotide resolution on a genome-wide scale. However, sodium bisulfite is known to severely degrade DNA, which, in combination with biases introduced during PCR amplification, leads to unbalanced base representation in the final sequencing libraries. Enzymatic conversion of unmethylated cytosines to uracils can achieve the same end product for sequencing as does bisulfite treatment and does not affect the integrity of the DNA; enzymatic methylation sequencing may, thus, provide advantages over bisulfite sequencing. Results Using an enzymatic methyl-seq (EM-seq) technique to selectively deaminate unmethylated cytosines to uracils, we generated and sequenced libraries based on different amounts of Arabidopsis input DNA and different numbers of PCR cycles, and compared these data to results from traditional whole-genome bisulfite sequencing. We found that EM-seq libraries were more consistent between replicates and had higher mapping and lower duplication rates, lower background noise, higher average coverage, and higher coverage of total cytosines. Differential methylation region (DMR) analysis showed that WGBS tended to over-estimate methylation levels especially in CHG and CHH contexts, whereas EM-seq detected higher CG methylation levels in certain highly methylated areas. These phenomena can be mostly explained by a correlation of WGBS methylation estimation with GC content and methylated cytosine density. We used EM-seq to compare methylation between leaves and flowers, and found that CHG methylation level is greatly elevated in flowers, especially in pericentromeric regions. Conclusion We suggest that EM-seq is a more accurate and reliable approach than WGBS to detect methylation. Compared to WGBS, the results of EM-seq are less affected by differences in library preparation conditions or by the skewed base composition in the converted DNA. It may therefore be more desirable to use EM-seq in methylation studies.

scholarly journals Major Revisions in Arthropod Phylogeny Through Improved Supermatrix, With Support for Two Possible Waves of Land Invasion by Chelicerates

2020 ◽  
Vol 16 ◽  
pp. 117693432090373 ◽  
Author(s):  
Katherine E Noah ◽  
Jiasheng Hao ◽  
Luyan Li ◽  
Xiaoyan Sun ◽  
Brian Foley ◽  
...  
Keyword(s):  
Codon Position ◽  
Amino Acid Level ◽  
Phylogenetic Reconstruction ◽  
Original Data ◽  
Data Sets ◽  
Multiple Sequence ◽  
Protein Coding ◽  
Individual Gene ◽  
The Third ◽  
New Hypothesis

Deep phylogeny involving arthropod lineages is difficult to recover because the erosion of phylogenetic signals over time leads to unreliable multiple sequence alignment (MSA) and subsequent phylogenetic reconstruction. One way to alleviate the problem is to assemble a large number of gene sequences to compensate for the weakness in each individual gene. Such an approach has led to many robustly supported but contradictory phylogenies. A close examination shows that the supermatrix approach often suffers from two shortcomings. The first is that MSA is rarely checked for reliability and, as will be illustrated, can be poor. The second is that, to alleviate the problem of homoplasy at the third codon position of protein-coding genes due to convergent evolution of nucleotide frequencies, phylogeneticists may remove or degenerate the third codon position but may do it improperly and introduce new biases. We performed extensive reanalysis of one of such “big data” sets to highlight these two problems, and demonstrated the power and benefits of correcting or alleviating these problems. Our results support a new group with Xiphosura and Arachnopulmonata (Tetrapulmonata + Scorpiones) as sister taxa. This favors a new hypothesis in which the ancestor of Xiphosura and the extinct Eurypterida (sea scorpions, of which many later forms lived in brackish or freshwater) returned to the sea after the initial chelicerate invasion of land. Our phylogeny is supported even with the original data but processed with a new “principled” codon degeneration. We also show that removing the 1673 codon sites with both AGN and UCN codons (encoding serine) in our alignment can partially reconcile discrepancies between nucleotide-based and AA-based tree, partly because two sequences, one with AGN and the other with UCN, would be identical at the amino acid level but quite different at the nucleotide level.

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