scholarly journals PerSVade: Personalized Structural Variation detection in your species of interest

2021 ◽  
Author(s):  
Miquel Angel Schikora-Tamarit ◽  
Toni Gabaldon
Keyword(s):  
Structural Variation ◽  
Reference Genome ◽  
Copy Number Variations ◽  
Genomic Variation ◽  
Optimal Parameters ◽  
Short Reads ◽  
Short Read Sequencing ◽  
Input Sample ◽  
Species Specific

Structural variants (SVs) like translocations, deletions, and other rearrangements underlie genetic and phenotypic variation. SVs are often overlooked due to difficult detection from short-read sequencing. Most algorithms yield low recall on humans, but the performance in other organisms is unclear. Similarly, despite remarkable differences across species genomes, most approaches use parameters optimized for humans. To overcome this and enable species-tailored approaches, we developed perSVade (personalized Structural Variation Detection), a pipeline that identifies SVs in a way that is optimized for any input sample. Starting from short reads, perSVade uses simulations on the reference genome to choose the best SV calling parameters. The output includes the optimally-called SVs and the accuracy, useful to assess the confidence in the results. In addition, perSVade can call small variants and copy-number variations. In summary, perSVade automatically identifies several types of genomic variation from short reads using sample-optimized parameters. We validated that perSVade increases the SV calling accuracy on simulated variants for six diverse eukaryotes, and on datasets of validated human variants. Importantly, we found no universal set of optimal parameters, which underscores the need for species-specific parameter optimization. PerSVade will improve our understanding about the role of SVs in non-human organisms.

scholarly journals DACCOR - Detection, charACterization, and reconstruction of Repetitive regions in bacterial genomes

2017 ◽  
Author(s):  
Alexander Seitz ◽  
Friederike Hanssen ◽  
Kay Nieselt
Keyword(s):  
Base Pair ◽  
Repetitive Sequence ◽  
Reference Genome ◽  
De Novo ◽  
Treponema Pallidum ◽  
Sequencing Data ◽  
Bacterial Genomes ◽  
Short Read ◽  
Short Reads ◽  
Short Read Sequencing

The reconstruction of genomes using mapping based approaches with short reads experiences difficulties when resolving repetitive regions. These repetitive regions in genomes result in low mapping qualities of the respective reads, which in turn lead to many unresolved bases of the genotypers. Currently, the reconstruction of these regions is often based on modified references in which the repetitive regions are masked. However, for many references such masked genomes are not available or are based on repetitive regions of other genomes. Our idea is to identify repetitive regions in the reference genome de novo. These regions can then be used to reconstruct them separately using short read sequencing data. Afterwards the reconstructed repetitive sequence can be inserted into the reconstructed genome. We present the program DACCOR, which performs these steps automatically. Our results show an increased base pair resolution of the repetitive regions in the reconstruction of Treponema pallidum samples, resulting in fewer unresolved bases.

scholarly journals DACCOR–Detection, characterization, and reconstruction of repetitive regions in bacterial genomes

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4742 ◽  
Author(s):  
Alexander Seitz ◽  
Friederike Hanssen ◽  
Kay Nieselt
Keyword(s):  
Base Pair ◽  
Repetitive Sequence ◽  
Reference Genome ◽  
De Novo ◽  
Treponema Pallidum ◽  
Sequencing Data ◽  
Bacterial Genomes ◽  
Short Read ◽  
Short Reads ◽  
Short Read Sequencing

The reconstruction of genomes using mapping-based approaches with short reads experiences difficulties when resolving repetitive regions. These repetitive regions in genomes result in low mapping qualities of the respective reads, which in turn lead to many unresolved bases. Currently, the reconstruction of these regions is often based on modified references in which the repetitive regions are masked. However, for many references, such masked genomes are not available or are based on repetitive regions of other genomes. Our idea is to identify repetitive regions in the reference genome de novo. These regions can then be used to reconstruct them separately using short read sequencing data. Afterward, the reconstructed repetitive sequence can be inserted into the reconstructed genome. We present the program detection, characterization, and reconstruction of repetitive regions, which performs these steps automatically. Our results show an increased base pair resolution of the repetitive regions in the reconstruction of Treponema pallidum samples, resulting in fewer unresolved bases.

scholarly journals DACCOR - Detection, charACterization, and reconstruction of Repetitive regions in bacterial genomes

2017 ◽  
Author(s):  
Alexander Seitz ◽  
Friederike Hanssen ◽  
Kay Nieselt
Keyword(s):  
Base Pair ◽  
Repetitive Sequence ◽  
Reference Genome ◽  
De Novo ◽  
Treponema Pallidum ◽  
Sequencing Data ◽  
Bacterial Genomes ◽  
Short Read ◽  
Short Reads ◽  
Short Read Sequencing

The reconstruction of genomes using mapping based approaches with short reads experiences difficulties when resolving repetitive regions. These repetitive regions in genomes result in low mapping qualities of the respective reads, which in turn lead to many unresolved bases of the genotypers. Currently, the reconstruction of these regions is often based on modified references in which the repetitive regions are masked. However, for many references such masked genomes are not available or are based on repetitive regions of other genomes. Our idea is to identify repetitive regions in the reference genome de novo. These regions can then be used to reconstruct them separately using short read sequencing data. Afterwards the reconstructed repetitive sequence can be inserted into the reconstructed genome. We present the program DACCOR, which performs these steps automatically. Our results show an increased base pair resolution of the repetitive regions in the reconstruction of Treponema pallidum samples, resulting in fewer unresolved bases.

A Problem Based Learning Exercise on Food Security: Understanding the Role of Genomic Variation and Plant Breeding

2018 ◽  
Author(s):  
Jolie WAX ◽  
Zhu Zhuo ◽  
Anna Bower ◽  
Jessica Cooper ◽  
Susan Gachara ◽  
...  
Keyword(s):  
Food Security ◽  
Plant Breeding ◽  
Problem Based Learning ◽  
Genomic Variation

Soil Chemical Pollution and Aggressive Pathologies

2018 ◽  
Vol 69 (8) ◽  
pp. 2278-2282
Author(s):  
Stelian Ioan Morariu ◽  
Letitia Doina Duceac ◽  
Alina Costina Luca ◽  
Florina Popescu ◽  
Liliana Pavel ◽  
...  
Keyword(s):  
Health Care Professionals ◽  
Scientific Progress ◽  
Volcanic Eruptions ◽  
Chemical Pollution ◽  
Optimal Parameters ◽  
Chemical Pollutants ◽  
Wide Range ◽  
Health Physician ◽  
Solid Liquid

Maintaining the soil in optimal parameters is vital for mankind, given its essential role in providing the alimentary base, as well as its extremely slow formation and regeneration (hundreds or thousands of years). The direct and indirect pollution of the soil and especially its chemical pollution represent a corollary of other types of pollution, given that it is produced by solid, liquid and gaseous residues. It may be involved in a wide range of diseases (respiratory, cardiovascular, digestive, renal, haematological, osteoarticular, neurological) of allergic, infectious, degenerative or neoplastic nature, from infancy to the old age. Although there are natural causes of soil pollution (e.g. volcanic eruptions), most pollutants come from human activities, which are the most incriminated in its pollution, degradation and erosion at an accelerated pace. The growing concern of all nations for the adoption of measures to limit the chemical pollution of the soil is partially found so far in viable and effective solutions intended to combat soil contamination and degradation and ensure its restoration. Chemical industrialization leads to technical and scientific progress, but at the same time it can develop related pathologies, which means that the role of the occupational health physician is essential in ensuring prophylaxis and the early detection of occupational diseases. Besides that, the role of the pediatrician is equally precious for the detection of specific diseases caused by chemical pollutants to children, because they will develop into adults with pathological stigma.The chemical pollution of the soil is a major challenge for ecologists, given that it is an important risk factor for many types of afflictions. It requires maximum attention from civil society, health care professionals and government institutions. The specialist in occupational medicine, as well as the pediatrician bear an essential responsibility in both, prevention and treatment.

scholarly journals Dietary Modulation of Bacteriophages as an Additional Player in Inflammation and Cancer

Cancers ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 2036
Author(s):  
Luigi Marongiu ◽  
Markus Burkard ◽  
Sascha Venturelli ◽  
Heike Allgayer
Keyword(s):  
Structural Damage ◽  
Folk Medicine ◽  
Gastrointestinal Diseases ◽  
Potential Contribution ◽  
Anticancer Properties ◽  
Specific Phage ◽  
Microbial Network ◽  
Inflammatory Bowel ◽  
Species Specific

Natural compounds such as essential oils and tea have been used successfully in naturopathy and folk medicine for hundreds of years. Current research is unveiling the molecular role of their antibacterial, anti-inflammatory, and anticancer properties. Nevertheless, the effect of these compounds on bacteriophages is still poorly understood. The application of bacteriophages against bacteria has gained a particular interest in recent years due to, e.g., the constant rise of antimicrobial resistance to antibiotics, or an increasing awareness of different types of microbiota and their potential contribution to gastrointestinal diseases, including inflammatory and malignant conditions. Thus, a better knowledge of how dietary products can affect bacteriophages and, in turn, the whole gut microbiome can help maintain healthy homeostasis, reducing the risk of developing diseases such as diverse types of gastroenteritis, inflammatory bowel disease, or even cancer. The present review summarizes the effect of dietary compounds on the physiology of bacteriophages. In a majority of works, the substance class of polyphenols showed a particular activity against bacteriophages, and the primary mechanism of action involved structural damage of the capsid, inhibiting bacteriophage activity and infectivity. Some further dietary compounds such as caffeine, salt or oregano have been shown to induce or suppress prophages, whereas others, such as the natural sweeter stevia, promoted species-specific phage responses. A better understanding of how dietary compounds could selectively, and specifically, modulate the activity of individual phages opens the possibility to reorganize the microbial network as an additional strategy to support in the combat, or in prevention, of gastrointestinal diseases, including inflammation and cancer.

scholarly journals In Search of Species-Specific SNPs in a Non-Model Animal (European Bison (Bison bonasus))—Comparison of De Novo and Reference-Based Integrated Pipeline of STACKS Using Genotyping-by-Sequencing (GBS) Data

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2226
Author(s):  
Sazia Kunvar ◽  
Sylwia Czarnomska ◽  
Cino Pertoldi ◽  
Małgorzata Tokarska
Keyword(s):  
Reference Genome ◽  
De Novo ◽  
Bos Taurus ◽  
Model Organism ◽  
Genotyping By Sequencing ◽  
Model Organisms ◽  
European Bison ◽  
Model Animal ◽  
Pcr Duplicates ◽  
Species Specific

The European bison is a non-model organism; thus, most of its genetic and genomic analyses have been performed using cattle-specific resources, such as BovineSNP50 BeadChip or Illumina Bovine 800 K HD Bead Chip. The problem with non-specific tools is the potential loss of evolutionary diversified information (ascertainment bias) and species-specific markers. Here, we have used a genotyping-by-sequencing (GBS) approach for genotyping 256 samples from the European bison population in Bialowieza Forest (Poland) and performed an analysis using two integrated pipelines of the STACKS software: one is de novo (without reference genome) and the other is a reference pipeline (with reference genome). Moreover, we used a reference pipeline with two different genomes, i.e., Bos taurus and European bison. Genotyping by sequencing (GBS) is a useful tool for SNP genotyping in non-model organisms due to its cost effectiveness. Our results support GBS with a reference pipeline without PCR duplicates as a powerful approach for studying the population structure and genotyping data of non-model organisms. We found more polymorphic markers in the reference pipeline in comparison to the de novo pipeline. The decreased number of SNPs from the de novo pipeline could be due to the extremely low level of heterozygosity in European bison. It has been confirmed that all the de novo/Bos taurus and Bos taurus reference pipeline obtained SNPs were unique and not included in 800 K BovineHD BeadChip.

scholarly journals Species-Specific Regulation of TRPM2 by PI(4,5)P2 via the Membrane Interfacial Cavity

2021 ◽  
Vol 22 (9) ◽  
pp. 4637
Author(s):  
Daniel Barth ◽  
Andreas Lückhoff ◽  
Frank J. P. Kühn
Keyword(s):  
Amino Acid Residues ◽  
Hek 293 ◽  
Complete Inactivation ◽  
293 Cells ◽  
Activation Mechanisms ◽  
Specific Regulation ◽  
Species Specific ◽  
Inside Out ◽  
Positively Charged

The human apoptosis channel TRPM2 is stimulated by intracellular ADR-ribose and calcium. Recent studies show pronounced species-specific activation mechanisms. Our aim was to analyse the functional effect of phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2), commonly referred to as PIP2, on different TRPM2 orthologues. Moreover, we wished to identify the interaction site between TRPM2 and PIP2. We demonstrate a crucial role of PIP2, in the activation of TRPM2 orthologues of man, zebrafish, and sea anemone. Utilizing inside-out patch clamp recordings of HEK-293 cells transfected with TRPM2, differential effects of PIP2 that were dependent on the species variant became apparent. While depletion of PIP2 via polylysine uniformly caused complete inactivation of TRPM2, restoration of channel activity by artificial PIP2 differed widely. Human TRPM2 was the least sensitive species variant, making it the most susceptible one for regulation by changes in intramembranous PIP2 content. Furthermore, mutations of highly conserved positively charged amino acid residues in the membrane interfacial cavity reduced the PIP2 sensitivity in all three TRPM2 orthologues to varying degrees. We conclude that the membrane interfacial cavity acts as a uniform PIP2 binding site of TRPM2, facilitating channel activation in the presence of ADPR and Ca2+ in a species-specific manner.

scholarly journals Genome diversity in Ukraine

GigaScience ◽  
2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Taras K Oleksyk ◽  
Walter W Wolfsberger ◽  
Alexandra M Weber ◽  
Khrystyna Shchubelka ◽  
Olga T Oleksyk ◽  
...  
Keyword(s):  
Sequence Data ◽  
Copy Number Variations ◽  
Genomic Variation ◽  
High Coverage ◽  
Genome Data ◽  
New Information ◽  
Genome Wide ◽  
Public Data ◽  
Genome Wide Data ◽  
Multiple Samples

Abstract Background The main goal of this collaborative effort is to provide genome-wide data for the previously underrepresented population in Eastern Europe, and to provide cross-validation of the data from genome sequences and genotypes of the same individuals acquired by different technologies. We collected 97 genome-grade DNA samples from consented individuals representing major regions of Ukraine that were consented for public data release. BGISEQ-500 sequence data and genotypes by an Illumina GWAS chip were cross-validated on multiple samples and additionally referenced to 1 sample that has been resequenced by Illumina NovaSeq6000 S4 at high coverage. Results The genome data have been searched for genomic variation represented in this population, and a number of variants have been reported: large structural variants, indels, copy number variations, single-nucletide polymorphisms, and microsatellites. To our knowledge, this study provides the largest to-date survey of genetic variation in Ukraine, creating a public reference resource aiming to provide data for medical research in a large understudied population. Conclusions Our results indicate that the genetic diversity of the Ukrainian population is uniquely shaped by evolutionary and demographic forces and cannot be ignored in future genetic and biomedical studies. These data will contribute a wealth of new information bringing forth a wealth of novel, endemic and medically related alleles.

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