scholarly journals Resolving the insertion sites of polymorphic duplications reveals a HERC2 haplotype under selection

2018 ◽  
Author(s):  
M. Saitou ◽  
O. Gokcumen
Keyword(s):  
Phenotypic Diversity ◽  
Human Populations ◽  
Related Gene ◽  
Partial Duplication ◽  
Future Studies ◽  
Evolutionary Forces ◽  
Genome Wide ◽  
Insertion Sites ◽  
Reference Genomes

ABSTRACTPolymorphic duplications in humans have been shown to contribute to phenotypic diversity. However, the evolutionary forces that maintain variable duplications across the human genome are largely unexplored. To understand the haplotypic architecture of the derived duplications, we developed a linkage-disequilibrium based method to detect insertion sites of polymorphic duplications not represented in reference genomes. This method also allows resolution of haplotypes harboring the duplications. Using this approach, we conducted genome-wide analyses and identified the insertion sites of 22 common polymorphic duplications. We found that the majority of these duplications are intrachromosomal and only one of them is an interchromosomal insertion. Further characterization of these duplications revealed significant associations to blood and skin phenotypes. Based on population genetics analyses, we found that the partial duplication of a well-characterized pigmentation-related gene, HERC2, may be selected against in European populations. We further demonstrated that the haplotype harboring the partial duplication significantly affects the expression of the HERC2P9 gene in multiple tissues. Our study sheds light onto the evolutionary impact of understudied polymorphic duplications in human populations and presents methodological insights for future studies.

scholarly journals Genome-wide microsatellite characteristics of five human Plasmodium species, focusing on Plasmodium malariae and P. ovale curtisi

Parasite ◽  
2020 ◽  
Vol 27 ◽  
pp. 34
Author(s):  
Vivek Bhakta Mathema ◽  
Supatchara Nakeesathit ◽  
Nicholas J. White ◽  
Arjen M. Dondorp ◽  
Mallika Imwong
Keyword(s):  
Plasmodium Species ◽  
Plasmodium Malariae ◽  
Base Pairs ◽  
Comprehensive Overview ◽  
Genome Wide ◽  
Malaria Species ◽  
Repeated Motifs ◽  
Reference Genomes ◽  
Human Plasmodium

Microsatellites can be utilized to explore genotypes, population structure, and other genomic features of eukaryotes. Systematic characterization of microsatellites has not been a focus for several species of Plasmodium, including P. malariae and P. ovale, as the majority of malaria elimination programs are focused on P. falciparum and to a lesser extent P. vivax. Here, five human malaria species (P. falciparum, P. vivax, P. malariae, P. ovale curtisi, and P. knowlesi) were investigated with the aim of conducting in-depth categorization of microsatellites for P. malariae and P. ovale curtisi. Investigation of reference genomes for microsatellites with unit motifs of 1–10 base pairs indicates high diversity among the five Plasmodium species. Plasmodium malariae, with the largest genome size, displays the second highest microsatellite density (1421 No./Mbp; 5% coverage) next to P. falciparum (3634 No./Mbp; 12% coverage). The lowest microsatellite density was observed in P. vivax (773 No./Mbp; 2% coverage). A, AT, and AAT are the most commonly repeated motifs in the Plasmodium species. For P. malariae and P. ovale curtisi, microsatellite-related sequences are observed in approximately 18–29% of coding sequences (CDS). Lysine, asparagine, and glutamic acids are most frequently coded by microsatellite-related CDS. The majority of these CDS could be related to the gene ontology terms “cell parts,” “binding,” “developmental processes,” and “metabolic processes.” The present study provides a comprehensive overview of microsatellite distribution and can assist in the planning and development of potentially useful genetic tools for further investigation of P. malariae and P. ovale curtisi epidemiology.

scholarly journals Genome-wide detection and characterization of positive selection in human populations

Nature ◽  
2007 ◽  
Vol 449 (7164) ◽  
pp. 913-918 ◽  
Author(s):  
Pardis C. Sabeti ◽  
◽  
Patrick Varilly ◽  
Ben Fry ◽  
Jason Lohmueller ◽  
...  
Keyword(s):  
Positive Selection ◽  
Human Populations ◽  
Genome Wide

scholarly journals Genome-wide Characterization of Shared and Distinct Genetic Components that Influence Blood Lipid Levels in Ethnically Diverse Human Populations

2013 ◽  
Vol 92 (6) ◽  
pp. 904-916 ◽  
Author(s):  
Marc A. Coram ◽  
Qing Duan ◽  
Thomas J. Hoffmann ◽  
Timothy Thornton ◽  
Joshua W. Knowles ◽  
...  
Keyword(s):  
Ethnically Diverse ◽  
Blood Lipid ◽  
Human Populations ◽  
Lipid Levels ◽  
Genetic Components ◽  
Genome Wide ◽  
Blood Lipid Levels

scholarly journals Presence and Transmission of Mitochondrial Heteroplasmic Mutations in Human Populations of European and African Ancestry

2020 ◽  
Author(s):  
Chunyu Liu ◽  
Jessica L. Fetterman ◽  
Yong Qian ◽  
Xianbang Sun ◽  
Kaiyu Yan ◽  
...  
Keyword(s):  
Tyrosine Phosphatase ◽  
African Ancestry ◽  
Functional Characterization ◽  
Nuclear Genome ◽  
Human Populations ◽  
Sibling Pairs ◽  
Coding Regions ◽  
Genome Wide ◽  
A Genome

ABSTRACTWe investigated the concordance of mitochondrial DNA heteroplasmic mutations (heteroplasmies) in different types of maternal pairs (n=6,745 pairs) of European (EA, n=4,718 pairs) and African (AA, n=2,027 pairs) Americans with whole genome sequences (WGSs). The average concordance rate of heteroplasmies was highest between mother-offspring pairs, followed by sibling-sibling pairs and more distantly related maternal pairs in both EA and AA participants. The allele fractions of concordant heteroplasmies exhibited high correlation (R2=0.8) between paired individuals. Compared to concordant heteroplasmies, discordant ones were more likely to locate in coding regions, be nonsynonymous or nonsynonymous-deleterious (p<0.001). The average number of heteroplasmies per individual (i.e. heteroplasmic burden) was at a similar level until older age (70-80 years old) and increased significantly thereafter (p<0.01). The burden of deleterious heteroplasmies (combined annotation-dependent depletion score≥15), however, was significantly correlated with advancing age (20-44, 45-64, ≥65 years, p-trend=0.01). A genome-wide association analysis of the heteroplasmic burden identified many significant (P<5e-8) common variants (minor allele frequency>0.05) at 11p11.12. Many of the top SNPs act as strong long-range cis regulators of protein tyrosine phosphatase receptor type J. This study provides further evidence that mtDNA heteroplasmies may be inherited or somatic. Somatic heteroplasmic variants increase with advancing age and are more likely to have an adverse impact on mitochondrial function. Further studies are warranted for functional characterization of the deleterious heteroplasmies occurring with advancing age and the association of the 11p11.12 region of the nuclear genome with mtDNA heteroplasmy.

scholarly journals Mining SNPs From EST Databases

1999 ◽  
Vol 9 (2) ◽  
pp. 167-174 ◽  
Author(s):  
Leslie Picoult-Newberg ◽  
Trey E. Ideker ◽  
Mark G. Pohl ◽  
Scott L. Taylor ◽  
Miriam A. Donaldson ◽  
...  
Keyword(s):  
Expressed Sequence Tag ◽  
De Novo ◽  
Cdna Libraries ◽  
Human Populations ◽  
Data Sets ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Using Data

There is considerable interest in the discovery and characterization of single nucleotide polymorphisms (SNPs) to enable the analysis of the potential relationships between human genotype and phenotype. Here we present a strategy that permits the rapid discovery of SNPs from publicly available expressed sequence tag (EST) databases. From a set of ESTs derived from 19 different cDNA libraries, we assembled 300,000 distinct sequences and identified 850 mismatches from contiguous EST data sets (candidate SNP sites), without de novo sequencing. Through a polymerase-mediated, single-base, primer extension technique, Genetic Bit Analysis (GBA), we confirmed the presence of a subset of these candidate SNP sites and have estimated the allele frequencies in three human populations with different ethnic origins. Altogether, our approach provides a basis for rapid and efficient regional and genome-wide SNP discovery using data assembled from sequences from different libraries of cDNAs.[The SNPs identified in this study can be found in the National Center of Biotechnology (NCBI) SNP database under submitter handles ORCHID (SNPS-981210-A) and debnick (SNPS-981209-A and SNPS-981209-B).]

scholarly journals Isolation and Characterization of Thermophilic Bacteria from Jordanian Hot Springs: Bacillus licheniformis and Thermomonas hydrothermalis Isolates as Potential Producers of Thermostable Enzymes

2017 ◽  
Vol 2017 ◽  
pp. 1-12 ◽  
Author(s):  
Balsam T. Mohammad ◽  
Hala I. Al Daghistani ◽  
Atef Jaouani ◽  
Saleh Abdel-Latif ◽  
Christian Kennes
Keyword(s):  
Bacillus Licheniformis ◽  
Hot Springs ◽  
Thermophilic Bacteria ◽  
Phenotypic Diversity ◽  
Thermostable Enzymes ◽  
Future Studies ◽  
Blast Search ◽  
Upgma Dendrogram ◽  
Isolation And Characterization

The aim of this study was the isolation and characterization of thermophilic bacteria from hot springs in Jordan. Ten isolates were characterized by morphological, microscopic, biochemical, molecular, and physiological characteristics. Sequencing of the 16S rDNA of the isolates followed by BLAST search revealed that nine strains could be identified as Bacillus licheniformis and one isolate as Thermomonas hydrothermalis. This is the first report on the isolation of Thermomonas species from Jordanian hot springs. The isolates showed an ability to produce some thermostable enzymes such as amylase, protease, cellulose, gelatins, and lecithin. Moreover, the UPGMA dendrogram of the enzymatic characteristics of the ten isolates was constructed; results indicated a high phenotypic diversity, which encourages future studies to explore further industrial and environmental applications.

scholarly journals Exploring functional variation affecting ceRNA regulation in humans

2015 ◽  
Author(s):  
Mulin Jun Li ◽  
Jiexing Wu ◽  
Peng Jiang ◽  
Wei Li ◽  
Yun Zhu ◽  
...  
Keyword(s):  
Genetic Effect ◽  
Systematic Investigation ◽  
Human Populations ◽  
Functional Variation ◽  
Regulatory Variants ◽  
Genome Wide ◽  
Competing Endogenous Rnas ◽  
Mirna Sponges ◽  
Cis And Trans

MicroRNA (miRNA) sponges have been shown to function as competing endogenous RNAs (ceRNAs) to regulate the expression of other miRNA targets in the network by sequestering available miRNAs. As the first systematic investigation of the genome-wide genetic effect on ceRNA regulation, we applied multivariate response regression and identified widespread genetic variations that are associated with ceRNA competition using 462 Geuvadis RNA-seq data in multiple human populations. We showed that SNPs in gene 3’UTRs at the miRNA seed binding regions can simultaneously regulate gene expression changes in both cis and trans by the ceRNA mechanism. We termed these loci as endogenous miRNA sponge expression quantitative trait loci or “emsQTLs”, and found that a large number of them were unexplored in conventional eQTL mapping. We identified many emsQTLs are undergoing recent positive selection in different human populations. Using GWAS results, we found that emsQTLs are significantly enriched in traits/diseases associated loci. Functional prediction and prioritization extend our understanding on causality of emsQTL allele in disease pathways. We illustrated that emsQTL can synchronously regulate the expression of tumor suppressor and oncogene through ceRNA competition in angiogenesis. Together these results provide a distinct catalog and characterization of functional noncoding regulatory variants that control ceRNA crosstalk.

scholarly journals Genome-wide identification and characterization of the BES/BZR gene family in wheat and foxtail millet

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Dan Liu ◽  
Yanjiao Cui ◽  
Zilong Zhao ◽  
Suying Li ◽  
Dan Liang ◽  
...  
Keyword(s):  
Gene Family ◽  
Molecular Mechanisms ◽  
Profile Analysis ◽  
Foxtail Millet ◽  
Future Studies ◽  
Expression Profile Analysis ◽  
Genome Wide ◽  
Leaf Tissues ◽  
Identification And Characterization

Abstract Background BES/BZR family genes have vital roles in plant growth, development, and adaptation to environmental stimuli. However, they have not yet been characterized and systematically analyzed in wheat and foxtail millet. Results In the current study, five common and two unique BES/BZR genes were identified by genome-wide analysis in wheat and foxtail millet, respectively. These genes were unevenly distributed on 14 and five chromosomes of wheat and foxtail millet, respectively, and clustered in two subgroups in a phylogenetic analysis. The BES/BZR gene family members in each subgroup contained similar conserved motifs. Investigation of cis-acting elements and expression profile analysis revealed that the BES/BZR genes were predominantly expressed in leaf tissues of wheat and foxtail millet seedlings and responded to brassinosteroid, abscisic acid, and NaCl treatments. Conclusions Our results provide a basis for future studies on the function and molecular mechanisms of the BES/BZR gene family in wheat, foxtail millet, and other plants.

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