scholarly journals The impact of linked selection on plant genomic variation

2014 ◽  
Vol 13 (4) ◽  
pp. 268-275 ◽  
Author(s):  
T. Slotte
Keyword(s):  
Genomic Variation ◽  
The Impact ◽  
Linked Selection

scholarly journals The ecology of ponds in the context of human activity and geography – environmental DNA and beyond

2021 ◽  
Vol 4 ◽  
Author(s):  
Karolina Bacela-Spychalska ◽  
Annette Taugbøl ◽  
Wiesław Babik ◽  
Maciej Pabijan ◽  
David Strand ◽  
...  
Keyword(s):  
Alien Species ◽  
Invasive Alien Species ◽  
Environmental Dna ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
Parasitic Fungus ◽  
Detailed Knowledge ◽  
Geographic Regions ◽  
The Impact ◽  
Pond Ecosystems

Pond ecosystems are hotspots of freshwater biodiversity, often containing many rare and protected species that are not commonly found elsewhere (Harper et al. 2018;Harper et al. 2019). However, even if they constitute c.a. 30% of freshwaters by area, still not enough effort has been put into pond monitoring and management and pond ecosystems are hence relatively poorly understood. Results of ECOPOND project will lead to add valuable knowledge upon pond diversity in geographic gradient taking for consideration human impact by comparing rural and urban areas. The sample design in ECOPOND includes six geographic regions, spanning from the south of Poland to the middle of Norway, where we will sample five replicates of urban and rural ponds in close geographic proximity, making it possible to test the impact of urbanization on biodiversity and biotic homogenization across latitude. We will sample all ponds at spring and late summer, making it possible to assess also seasonality in biodiversity. ECOPOND will utilize environmental DNA and RNA to perform biodiversity screening. The extracted eDNA and eRNA fragments will be amplified with the use of several selected markers for vertebrates, invertebrates, fungi and bacteria. Comparisons between eDNA and eRNA metabarcoding are hypothesized to allow inference between present and past diversity, as eRNA is thought to be only available from live organisms in the community. Moreover, ECOPOND aims at testing the effects of selected invasives species that can have on whole ecosystems. By sampling a range of biotic and abiotic parameters describing studied ponds, we will incorporate the available data for the ponds and employ occupancy modelling methods to assess the habitat preferences of selected invasive alien species. Then we will develop a method that can contribute towards an earlywarning system of evaluating threats to ecosystem status. One of the focus species will be the parasitic fungus Batrachochytrium dendrobatidis (Bd), an infectious fungal pathogen that has caused a number of amphibian declines and extinctions. The European amphibians seem less affected by the parasite at present. However, the fungi could be a direct driver of reduced genetic variation due to selection, or directly reduce the infected amphibian’s overall fitness by reducing the microbiotic diversity on their skin, which in many cases acts as a second immune system. ECOPOND will therefore provide data on genomic variation (using RADseq) for two amphibian species: the smooth newt (Lissotriton vulgaris) and the common toad (Bufo bufo). We will investigate populations of these species inhabiting ponds that are infected and not infected by Bd as well as collect data on their skin microbes (identified using metabarcoding). We will also contrast the genomic diversity between the replicated urban/rural setup and look for repeatable genomic changes. This setup will also be compared for the genomic variation for a potential native prey, the blue-tailed dragonfly, as will ponds with and without fish and/or amphibians (possibly also comparing between native and IAS top-predators) in order to look for predatory selective sweeps in the genome and transcriptome (experimental setup). All ponds will also be analyzed for over 20 water quality parameters and include data on a range of site characteristics that will be used as explanatory variables in all models. ECOPOND will compare large datasets across large geographic regions and will provide detailed knowledge of biodiversity patterns in vertebrates, invertebrates, fungal and microbial species, as well as genomic composition and skin biodiversity for animals inhabiting the same ponds set in an urban context. As a total, ECOPOND will obtain data on the location and status of biodiversity interests, gather data that can help in preventing the establishment of invasive alien species, and eradicating or controlling species that have already become established. And finally, ECOPOND will work closely with stakeholders and develop statistical techniques that can be used for monitoring, detection and protection of biodiversity.

Linked selection shapes the landscape of genomic variation in three oak species

2021 ◽  
Author(s):  
Yi‐Ye Liang ◽  
Yong Shi ◽  
Shuai Yuan ◽  
Biao‐Feng Zhou ◽  
Xue‐Yan Chen ◽  
...  
Keyword(s):  
Genomic Variation ◽  
Linked Selection

Impact of Privacy Issues on Successful Implementation of Personalized Medicare System

2019 ◽  
Vol 10 (3) ◽  
pp. 96-115
Author(s):  
Sandip Bisui ◽  
Subhas C. Misra
Keyword(s):  
Large Scale ◽  
Healthcare Management ◽  
Genomic Variation ◽  
Successful Implementation ◽  
Related Factors ◽  
Privacy Concerns ◽  
Novel Approach ◽  
Impact Of Technology ◽  
The Impact ◽  
Privacy Issues

Personalized medicare systems is an emerging field of research, which bears the potential to significantly reduce healthcare expenditures and treatment errors and thereby to revolutionize the entire treatment procedure. In this novel approach, genomic variation in different individuals is duly taken into consideration. However, there exist several serious issues (e.g. privacy concerns) that provide hindrance to large-scale adoption of this medicare system. The main objective of this study has been to identify the privacy issues and to evaluate their impact on successful implementation of this novel medical treatment. The methodology used is empirical and is based on a survey-based post facto procedure. The data collected from the survey are analyzed by using the method of structural modelling analysis. This is an original study in the realm of healthcare management, which reveals that the technology related factors and privacy concerns have considerable impact on the successful implementation of personalized medicare system on a large scale. But the privacy concerns have no significant moderating effect on the impact of technology related factors, so far, the success of implementation of personalized medicine is concerned.

scholarly journals Fido-SNP: the first webserver for scoring the impact of single nucleotide variants in the dog genome

2019 ◽  
Vol 47 (W1) ◽  
pp. W136-W141 ◽  
Author(s):  
Emidio Capriotti ◽  
Ludovica Montanucci ◽  
Giuseppe Profiti ◽  
Ivan Rossi ◽  
Diana Giannuzzi ◽  
...  
Keyword(s):  
Matthews Correlation Coefficient ◽  
Genomic Variation ◽  
Gradient Boosting ◽  
Binary Classifier ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Coding Regions ◽  
Variation Data ◽  
Boosting Algorithm ◽  
The Impact

Abstract As the amount of genomic variation data increases, tools that are able to score the functional impact of single nucleotide variants become more and more necessary. While there are several prediction servers available for interpreting the effects of variants in the human genome, only few have been developed for other species, and none were specifically designed for species of veterinary interest such as the dog. Here, we present Fido-SNP the first predictor able to discriminate between Pathogenic and Benign single-nucleotide variants in the dog genome. Fido-SNP is a binary classifier based on the Gradient Boosting algorithm. It is able to classify and score the impact of variants in both coding and non-coding regions based on sequence features within seconds. When validated on a previously unseen set of annotated variants from the OMIA database, Fido-SNP reaches 88% overall accuracy, 0.77 Matthews correlation coefficient and 0.91 Area Under the ROC Curve.

scholarly journals Polymorphisms and Splice Variants Influence the Antiretroviral Activity of Human APOBEC3H

2008 ◽  
Vol 83 (1) ◽  
pp. 295-303 ◽  
Author(s):  
Ariana Harari ◽  
Marcel Ooms ◽  
Lubbertus C. F. Mulder ◽  
Viviana Simon
Keyword(s):  
Alternative Splicing ◽  
Mononuclear Cells ◽  
Splice Variants ◽  
Genomic Variation ◽  
Endogenous Retroviruses ◽  
Site Directed Mutagenesis ◽  
Wide Range ◽  
The Impact ◽  
Hiv 1 ◽  
Antiretroviral Activity

ABSTRACT Human APOBEC3H belongs to the APOBEC3 family of cytidine deaminases that potently inhibit exogenous and endogenous retroviruses. The impact of single nucleotide polymorphisms (SNP) and alternative splicing on the antiretroviral activity of human APOBEC3H is currently unknown. In this study, we show that APOBEC3H transcripts derived from human peripheral blood mononuclear cells are polymorphic in sequence and subject to alternative splicing. We found that APOBEC3H variants encoding a SNP cluster (G105R, K121D and E178D, hapII-RDD) restricted human immunodeficiency virus type 1 (HIV-1) more efficiently than wild-type APOBEC3H (hapI-GKE). All APOBEC3H variants tested were resistant to HIV-1 Vif, the viral protein that efficiently counteracts APOBEC3G/3F activity. Alternative splicing of APOBEC3H was common and resulted in variants with distinct C-terminal regions and variable antiretroviral activities. Splice variants of hapI-GKE displayed a wide range of antiviral activities, whereas similar splicing events in hapII-RDD resulted in proteins that uniformly and efficiently restricted viral infectivity (>20-fold). Site-directed mutagenesis identified G105R in hapI-GKE and D121K in hapII-RDD as critical substitutions leading to an average additional 10-fold increase in antiviral activity. APOBEC3H variants were catalytically active and, similarly to APOBEC3F, favored a GA dinucleotide context. HIV-1 mutagenesis as a mode of action for APOBEC3H is suggested by the decrease of restriction observed with a cytidine deaminase domain mutant and the inverse correlation between G-to-A mutations and infectivity. Thus, the anti-HIV activity of APOBEC3H seems to be regulated by a combination of genomic variation and alternative splicing. Since prevalence of hapII-RDD is high in populations of African descent, these findings raise the possibility that some individuals may harbor effective as well as HIV-1 Vif-resistant intracellular antiviral defense mechanisms.

scholarly journals Testing for evolutionary change in restoration: a genomic comparison betweenex situ, native and commercial seed sources ofHelianthus maximiliani

2021 ◽  
Author(s):  
Joseph E Braasch ◽  
Lionel N Di Santo ◽  
Zach Tarble ◽  
Jarrad R Prasifka ◽  
Jill A Hamilton
Keyword(s):  
Isolation By Distance ◽  
Genomic Variation ◽  
Ex Situ ◽  
Wild Populations ◽  
Restoration Process ◽  
Seed Material ◽  
Seed Sources ◽  
Restoration Success ◽  
Commercial Seed ◽  
The Impact

AbstractGlobally imperiled ecosystems often depend upon collection, propagation, and storage of seed material for use in restoration. However, during the restoration process demographic changes, population bottlenecks, and selection can alter the genetic composition of seed material, with potential impacts for restoration success. The evolutionary outcomes associated with these processes have been demonstrated using theoretical and experimental frameworks, but no studies to date have examined the impact these processes have had on the seed material maintained for conservation and restoration. In this study, we compare genomic variation across seed sources used in conservation and restoration for the perennial prairie plantHelianthus maximiliani, a key component of restorations across North American grasslands. We compare individuals sourced from contemporary wild populations,ex situconservation collections, commercially produced restoration material, and two populations selected for agronomic traits. Overall, we observed thatex situand contemporary wild populations exhibited a similar genomic composition, while four of five commercial populations and selected lines were differentiated from each other and other seed source populations. Genomic differences across seed sources could not be explained solely by isolation by distance nor directional selection. We did find evidence of sampling effects forex situcollections, which exhibited significantly increased coancestry relative to commercial populations, suggesting increased relatedness. Interestingly, commercially sourced seed appeared to maintain an increased number of rare alleles relative toex situand wild contemporary seed sources. However, while commercial seed populations were not genetically depauperate, the genomic distance between wild and commercially produced seed suggests differentiation in the genomic composition could impact restoration success. Our results point towards the importance of genetic monitoring of species used for conservation and restoration as they are expected to be influenced by the evolutionary processes that contribute to divergence during the restoration process.

scholarly journals Heterogeneity in effective size across the genome: effects on the Inverse Instantaneous Coalescence Rate (IICR) and implications for demographic inference under linked selection.

2021 ◽  
Author(s):  
Simon Boitard ◽  
Armando Arredondo ◽  
Camille Noûs ◽  
Lounes Chikhi ◽  
Olivier Mazet
Keyword(s):  
Genetic Diversity ◽  
Balancing Selection ◽  
Effective Population ◽  
Recombination Rates ◽  
Genome Wide ◽  
Coalescence Rate ◽  
Demographic Inference ◽  
The Impact ◽  
Linked Selection ◽  
Coalescence Times

The relative contribution of selection and neutrality in shaping species genetic diversity is one of the most central and controversial questions in evolutionary theory. Genomic data provide growing evidence that linked selection, i.e. the modification of genetic diversity at neutral sites through linkage with selected sites, might be pervasive over the genome. Several studies proposed that linked selection could be modelled as first approximation by a local reduction (e.g. purifying selection, selective sweeps) or increase (e.g. balancing selection) of effective population size (Ne). At the genome-wide scale, this leads to a large variance of Ne from one region to another, reflecting the heterogeneity of selective constraints and recombination rates between regions. We investigate here the consequences of this variation of Ne on the genome-wide distribution of coalescence times. The underlying motivation concerns the impact of linked selection on demographic inference, because the distribution of coalescence times is at the heart of several important demographic inference approaches. Using the concept of Inverse Instantaneous Coalescence Rate, we demonstrate that in a panmictic population, linked selection always results in a spurious apparent decrease of Ne along time. Balancing selection has a particularly large effect, even when it concerns a very small part of the genome. We quantify the expected magnitude of the spurious decrease of Ne in humans and Drosophila melanogaster, based on Ne distributions inferred from real data in these species. We also find that the effect of linked selection can be significantly reduced by that of population structure.

The Impact of Constitutional Copy Number Variants in Myeloma

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 496-496
Author(s):  
Matthew W Jenner ◽  
David C Johnson ◽  
Paola E Leone ◽  
Brian A Walker ◽  
David Gonzalez ◽  
...  
Keyword(s):  
Copy Number ◽  
Copy Number Change ◽  
Copy Number Variations ◽  
Genomic Variation ◽  
Chromosome 21 ◽  
Nucleotide Polymorphisms ◽  
Copy Number Changes ◽  
The Impact ◽  
First Time ◽  
Tumor Dna

Abstract Single nucleotide polymorphisms (SNPs) have been long regarded as being important in determining variation and disease predisposition. Recently, chromosomal structural variation in the form of deletions, insertions and duplifications have been identified frequently in the genome of the general population. Such copy number variations (CNVs) have been shown to contribute to a range of human diseases. In recent studies we have utilized Affymetrix 50K and 500K arrays to identify acquired copy number change in myeloma tumor samples. In those studies we had access to paired constitutional DNA and in the present study have been able to report for the first time a CNV map of the constitutional genome of myeloma patients. Affymetrix 500K mapping arrays were used to identify copy number changes in 63 paired samples using DNA from peripheral blood and CD138 selected plasma cells. Tumor samples were analyzed in CNAG using both a paired and unpaired analysis to distinguish between inherited and acquired copy number change. Constitutional DNA was analyzed by both CNAG and GEMCA using 90 Caucasian samples from the Hapmap database as a reference set. For maximum calling accuracy, only those regions identified by both algorithms were called as CNVs. As with similar studies, overlapping CNVs identified using this approach were merged to generate a list of CNV regions (CNVRs) characteristic of the constitutional DNA of these myeloma cases. Using this approach, we identified 292 CNVs across 63 cases, with a median of 4 regions per sample. There were 155 discrete CNVRs, of which 46 were recurrent. The recurrent CNVRs were found most frequently in the pericentric regions of chromosome 14 and 15 in keeping with other studies. We then compared these recurrent CNVRs with a comparable dataset of normal individuals generated using Affymetrix 500K arrays. In this analysis, 25/46 recurrent CNVRs in the myeloma cases were novel. The two most frequent novel CNVRs in the myeloma cases were gains on chromosome 21 and 15. We also compared the characteristics of the constitutional CNVs with the acquired copy number changes in the corresponding tumor samples and identified that the constitutional CNVs were generally considerably smaller. However, using unpaired analysis it was possible to determine the presence of the constitutional CNV in the tumor sample, providing validation of the CNVs. We were also able to demonstrate that acquired copy number change in the tumor cells can either exaggerate or ameliorate the effect of the inherited CNV in the tumor genome, such as cases with acquired trisomy 15 and deletion or gain of regions of 15q in the constitutional DNA. These findings also reinforce the need for paired non-tumor DNA when undertaking copy number analysis of tumor DNA using SNP arrays. In this study we have been able to identify for the first time the presence of CNVs in the constitutional genome of individuals with myeloma. We have been able to systematically catalogue these CNVRs. These results provide the basis for future studies aimed at identifying how this type of genomic variation may influence the development of and outcome of myeloma and a broad range of other hematological conditions.

scholarly journals Genome assembly of primitive cultivated potato Solanum stenotomum provides insights into potato evolution

2021 ◽  
Author(s):  
Lang Yan ◽  
Yizheng Zhang ◽  
Guangze Cai ◽  
Yuan Qing ◽  
Jiling Song ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Families ◽  
Defense Responses ◽  
Genomic Variation ◽  
Raw Material ◽  
Specific Gene ◽  
Solanum Stenotomum ◽  
Cultivated Potato ◽  
Solanaceae Species ◽  
The Impact

Abstract Genetic diversity is the raw material for germplasm enhancement. Landraces and wild species relatives of potato, which contain a rich gene pool of valuable agronomic traits, can provide insights into the genetic diversity behind the adaptability of the common potato. The diploid plant, Solanum stenotomum (Sst), is believed to have an ancestral relationship with modern potato cultivars and be a potential source of resistance against disease. Sequencing of the Sst genome generated an assembly of 852.85 Mb (N50 scaffold size, 3.7 Mb). Pseudomolecule construction anchored 788.75 Mb of the assembly onto 12 pseudochromosomes, with an anchor rate of 92.4%. Genome annotation yielded 41,914 high-confidence protein-coding gene models and comparative analyses with closely related Solanaceae species identified 358 Sst-specific gene families, 885 gene families with expansion along the Sst lineage, and 149 genes experiencing accelerated rates of protein sequence evolution in Sst, the functions of which were mainly associated with defense responses, particularly against bacterial and fungal infection. Insights into the Sst genome and the genomic variation of cultivated potato taxa are valuable in elaborating the impact of potato evolution in early landrace diploid and facilitate modern potato breeding.

Sign in / Sign up

Export Citation Format

Share Document