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1.
Nat Commun ; 11(1): 3795, 2020 07 30.
Artículo en Inglés | MEDLINE | ID: mdl-32732942

RESUMEN

Angiosperms have become the dominant terrestrial plant group by diversifying for ~145 million years into a broad range of environments. During the course of evolution, numerous morphological innovations arose, often preceded by whole genome duplications (WGD). The mustard family (Brassicaceae), a successful angiosperm clade with ~4000 species, has been diversifying into many evolutionary lineages for more than 30 million years. Here we develop a species inventory, analyze morphological variation, and present a maternal, plastome-based genus-level phylogeny. We show that increased morphological disparity, despite an apparent absence of clade-specific morphological innovations, is found in tribes with WGDs or diversification rate shifts. Both are important processes in Brassicaceae, resulting in an overall high net diversification rate. Character states show frequent and independent gain and loss, and form varying combinations. Therefore, Brassicaceae pave the way to concepts of phylogenetic genome-wide association studies to analyze the evolution of morphological form and function.


Asunto(s)
Evolución Biológica , Brassicaceae/clasificación , Brassicaceae/genética , Evolución Molecular , Genoma de Planta/genética , Variación Genética/genética , Estudio de Asociación del Genoma Completo , Filogenia
2.
Nat Commun ; 11(1): 4020, 2020 08 11.
Artículo en Inglés | MEDLINE | ID: mdl-32782262

RESUMEN

While variance components analysis has emerged as a powerful tool in complex trait genetics, existing methods for fitting variance components do not scale well to large-scale datasets of genetic variation. Here, we present a method for variance components analysis that is accurate and efficient: capable of estimating one hundred variance components on a million individuals genotyped at a million SNPs in a few hours. We illustrate the utility of our method in estimating and partitioning variation in a trait explained by genotyped SNPs (SNP-heritability). Analyzing 22 traits with genotypes from 300,000 individuals across about 8 million common and low frequency SNPs, we observe that per-allele squared effect size increases with decreasing minor allele frequency (MAF) and linkage disequilibrium (LD) consistent with the action of negative selection. Partitioning heritability across 28 functional annotations, we observe enrichment of heritability in FANTOM5 enhancers in asthma, eczema, thyroid and autoimmune disorders.


Asunto(s)
Variación Genética/genética , Genoma Humano/genética , Modelos Genéticos , Alelos , Frecuencia de los Genes , Genotipo , Humanos , Desequilibrio de Ligamiento , Herencia Multifactorial/genética , Fenotipo , Polimorfismo de Nucleótido Simple , Carácter Cuantitativo Heredable
3.
PLoS One ; 15(7): e0235434, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32649700

RESUMEN

The genetic diversity of North American soybean cultivars has been largely influenced by a small number of ancestors. High yielding breeding lines that possess exotic pedigrees have been developed, but identifying beneficial exotic alleles has been difficult as a result of complex interactions of yield alleles with genetic backgrounds and environments as well as the highly quantitative nature of yield. PI 416937 has been utilized in the development of many high yielding lines that have been entered into the USDA Southern States Uniform Tests over the past ~20 years. The primary goal of this research was to identify genomic regions under breeding selection from PI 416937 and introduce a methodology for identifying and potentially utilizing beneficial diversity from lines prevalent in the ancestry of elite cultivars. Utilizing SoySNP50K Infinium BeadChips, 52 high yielding PI 416937-derived lines as well as their parents were genotyped to identify PI 416937 alleles under breeding selection. Nine genomic regions across three chromosomes and 17 genomic regions across seven chromosomes were identified where PI 416937 alleles were under positive or negative selection. Minimal significant associations between PI 416937 alleles and yield were observed in replicated yield trials of five RIL populations, highlighting the difficulty of consistently detecting yield associations.


Asunto(s)
Cruzamiento , Variación Genética/genética , Soja/genética , Alelos , Mapeo Cromosómico , Cromosomas de las Plantas , Genoma de Planta/genética , Genómica , Genotipo , Humanos , Sitios de Carácter Cuantitativo/genética , Semillas/genética , Semillas/crecimiento & desarrollo , Soja/crecimiento & desarrollo , Estados Unidos
4.
Genome Med ; 12(1): 57, 2020 06 30.
Artículo en Inglés | MEDLINE | ID: mdl-32605661

RESUMEN

BACKGROUND: COVID-19 (coronavirus disease 2019) has caused a major epidemic worldwide; however, much is yet to be known about the epidemiology and evolution of the virus partly due to the scarcity of full-length SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) genomes reported. One reason is that the challenges underneath sequencing SARS-CoV-2 directly from clinical samples have not been completely tackled, i.e., sequencing samples with low viral load often results in insufficient viral reads for analyses. METHODS: We applied a novel multiplex PCR amplicon (amplicon)-based and hybrid capture (capture)-based sequencing, as well as ultra-high-throughput metatranscriptomic (meta) sequencing in retrieving complete genomes, inter-individual and intra-individual variations of SARS-CoV-2 from serials dilutions of a cultured isolate, and eight clinical samples covering a range of sample types and viral loads. We also examined and compared the sensitivity, accuracy, and other characteristics of these approaches in a comprehensive manner. RESULTS: We demonstrated that both amplicon and capture methods efficiently enriched SARS-CoV-2 content from clinical samples, while the enrichment efficiency of amplicon outran that of capture in more challenging samples. We found that capture was not as accurate as meta and amplicon in identifying between-sample variations, whereas amplicon method was not as accurate as the other two in investigating within-sample variations, suggesting amplicon sequencing was not suitable for studying virus-host interactions and viral transmission that heavily rely on intra-host dynamics. We illustrated that meta uncovered rich genetic information in the clinical samples besides SARS-CoV-2, providing references for clinical diagnostics and therapeutics. Taken all factors above and cost-effectiveness into consideration, we proposed guidance for how to choose sequencing strategy for SARS-CoV-2 under different situations. CONCLUSIONS: This is, to the best of our knowledge, the first work systematically investigating inter- and intra-individual variations of SARS-CoV-2 using amplicon- and capture-based whole-genome sequencing, as well as the first comparative study among multiple approaches. Our work offers practical solutions for genome sequencing and analyses of SARS-CoV-2 and other emerging viruses.


Asunto(s)
Betacoronavirus/genética , Genoma Viral/genética , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Secuenciación Completa del Genoma/métodos , Infecciones por Coronavirus , Variación Genética/genética , Interacciones Huésped-Patógeno/genética , Humanos , Reacción en Cadena de la Polimerasa Multiplex/métodos , Pandemias , Neumonía Viral , ARN Viral/genética
5.
PLoS Comput Biol ; 16(7): e1007504, 2020 07.
Artículo en Inglés | MEDLINE | ID: mdl-32692749

RESUMEN

NGS studies have uncovered an ever-growing catalog of human variation while leaving an enormous gap between observed variation and experimental characterization of variant function. High-throughput screens powered by NGS have greatly increased the rate of variant functionalization, but the development of comprehensive statistical methods to analyze screen data has lagged. In the massively parallel reporter assay (MPRA), short barcodes are counted by sequencing DNA libraries transfected into cells and the cell's output RNA in order to simultaneously measure the shifts in transcription induced by thousands of genetic variants. These counts present many statistical challenges, including overdispersion, depth dependence, and uncertain DNA concentrations. So far, the statistical methods used have been rudimentary, employing transformations on count level data and disregarding experimental and technical structure while failing to quantify uncertainty in the statistical model. We have developed an extensive framework for the analysis of NGS functionalization screens available as an R package called malacoda (available from github.com/andrewGhazi/malacoda). Our software implements a probabilistic, fully Bayesian model of screen data. The model uses the negative binomial distribution with gamma priors to model sequencing counts while accounting for effects from input library preparation and sequencing depth. The method leverages the high-throughput nature of the assay to estimate the priors empirically. External annotations such as ENCODE data or DeepSea predictions can also be incorporated to obtain more informative priors-a transformative capability for data integration. The package also includes quality control and utility functions, including automated barcode counting and visualization methods. To validate our method, we analyzed several datasets using malacoda and alternative MPRA analysis methods. These data include experiments from the literature, simulated assays, and primary MPRA data. We also used luciferase assays to experimentally validate several hits from our primary data, as well as variants for which the various methods disagree and variants detectable only with the aid of external annotations.


Asunto(s)
Biología Computacional/métodos , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Modelos Estadísticos , Análisis de Secuencia de ADN/métodos , Programas Informáticos , Teorema de Bayes , Variación Genética/genética , Humanos
6.
Medicine (Baltimore) ; 99(26): e20716, 2020 Jun 26.
Artículo en Inglés | MEDLINE | ID: mdl-32590746

RESUMEN

Genome-wide association studies (GWAS) have identified multiple independent cancer susceptibility loci at chromosome 8q24. We aimed to evaluate the associations between variants in the 8q24 region and cancer susceptibility. A comprehensive research synopsis and meta-analysis was performed to evaluate associations between 28 variants in 8q24 and risk of 7 cancers using data from 103 eligible articles totaling 146,932 cancer cases and 219,724 controls. Results: 20 variants were significantly associated with risk of prostate cancer, colorectal cancer, thyroid cancer, breast cancer, bladder cancer, stomach cancer, and glioma, including 1 variant associated with prostate cancer, colorectal cancer, and thyroid cancer. Cumulative epidemiological evidence of an association was graded as strong for DG8S737 -8 allele, rs10090154, rs7000448 in prostate cancer, rs10808556 in colorectal cancer, rs55705857 in gliomas, rs9642880 in bladder cancer, moderate for rs16901979, rs1447295, rs6983267, rs7017300, rs7837688, rs1016343, rs620861, rs10086908 associated in prostate cancer, rs10505477, rs6983267 in colorectal cancer, rs6983267 in thyroid cancer, rs13281615 in breast cancer, and rs1447295 in stomach cancer, weak for rs6983561, rs13254738, rs7008482, rs4242384 in prostate cancer. Data from ENCODE suggested that these variants with strong evidence and other correlated variants might fall within putative functional regions. Our study provides summary evidence that common variants in the 8q24 are associated with risk of multiple cancers in this large-scale research synopsis and meta-analysis. Further studies are needed to explore the mechanisms underlying variants in the 8q24 involved in various human cancers.


Asunto(s)
Predisposición Genética a la Enfermedad/epidemiología , Variación Genética/genética , Neoplasias/genética , Estudio de Asociación del Genoma Completo , Humanos , Neoplasias/clasificación , Neoplasias/epidemiología
8.
Aging Cell ; 19(7)2020 07.
Artículo en Inglés | MEDLINE | ID: mdl-32558150

RESUMEN

The COVID-19 coronavirus is now spreading worldwide. Its pathogen, SARS-CoV-2, has been shown to use angiotensin-converting enzyme 2 (ACE2) as its host cell receptor, same as the severe acute respiratory syndrome coronavirus (SARS-CoV) in 2003. Epidemiology studies found males although only slightly more likely to be infected than females account for the majority of the severely ill and fatality, which also bias for people older than 60 years or with metabolic and cardiovascular diseases. Here by analyzing GTEx and other public data in 30 tissues across thousands of individuals, we found a significantly higher level in Asian females, an age-dependent decrease in all ethnic groups, and a highly significant decrease in type II diabetic patients of ACE2 expression. Consistently, the most significant expression quantitative loci (eQTLs) contributing to high ACE2 expression are close to 100% in East Asians, >30% higher than other ethnic groups. A shockingly common enrichment of viral infection pathways was found among ACE2 anti-expressed genes, and multiple binding sites of virus infection related transcription factors and sex hormone receptors locate at ACE2 regulatory regions. Human and mice data analysis further revealed ACE2 expression is reduced in T2D patients and with inflammatory cytokine treatment and upregulated by estrogen and androgen (both decrease with age). Our findings revealed a negative correlation between ACE2 expression and COVID-19 fatality at both population and molecular levels. These results will be instrumental when designing potential prevention and treatment strategies for ACE2 binding coronaviruses in general.


Asunto(s)
Betacoronavirus/metabolismo , Infecciones por Coronavirus/genética , Infecciones por Coronavirus/virología , Regulación de la Expresión Génica , Variación Genética/genética , Peptidil-Dipeptidasa A/genética , Peptidil-Dipeptidasa A/metabolismo , Neumonía Viral/genética , Neumonía Viral/virología , Betacoronavirus/patogenicidad , Biología Computacional , Femenino , Humanos , Masculino , Pandemias , Receptores Virales/genética , Receptores Virales/metabolismo , Testículo/metabolismo , Testículo/virología
9.
Nat Commun ; 11(1): 2927, 2020 06 10.
Artículo en Inglés | MEDLINE | ID: mdl-32522982

RESUMEN

Structural variants (SVs) and short tandem repeats (STRs) comprise a broad group of diverse DNA variants which vastly differ in their sizes and distributions across the genome. Here, we identify genomic features of SV classes and STRs that are associated with gene expression and complex traits, including their locations relative to eGenes, likelihood of being associated with multiple eGenes, associated eGene types (e.g., coding, noncoding, level of evolutionary constraint), effect sizes, linkage disequilibrium with tagging single nucleotide variants used in GWAS, and likelihood of being associated with GWAS traits. We identify a set of high-impact SVs/STRs associated with the expression of three or more eGenes via chromatin loops and show that they are highly enriched for being associated with GWAS traits. Our study provides insights into the genomic properties of structural variant classes and short tandem repeats that are associated with gene expression and human traits.


Asunto(s)
Repeticiones de Microsatélite/genética , Línea Celular , Variación Genética/genética , Estudio de Asociación del Genoma Completo , Humanos , Desequilibrio de Ligamiento/genética , Herencia Multifactorial , Polimorfismo de Nucleótido Simple/genética , Sitios de Carácter Cuantitativo/genética
10.
PLoS One ; 15(6): e0233516, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32479498

RESUMEN

The Balkans endemic species Alkanna primuliflora Griseb., A. stribrnyi Velen., and A. graeca Boiss. & Spruner have limited distribution in the Balkan Peninsula and a large variation in the morphological characteristics. The populations of the three Alkanna species in the Bulgarian flora are small and fragmented. There are no previous reports on the chemical profile or on the embryology of these species. The hypothesis was that the limited distribution of A. primuliflora, A. stribrnyi, and A. graeca was due to their reproductive capacity and genetic diversity. Furthermore, we hypothesized that the three species will contain pyrrolizidine alkaloids (PAs), as other species of the genus Alkanna (Boraginaceae), but they would have differential alkaloids composition. The population genetic structure and differentiation showed a clear distinction between species and revealed average levels of genetic diversity among the natural populations of the three Alkanna species. The embryological investigation observed stability of the processes in the male and female generative spheres and high viability of mature pollen and embryo of the three species. The normal formation of male and female gametophytes without deviations or degenerative processes, and observed levels of genetic diversity between Alkanna individuals are important in maintaining the size and resilience of the Alkanna populations. Eight alkaloids were identified by GC-MS in A. primuliflora and A. graeca and six alkaloids in A. stribrnyi. The main pyrrolizidine alkaloids (PAs) in all investigated species was triangularine. A. primuliflora and A. graeca showed similar chemical composition that comprised 9-angeloylretronecine, 7-tigloylretronecine, 9-tigloylretronecine, triangularicine, dihydroxytriangularine, dihydroxytriangularicine, whereas, in A. stribrnyi 9-tigloylretronecine, triangularicine and dihydroxytriangularicine were not found. This is the first report on the presence of PAs in A. primuliflora, A. stribrnyi and A. graeca. Besides, this is the first report on the embryology of these endemic species. The results contribute to the knowledge of the three endemic Alkanna species and will facilitate policy-making and defining new strategies for their conservation.


Asunto(s)
Boraginaceae/química , Boraginaceae/genética , Alcaloides/análisis , Peninsula Balcánica , Boraginaceae/metabolismo , Bulgaria , Cromatografía Líquida de Alta Presión/métodos , Cromatografía de Gases y Espectrometría de Masas/métodos , Variación Genética/genética , Extractos Vegetales/química , Alcaloides de Pirrolicidina/química , Reproducción/fisiología , Especificidad de la Especie
11.
PLoS One ; 15(6): e0233377, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32502155

RESUMEN

The biology of how faces are built and come to differ from one another is complex. Discovering normal variants that contribute to differences in facial morphology is one key to untangling this complexity, with important implications for medicine and evolutionary biology. This study maps quantitative trait loci (QTL) for skeletal facial shape using Diversity Outbred (DO) mice. The DO is a randomly outcrossed population with high heterozygosity that captures the allelic diversity of eight inbred mouse lines from three subspecies. The study uses a sample of 1147 DO animals (the largest sample yet employed for a shape QTL study in mouse), each characterized by 22 three-dimensional landmarks, 56,885 autosomal and X-chromosome markers, and sex and age classifiers. We identified 37 facial shape QTL across 20 shape principal components (PCs) using a mixed effects regression that accounts for kinship among observations. The QTL include some previously identified intervals as well as new regions that expand the list of potential targets for future experimental study. Three QTL characterized shape associations with size (allometry). Median support interval size was 3.5 Mb. Narrowing additional analysis to QTL for the five largest magnitude shape PCs, we found significant overrepresentation of genes with known roles in growth, skeletal and facial development, and sensory organ development. For most intervals, one or more of these genes lies within 0.25 Mb of the QTL's peak. QTL effect sizes were small, with none explaining more than 0.5% of facial shape variation. Thus, our results are consistent with a model of facial diversity that is influenced by key genes in skeletal and facial development and, simultaneously, is highly polygenic.


Asunto(s)
Desarrollo Óseo/genética , Huesos Faciales/anatomía & histología , Desarrollo Maxilofacial/genética , Alelos , Animales , Huesos/anatomía & histología , Mapeo Cromosómico/métodos , Ratones de Colaboración Cruzada/genética , Cara/anatomía & histología , Femenino , Variación Genética/genética , Genotipo , Masculino , Ratones , Fenotipo , Polimorfismo de Nucleótido Simple/genética , Sitios de Carácter Cuantitativo/genética
12.
Toxicology ; 441: 152505, 2020 08.
Artículo en Inglés | MEDLINE | ID: mdl-32450112

RESUMEN

The majority of single nucleotide variants (SNVs) identified in Genome Wide Association Studies (GWAS) fall within non-protein coding DNA and have the potential to alter gene expression. Non-protein coding DNA can control gene expression by acting as transcription factor (TF) binding sites or by regulating the organization of DNA into chromatin. SNVs in non-coding DNA sequences can disrupt TF binding and chromatin structure and this can result in pathology. Further, environmental health studies have shown that exposure to xenobiotics can disrupt the ability of TFs to regulate entire gene networks and result in pathology. However, there is a large amount of interindividual variability in exposure-linked health outcomes. One explanation for this heterogeneity is that genetic variation and exposure combine to disrupt gene regulation, and this eventually manifests in disease. Many resources exist that annotate common variants from GWAS and combine them with conservation, functional genomics, and TF binding data. These annotation tools provide clues regarding the biological implications of an SNV, as well as lead to the generation of hypotheses regarding potentially disrupted target genes, epigenetic markers, pathways, and cell types. Collectively this information can be used to predict how SNVs can alter an individual's response to exposure and disease risk. A basic understanding of the regulatory information contained within non-protein coding DNA is needed to predict the biological consequences of SNVs, and to determine how these SNVs impact exposure-related disease. We hope that this review will aid in the characterization of disease-associated genetic variation in the non-protein coding genome.


Asunto(s)
Interacción Gen-Ambiente , Variación Genética , Genómica/métodos , Regiones no Traducidas , Animales , Expresión Génica , Variación Genética/genética , Estudio de Asociación del Genoma Completo , Humanos , Polimorfismo de Nucleótido Simple/genética , Regiones no Traducidas/efectos de los fármacos
13.
Nature ; 581(7809): 434-443, 2020 05.
Artículo en Inglés | MEDLINE | ID: mdl-32461654

RESUMEN

Genetic variants that inactivate protein-coding genes are a powerful source of information about the phenotypic consequences of gene disruption: genes that are crucial for the function of an organism will be depleted of such variants in natural populations, whereas non-essential genes will tolerate their accumulation. However, predicted loss-of-function variants are enriched for annotation errors, and tend to be found at extremely low frequencies, so their analysis requires careful variant annotation and very large sample sizes1. Here we describe the aggregation of 125,748 exomes and 15,708 genomes from human sequencing studies into the Genome Aggregation Database (gnomAD). We identify 443,769 high-confidence predicted loss-of-function variants in this cohort after filtering for artefacts caused by sequencing and annotation errors. Using an improved model of human mutation rates, we classify human protein-coding genes along a spectrum that represents tolerance to inactivation, validate this classification using data from model organisms and engineered human cells, and show that it can be used to improve the power of gene discovery for both common and rare diseases.


Asunto(s)
Exoma/genética , Genes Esenciales/genética , Variación Genética/genética , Genoma Humano/genética , Adulto , Encéfalo/metabolismo , Enfermedades Cardiovasculares/genética , Estudios de Cohortes , Bases de Datos Genéticas , Femenino , Predisposición Genética a la Enfermedad/genética , Estudio de Asociación del Genoma Completo , Humanos , Mutación con Pérdida de Función/genética , Masculino , Tasa de Mutación , Proproteína Convertasa 9/genética , ARN Mensajero/genética , Reproducibilidad de los Resultados , Secuenciación del Exoma Completo , Secuenciación Completa del Genoma
14.
PLoS One ; 15(5): e0232818, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32407352

RESUMEN

Breeding for yield and fruit quality traits in passion fruits is complex due to the polygenic nature of these traits and the existence of genetic correlations among them. Therefore, studies focused on crop management practices and breeding using modern quantitative genetic approaches are still needed, especially for Passiflora alata, an understudied crop, popularly known as the sweet passion fruit. It is highly appreciated for its typical aroma and flavor characteristics. In this study, we aimed to reevaluate 30 genotypes previously selected for fruit quality from a 100 full-sib sweet passion fruit progeny in three environments, with a view to estimating the heritability and genetic correlations, and investigating the GEI and response to selection for nine fruit traits (weight, diameter and length of the fruit; thickness and weight of skin; weight and yield of fruit pulp; soluble solids, and yield). Pairwise genetic correlations among the fruit traits showed mostly intermediate to high values, especially those associated with fruit size and shape. Different genotype rankings were obtained regarding the predicted genetic values of weight of skin, thickness of skin and weight of pulp in each environment. Finally, we used a multiplicative selection index to select simultaneously for weight of pulp and against fruit skin thickness and weight. The response to selection was positive for all traits except soluble solids, and the 20% superior (six) genotypes were ranked. Based on the assumption that incompatibility mechanisms exist in P. alata, the selected genotypes were intercrossed in a complete diallel mating scheme. It is worth noting that all genotypes produced fruits, which is essential to guarantee yields in commercial orchards.


Asunto(s)
Frutas/genética , Interacción Gen-Ambiente , Passiflora/genética , Cruzamiento , Capsicum/genética , Capsicum/crecimiento & desarrollo , Frutas/crecimiento & desarrollo , Variación Genética/genética , Genotipo , Passiflora/crecimiento & desarrollo , Selección Genética/genética
15.
Gene ; 753: 144804, 2020 Aug 30.
Artículo en Inglés | MEDLINE | ID: mdl-32445920

RESUMEN

We have investigated 765 unrelated individuals from Azerbaijan using AmpFlSTR® Identifiler® Plus PCR Amplification Kit. For each STR locus basic population-genetic and forensic parameters were determined. The calculated P-values (PHWE) for the accuracy of the Hardy-Weinberg equilibrium (HWE) tests, showed that this parameter had a statistically significant value (PHWE = 0.0000) only for the THO1, D18S51 and FGA loci. The values of parameters for the set of 15 STR loci such as CPE, CPD, CTPI and the PP showed that the given set of loci can be confidently used to solve identification problems for the studied population. Multiple population differentiation tests performed between Azerbaijan and other 17 world populations revealed that between Azerbaijan and Iraqi, Iranian, Turkish populations there were no significant differences on all STR loci. Additionally, comparisons of Fischer genetic distance indices (FST) P-values did not reveal any statistically significant difference between Azerbaijan and Iranian populations at P < 0.05. However, with South African black population differences at all STR loci were detected. Both tests did not reveal a locus by which our population would differ from all the other compared populations. PCA and PCoA analyzes showed that the Azerbaijani population was grouped with different populations in different quarters, showing a negative and zero correlation, respectively. Regarding the location of the Azerbaijan population, there are some differences between NJ and UPGMA phylogenetic trees. For example, in the NJ tree, Azerbaijan population was grouped with Iranian, but in the UPGMA tree, it was grouped with the Turkish population. Based on Nei's genetic distance between populations the second tree has a more realistic outcome.


Asunto(s)
Variación Genética/genética , Genética de Población/métodos , Repeticiones de Microsatélite/genética , Adulto , Alelos , Azerbaiyán/etnología , Femenino , Fibrinógeno/genética , Frecuencia de los Genes/genética , Sitios Genéticos/genética , Humanos , Irán , Masculino , Proteínas Nucleares/genética , Filogenia , Reacción en Cadena de la Polimerasa , Turquia
16.
Gene ; 753: 144800, 2020 Aug 30.
Artículo en Inglés | MEDLINE | ID: mdl-32454179

RESUMEN

Sugarcane is one among the most important commercial crops used to produce sugar, ethanol, and other byproducts, which significantly contributes in the GDP of India and many other countries around the world. Genetic diversity is a platform for any breeding program of a plant species. Estimation of the genetic variability and population structure play a vital role for conservation planning and management of plant genetic resources. Genetic variability serves as a source of noble alleles responsible for key agronomic and quality traits, which ultimately form basis for identification and selection of promising parents for breeding programs. In the present study genetic diversity and population structure of 139 accessions of the genus Saccharum, allied genera of family Poaceae and cultivars were assessed using informative microsatellite (SSR) markers. A sum of 427 alleles was produced using 61 polymorphic primers and number of alleles generated was ranged from 2 to 13 with an average of 7 alleles per locus. PIC values were ranged from 0.35 to 0.90, with a mean value of 0.66 for all the markers evaluated. Cluster analysis based on UPGMA method revealed three major clusters which were further subdivided into nine subclusters. Population structure analysis also established three subpopulations of used accession set, however there were no correlation of sub-groupings with that of place of origin. AMOVA analysis also confirmed that 83% and 17% of total variations were attributed to the within- and between-populations, correspondingly, demonstrating greater exchange of gene pool across places of origin. The principal component analysis (PCA) demonstrated the distribution of accessions in the scatter-plot was substantially dispersed, revealing rich genetic diversity among accessions of different species. The findings from this study will be useful in breeding programs for introgression of noble alleles into modern cultivars by exploiting natural genetic variation existing in sugarcane genetic resources.


Asunto(s)
Variación Genética/genética , Repeticiones de Microsatélite/genética , Saccharum/genética , Alelos , Análisis por Conglomerados , ADN de Plantas/genética , Frecuencia de los Genes/genética , Genotipo , India , Fenotipo , Filogenia , Fitomejoramiento/métodos
17.
Arch Virol ; 165(8): 1749-1757, 2020 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-32435857

RESUMEN

The aim of this study was to assess the vaccine-matching and antigenic properties of foot-and-mouth disease virus (FMDV) isolates collected from Ethiopia between 2011 and 2014. Samples (n = 51) were collected from cattle and pigs with clinical signs consistent with foot-and-mouth disease (FMD) on farms in Debre-Berhan, Debre-Zeit/Bishoftu, Sidamo, Mekelle, and Addis Ababa. Infectious FMDV was isolated using BHK-21 cell cultures from 38 of the 51 field samples (74.5%). All of these FMDV-positive samples were characterized as serotype O, belonging to two East Africa topotypes (EA-3 and EA-4), and their VP1-encoding sequences demonstrated amino acid sequence variability encompassing 27 positions in comparison to the vaccine strain (O/ETH/38/2005) currently provided by the National Veterinary Institute of Ethiopia. One-dimensional virus neutralization test (1 dm VNT) results showed that O/ETH/38/2005 was antigenically matched to 10 of the 16 serotype O viruses. These findings indicate that the O/ETH/38/2005 vaccine strain can provide protection against outbreaks caused by the O/EA-3 topotype, although poorer vaccine-matching results for the O/EA-4 topotype reinforce the importance of using a good-quality vaccine with high coverage in the susceptible herds with supporting post-vaccination serosurveillance to ensure that sufficient antibody titers are generated in the vaccinated animals.


Asunto(s)
Virus de la Fiebre Aftosa/genética , Virus de la Fiebre Aftosa/inmunología , Variación Genética/genética , Vacunas Virales/inmunología , Animales , Bovinos , Enfermedades de los Bovinos/inmunología , Brotes de Enfermedades/veterinaria , Etiopía , Fiebre Aftosa/inmunología , Fiebre Aftosa/virología , Variación Genética/inmunología , Filogenia , Serogrupo , Porcinos
18.
Int J Food Microbiol ; 325: 108647, 2020 Jul 16.
Artículo en Inglés | MEDLINE | ID: mdl-32361480

RESUMEN

Yeasts are one of the main organisms in the food industry and effective components of many ecosystems. The method for identifying and detecting certain yeast species or strains is a crucial step for the food industry and should be simple, reliable, fast, and inexpensive. In our study, inter-priming binding sites (iPBS) retrotransposon marker system was employed to elucidate the genetic variability at intraspecies and interspecies levels among 112 yeast strains belonging to eight species previously obtained from fermented foods. The molecular identification of yeast strains was firstly confirmed by sequencing the D1/D2 domain of the 26S rRNA. The eight selected retrotransposon-based primers produced 278 bands, all of which were polymorphic with an average of 34.75 polymorphic fragments per primer. The averages of polymorphism information contents and the resolving power values for the iPBS marker system were 0.23 and 10.11, respectively. The genetic parameters within each yeast species obtained from iPBS markers were observed as; the percentage of polymorphic loci for each species ranging from 19.23% to 71.21%, Nei's gene diversity from 0.085 to 0.228, while Shannon's information index values ranging from 0.125 to 0.349. The value of gene flow (0.09) and genetic variation among the populations (0.85) showed higher genetic variation among the species. UPGMA analyses demonstrated considerable genetic variability in the yeast strains, clustered them according to their species, and revealed the intraspecific variation. Each of the selected iPBS primer provided enough species-discrimination. Present evaluations suggest the utility of iPBS marker system to estimate the genetic variation of yeast strains. This study is a preliminary point for further studies on the identification methodology, and population genetics of yeast species having importance in the food industry with iPBS markers.


Asunto(s)
Retroelementos/genética , Saccharomycetales/genética , Levadura Seca/genética , Sitios de Unión , Cartilla de ADN/genética , Ecosistema , Variación Genética/genética , Filogenia , Polimorfismo Genético/genética , Saccharomycetales/clasificación
19.
PLoS Comput Biol ; 16(5): e1007797, 2020 05.
Artículo en Inglés | MEDLINE | ID: mdl-32365089

RESUMEN

Copy number variants (CNVs) are the gain or loss of DNA segments in the genome that can vary in dosage and length. CNVs comprise a large proportion of variation in human genomes and impact health conditions. To detect rare CNV associations, kernel-based methods have been shown to be a powerful tool due to their flexibility in modeling the aggregate CNV effects, their ability to capture effects from different CNV features, and their accommodation of effect heterogeneity. To perform a kernel association test, a CNV locus needs to be defined so that locus-specific effects can be retained during aggregation. However, CNV loci are arbitrarily defined and different locus definitions can lead to different performance depending on the underlying effect patterns. In this work, we develop a new kernel-based test called CONCUR (i.e., copy number profile curve-based association test) that is free from a definition of locus and evaluates CNV-phenotype associations by comparing individuals' copy number profiles across the genomic regions. CONCUR is built on the proposed concepts of "copy number profile curves" to describe the CNV profile of an individual, and the "common area under the curve (cAUC) kernel" to model the multi-feature CNV effects. The proposed method captures the effects of CNV dosage and length, accounts for the numerical nature of copy numbers, and accommodates between- and within-locus etiological heterogeneity without the need to define artificial CNV loci as required in current kernel methods. In a variety of simulation settings, CONCUR shows comparable or improved power over existing approaches. Real data analyses suggest that CONCUR is well powered to detect CNV effects in the Swedish Schizophrenia Study and the Taiwan Biobank.


Asunto(s)
Biología Computacional/métodos , Variaciones en el Número de Copia de ADN/genética , Algoritmos , Área Bajo la Curva , Predisposición Genética a la Enfermedad/genética , Variación Genética/genética , Genoma Humano/genética , Estudio de Asociación del Genoma Completo/métodos , Genómica/métodos , Humanos , Polimorfismo de Nucleótido Simple/genética , Análisis Espacial
20.
PLoS One ; 15(4): e0232092, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32352995

RESUMEN

Human adenovirus (HAdV-7) is a highly contagious pathogen that causes severe respiratory illnesses. However, the epidemic patterns and genetic variability of HAdV-7 circulating in mainland China have not been well elucidated. In this study, we used Chinese HAdV sentinel surveillance data obtained from 2012-2015 to investigate the clinical features of 122 HAdV-7-positive cases and performed amplification and sequence determination of three capsid genes (penton base, hexon, and fiber) from 69 isolated viruses covering from seven provinces of China. Additionally, we compared with data from representative sequences of 21 strains covering seven more provinces in China and 32 international HAdV-7 strains obtained from GenBank database to determine the phylogenetic, sequence variations, and molecular evolution of HAdV-7. The results indicated that HAdV-7 infection occurred throughout the year, and a high proportion of severe cases (27 cases, 22.1%) exhibited infantile pneumonia. Moreover, phylogenetic analysis showed that all HAdV-7 strains could be divided into two major evolutionary branches, including subtype 1 and subtype 2, and subtype 3 was also formed according to analysis of the penton base gene. Subtypes 1 and 2 co-circulated in China before 2008, and HAdV-7 strains currently circulating in China belonged to subtype 2, which was also the predominant strain circulating worldwide in recent years. Further sequence variation analysis indicated that three genes of HAdV-7 were relatively stable across time and geographic space, particularly for viruses within subtypes, which shared almost the same variation sites. Owing to continuous outbreaks caused by HAdV-7, resulting in increased illness severity and fatality rates in China, the establishment of a national HAdV surveillance system is urgently needed for the development of effective preventive and infection-control interventions for adenovirus respiratory infections in China.


Asunto(s)
Infecciones por Adenovirus Humanos/genética , Adenovirus Humanos/genética , Proteínas de la Cápside/genética , Adenoviridae/genética , Infecciones por Adenovirus Humanos/epidemiología , Infecciones por Adenovirus Humanos/virología , China/epidemiología , Brotes de Enfermedades , Evolución Molecular , Variación Genética/genética , Humanos , Filogenia , Infecciones del Sistema Respiratorio/epidemiología , Análisis de Secuencia de ADN/métodos
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