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1.
Gene ; 766: 145118, 2021 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-32896588

RESUMEN

Insulin-like growth factor 1 (IGF1) is a multifunctional cell proliferation regulator that plays a critical role in regulating animal growth and development. In this study, the expression level of IGF1 gene in different tissues of Dezhou donkey in different periods was investigated by RT-qPCR. Meanwhile, two mutation sites were identified within the IGF1 gene and its effect on body size traits of Dezhou donkey was analysed. The results showed that the expression level of the adult donkey IGF1 gene in heart, liver, spleen, lung, renal and gastric tissues is higher than that of the young donkeys, but the young donkeys are significantly higher in muscle tissues than the adult donkeys. The IGF1-1 and IGF1-2 loci showed a trend that the GG mutant was larger than other genotypes in the growth traits of both male and female donkeys, among which the IGF1-1 loci had a significant association with the chest circumference and chest depth of male donkeys (P < 0.05), and the IGF1-2 loci had a significant association with the chest circumference of female donkeys. Haplotype combination Hap1Hap1 (GG-GG) showed a greater tendency than Hap2Hap2 (AA-GG) combination in terms of growth traits, reflecting that the results were consistent with the analysis results of genotypes, which also proved the analysis results of genotypes and growth traits had certain reliability. In summary, the IGF1 gene is a candidate gene for growth and development, and its polymorphisms can be used as the molecular markers for Dezhou donkey breeding.


Asunto(s)
Tamaño Corporal/genética , Equidae/genética , Factor I del Crecimiento Similar a la Insulina/genética , Transcriptoma/genética , Animales , Cruzamiento/métodos , Femenino , Genotipo , Haplotipos/genética , Masculino , Fenotipo , Polimorfismo de Nucleótido Simple/genética
2.
Gene ; 766: 145143, 2021 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-32911028

RESUMEN

We aimed to test the hypothesis that apelin (APLN) and its receptor AGTRL1 (APLNR) genes may contribute to the pathogenesis of myocardial infarction in Han Chinese. This is a hospital-based, case-control association study, involving 1067 patients with myocardial infarction and 942 healthy controls. Myocardial infarction is diagnosed by electrocardiogram or anatomopathological examination. Eight polymorphisms in APLN gene and 5 in APLNR gene were genotyped using the TaqMan assay. Risk was summarized as odds ratio (OR) and 95% confidence interval (CI). In males, rs56204867-G allele (adjusted OR, 95% CI, p: 0.21, 0.08-0.55, 0.002) and rs2235309-T allele (0.60, 0.42-0.84, 0.004) was associated with a significantly reduced risk of myocardial infarction, and the mutations of rs2235310 was associated with an increased risk (1.41, 1.06-2.52, 0.021), as well as for rs948847-GG genotype (1.85, 1.23-2.91, 0.007). In females, the presence of rs56204867-AG and -GG genotypes was significantly associated with 44% and 50% reduced risk (0.56 and 0.50, 0.40-8.04 and 0.29-0.86, 0.007 and 0.036), respectively; for rs2235310, CC genotype was associated with 72% increased risk (1.72, 1.09-3.22, 0.016), and the odds of myocardial infarction was 3.47 for rs9943582-TT genotype (95% CI: 1.53-7.57, 0.009). The gender-specific association of APLN and APLNR genes with myocardial infarction was reinforced by further linkage and haplotype analyses. Finally, nomograms based on significant polymorphisms are satisfactory, with the C-indexes over 80% for both genders. Taken together, our findings indicate that APLN and APLNR genes are potential candidates in the pathogenesis of myocardial infarction in Han Chinese, and importantly their contribution is gender-dependent.


Asunto(s)
Receptores de Apelina/genética , Apelina/genética , Grupo de Ascendencia Continental Asiática/genética , Predisposición Genética a la Enfermedad/genética , Infarto del Miocardio/genética , Polimorfismo de Nucleótido Simple/genética , Anciano , Alelos , Estudios de Casos y Controles , Femenino , Frecuencia de los Genes/genética , Genotipo , Haplotipos/genética , Humanos , Masculino , Persona de Mediana Edad
3.
Gene ; 766: 145158, 2021 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-32949694

RESUMEN

The reproductive performance (e.g. fertility) of dairy cows, which declined over past few decades due to the intense and intensive selection, needs to be improved. Previous genome-wide association study (GWAS) of female Holstein screened the Adenylate cyclase 5 (ADCY5) as the candidate gene for cow fertility. As a member of the adenylyl cyclases family, adenylate cyclase 5 (ADCY5) is famous for regulating extrapyramidal motor system related various neuropsychiatric diseases, and its genetic variant is reported to associate with lower birth and placenta weight which leads to asymmetric fetal growth restriction. It was hypothesized that ADCY5 may affect the fertility of cows by regulating the processes of ovarian development. Herein, genomic DNA from 768 ovaries samples of healthy unrelated Holstein cow were used to screen potential insertion/deletion (indel) mutations using eight pairs of primers, and we found three novel polymorphic indel variants, namely, rs385624978 (P3-D11-bp), rs433028962 (P5-I19-bp) and rs382393457 (P8-D19-bp). The minor allelic frequencies (MAF) of P3-D11-bp, P5-I19-bp and P8-D19-bp loci were 0.188, 0.365 and 0.06, respectively, and there were 7 different haplotypes. Additionally, linkage disequilibrium analysis demonstrated no linkage among them. Importantly, P3-D11-bp locus was significantly related to both ovarian width (P = 1.0E-6) and corpus luteum diameter (P = 0.015); P5-I19-bp locus had a significant relation with corpus albicans diameter (P = 0.030) and ovaries with mutational homozygous genotype produced a superior corpus albicans diameter than those with other genotypes. Briefly, three novel indel mutations of bovine ADCY5 gene were identified and two of them were uncovered to be significantly correlated with ovarian phenotypic traits or corpus luteum or albicans traits. These findings contributed to the application of molecular marker-assisted selection (MAS) in improving female fertility in cattle, which could accelerate the development of the cattle industry.


Asunto(s)
Adenilil Ciclasas/genética , Ovario/fisiología , Polimorfismo de Nucleótido Simple/genética , Animales , Bovinos , Femenino , Fertilidad/genética , Frecuencia de los Genes/genética , Estudio de Asociación del Genoma Completo/métodos , Genotipo , Haplotipos/genética , Mutación INDEL/genética , Desequilibrio de Ligamiento/genética , Fenotipo , Reproducción/genética
4.
Nat Commun ; 11(1): 4954, 2020 10 02.
Artículo en Inglés | MEDLINE | ID: mdl-33009396

RESUMEN

Genetic variation is of crucial importance for crop improvement. Landraces are valuable sources of diversity, but for quantitative traits efficient strategies for their targeted utilization are lacking. Here, we map haplotype-trait associations at high resolution in ~1000 doubled-haploid lines derived from three maize landraces to make their native diversity for early development traits accessible for elite germplasm improvement. A comparative genomic analysis of the discovered haplotypes in the landrace-derived lines and a panel of 65 breeding lines, both genotyped with 600k SNPs, points to untapped beneficial variation for target traits in the landraces. The superior phenotypic performance of lines carrying favorable landrace haplotypes as compared to breeding lines with alternative haplotypes confirms these findings. Stability of haplotype effects across populations and environments as well as their limited effects on undesired traits indicate that our strategy has high potential for harnessing beneficial haplotype variation for quantitative traits from genetic resources.


Asunto(s)
Haplotipos/genética , Carácter Cuantitativo Heredable , Zea mays/genética , Biblioteca de Genes , Variación Genética , Genoma de Planta , Estudio de Asociación del Genoma Completo , Haploidia , Fitomejoramiento , Análisis de Componente Principal , Zea mays/crecimiento & desarrollo
5.
Zootaxa ; 4767(1): zootaxa.4767.1.2, 2020 Apr 23.
Artículo en Inglés | MEDLINE | ID: mdl-33056572

RESUMEN

To date, only seven species of Macrobiotidae (Parachela; Eutardigrada; Tardigrada) have been reported from Japan, including the recently described Macrobiotus shonaicus Stec et al., 2018 from the Shonai region of Japan. This species has flexible filaments on the egg processes and is known to proliferate only through sexual reproduction. Here, we report a multifaceted analysis of nine populations of M. shonaicus found on four Japanese islands. DNA sequencing of the cytochrome oxidase subunit I (COI) and internal transcribed spacer 2 (ITS-2) of the nine populations revealed 8 and 11 haplotypes, respectively. The extensive morphometric analysis showed considerably greater variability in the morphology of eggs than of animals. In addition to the morphological and molecular data, we confirmed the karyotype and found that all populations had a chromosome number of n = 6. Moreover, we observed and filmed mating behaviour between all studied populations of M. shonaicus. Our results clearly indicated that M. shonaicus is widely distributed throughout Japan.


Asunto(s)
Tardigrada , Animales , Haplotipos , Japón , Reproducción
6.
Nat Commun ; 11(1): 4916, 2020 10 01.
Artículo en Inglés | MEDLINE | ID: mdl-33004803

RESUMEN

Self-incompatibility (SI) is a breeding system that promotes cross-fertilization. In Brassica, pollen rejection is induced by a haplotype-specific interaction between pistil determinant SRK (S receptor kinase) and pollen determinant SP11 (S-locus Protein 11, also named SCR) from the S-locus. Although the structure of the B. rapa S9-SRK ectodomain (eSRK) and S9-SP11 complex has been determined, it remains unclear how SRK discriminates self- and nonself-SP11. Here, we uncover the detailed mechanism of self/nonself-discrimination in Brassica SI by determining the S8-eSRK-S8-SP11 crystal structure and performing molecular dynamics (MD) simulations. Comprehensive binding analysis of eSRK and SP11 structures reveals that the binding free energies are most stable for cognate eSRK-SP11 combinations. Residue-based contribution analysis suggests that the modes of eSRK-SP11 interactions differ between intra- and inter-subgroup (a group of phylogenetically neighboring haplotypes) combinations. Our data establish a model of self/nonself-discrimination in Brassica SI.


Asunto(s)
Brassica rapa/fisiología , Fitomejoramiento , Proteínas de Plantas/metabolismo , Proteínas Quinasas/metabolismo , Animales , Cristalografía , Flores/metabolismo , Haplotipos , Simulación de Dinámica Molecular , Proteínas de Plantas/genética , Proteínas de Plantas/ultraestructura , Polen/metabolismo , Unión Proteica/fisiología , Dominios Proteicos/fisiología , Proteínas Quinasas/genética , Proteínas Quinasas/ultraestructura , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Proteínas Recombinantes/ultraestructura , Células Sf9 , Spodoptera
7.
Plant Genome ; 13(1): e20009, 2020 03.
Artículo en Inglés | MEDLINE | ID: mdl-33016627

RESUMEN

Successful management and utilization of increasingly large genomic datasets is essential for breeding programs to accelerate cultivar development. To help with this, we developed a Sorghum bicolor Practical Haplotype Graph (PHG) pangenome database that stores haplotypes and variant information. We developed two PHGs in sorghum that were used to identify genome-wide variants for 24 founders of the Chibas sorghum breeding program from 0.01x sequence coverage. The PHG called single nucleotide polymorphisms (SNPs) with 5.9% error at 0.01x coverage-only 3% higher than PHG error when calling SNPs from 8x coverage sequence. Additionally, 207 progenies from the Chibas genomic selection (GS) training population were sequenced and processed through the PHG. Missing genotypes were imputed from PHG parental haplotypes and used for genomic prediction. Mean prediction accuracies with PHG SNP calls range from .57-.73 and are similar to prediction accuracies obtained with genotyping-by-sequencing or targeted amplicon sequencing (rhAmpSeq) markers. This study demonstrates the use of a sorghum PHG to impute SNPs from low-coverage sequence data and shows that the PHG can unify genotype calls across multiple sequencing platforms. By reducing input sequence requirements, the PHG can decrease the cost of genotyping, make GS more feasible, and facilitate larger breeding populations. Our results demonstrate that the PHG is a useful research and breeding tool that maintains variant information from a diverse group of taxa, stores sequence data in a condensed but readily accessible format, unifies genotypes across genotyping platforms, and provides a cost-effective option for genomic selection.


Asunto(s)
Sorghum , Análisis Costo-Beneficio , Genoma , Genómica , Haplotipos , Sorghum/genética
9.
Nan Fang Yi Ke Da Xue Xue Bao ; 40(10): 1493-1499, 2020 Oct 30.
Artículo en Chino | MEDLINE | ID: mdl-33118521

RESUMEN

OBJECTIVE: Haplotype amplification on germline variants is suggested to imply potential selective advantages and clonal expansion susceptibility and has become an important signature for seeking cancer susceptibility gene.Here we propose an improved association method that fully considers the haplotype amplification status. METHODS: The haplotype amplification status was estimated by the variant allelic frequencies.We adopted a permutation test on variant allelic frequencies to divide the candidate variants into multiple groups.A likelihood clustering method was then applied to establish the neighborhood system of the hidden Markov random field framework.A filtering pipeline was introduced into the proposed method to further refine the candidate variants, including a Wilson's interval filter and a false discovery rate controller.The final candidate set along with the haplotype amplification status was collapsed into the weighted virtual sites for association tests. RESULTS: Through simulated tests on a series of datasets, we compared the type Ⅰ error rates of different minor allele frequencies, which stably fell within 2%, suggesting good robustness of the algorithm.In addition, we compared another 5 published association approaches for Type-Ⅰ and Type-Ⅱ error rates with the proposed method, which resulted in the error rates all within 2%, demonstrating significant advantages and a good statistical ability of the proposed method. CONCLUSIONS: The proposed method can accurately identify tumor susceptibility variants in haplotype amplification area with good robustness and stability.


Asunto(s)
Algoritmos , Neoplasias , Análisis por Conglomerados , Amplificación de Genes , Frecuencia de los Genes , Haplotipos , Humanos , Neoplasias/genética , Polimorfismo de Nucleótido Simple
10.
BMC Bioinformatics ; 21(1): 451, 2020 Oct 12.
Artículo en Inglés | MEDLINE | ID: mdl-33045983

RESUMEN

BACKGROUND: DNA methylation is an important epigenetic modification that plays a critical role in most eukaryotic organisms. Parental alleles in haploid genomes may exhibit different methylation patterns, which can lead to different phenotypes and even different therapeutic and drug responses to diseases. However, to our knowledge, no software is available for the identification of DNA methylation haplotype regions with combined allele-specific DNA methylation, single nucleotide polymorphisms (SNPs) and high-throughput chromosome conformation capture (Hi-C) data. RESULTS: In this paper, we developed a new method, MethHaplo, that identify DNA methylation haplotype regions with allele-specific DNA methylation and SNPs from whole-genome bisulfite sequencing (WGBS) data. Our results showed that methylation haplotype regions were ten times longer than haplotypes with SNPs only. When we integrate WGBS and Hi-C data, MethHaplo could call even longer haplotypes. CONCLUSIONS: This study illustrates the usefulness of methylation haplotypes. By constructing methylation haplotypes for various cell lines, we provide a clearer picture of the effect of DNA methylation on gene expression, histone modification and three-dimensional chromosome structure at the haplotype level. Our method could benefit the study of parental inheritance-related disease and hybrid vigor in agriculture.


Asunto(s)
Alelos , Metilación de ADN , Haplotipos/genética , Polimorfismo de Nucleótido Simple , Secuenciación Completa del Genoma , Epigénesis Genética , Programas Informáticos
11.
PLoS One ; 15(10): e0241172, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-33091066

RESUMEN

The novel coronavirus 2019 (COVID-19) global pandemic has drastically affected the world economy, raised public anxiety, and placed a substantial psychological burden on the governments and healthcare professionals by affecting over 4.7 million people worldwide. As a preventive measure to minimise the risk of community transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in India, a nationwide lockdown was imposed initially for 21 days to limit the movement of 1.3 billion people. These restrictions continue in most areas, with a conditional relaxation occurring in a few Indian states. In an attempt to assess the emerging mutants of SARS-CoV-2 and determine their spread in India, we analysed 112 complete genomes of SARS-CoV-2 in a time-lapse manner. We found 72 distinct SARS-CoV-2 haplotypes, defined by 143 polymorphic sites and high haplotype diversity, suggesting that this virus possesses a high evolutionary potential. We also demonstrated that early introduction of SARS-CoV-2 into India was from China, Italy and Iran and observed signs of community spread of the virus following its rapid demographic expansion since its first outbreak in the country. Additionally, we identified 18 mutations in the SARS-CoV-2 spike glycoprotein and a few selected mutations showed to increase stability, binding affinity, and molecular flexibility in the overall tertiary structure of the protein that may facilitate interaction between the receptor binding domain (RBD) of spike protein and the human angiotensin-converting enzyme 2 (ACE2) receptor. The study provides a pragmatic view of haplotype-dependent spread of SARS-CoV-2 in India which could be important in tailoring the pharmacologic treatments to be more effective for those infected with the most common haplotypes. The findings based on the time-lapse sentinel surveillance of SARS-CoV-2 will aid in the development of a real-time practical framework to tackle the ongoing, fast-evolving epidemic challenges in the country.


Asunto(s)
Betacoronavirus/genética , Infecciones por Coronavirus/epidemiología , Infecciones por Coronavirus/transmisión , Neumonía Viral/epidemiología , Neumonía Viral/transmisión , Vigilancia de Guardia , Infecciones por Coronavirus/prevención & control , Infecciones por Coronavirus/virología , Genoma Viral/genética , Haplotipos , Humanos , India/epidemiología , Simulación del Acoplamiento Molecular , Mutación , Pandemias/prevención & control , Peptidil-Dipeptidasa A/metabolismo , Filogenia , Neumonía Viral/prevención & control , Neumonía Viral/virología , Polimorfismo Genético , Estructura Terciaria de Proteína , Cuarentena/métodos , Glicoproteína de la Espiga del Coronavirus/química , Glicoproteína de la Espiga del Coronavirus/genética , Glicoproteína de la Espiga del Coronavirus/metabolismo
12.
mBio ; 11(5)2020 10 13.
Artículo en Inglés | MEDLINE | ID: mdl-33051368

RESUMEN

Despite numerous barriers to transmission, zoonoses are the major cause of emerging infectious diseases in humans. Among these, severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and ebolaviruses have killed thousands; the human immunodeficiency virus (HIV) has killed millions. Zoonoses and human-to-animal cross-species transmission are driven by human actions and have important management, conservation, and public health implications. The current SARS-CoV-2 pandemic, which presumably originated from an animal reservoir, has killed more than half a million people around the world and cases continue to rise. In March 2020, New York City was a global epicenter for SARS-CoV-2 infections. During this time, four tigers and three lions at the Bronx Zoo, NY, developed mild, abnormal respiratory signs. We detected SARS-CoV-2 RNA in respiratory secretions and/or feces from all seven animals, live virus in three, and colocalized viral RNA with cellular damage in one. We produced nine whole SARS-CoV-2 genomes from the animals and keepers and identified different SARS-CoV-2 genotypes in the tigers and lions. Epidemiologic and genomic data indicated human-to-tiger transmission. These were the first confirmed cases of natural SARS-CoV-2 animal infections in the United States and the first in nondomestic species in the world. We highlight disease transmission at a nontraditional interface and provide information that contributes to understanding SARS-CoV-2 transmission across species.IMPORTANCE The human-animal-environment interface of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an important aspect of the coronavirus disease 2019 (COVID-19) pandemic that requires robust One Health-based investigations. Despite this, few reports describe natural infections in animals or directly link them to human infections using genomic data. In the present study, we describe the first cases of natural SARS-CoV-2 infection in tigers and lions in the United States and provide epidemiological and genetic evidence for human-to-animal transmission of the virus. Our data show that tigers and lions were infected with different genotypes of SARS-CoV-2, indicating two independent transmission events to the animals. Importantly, infected animals shed infectious virus in respiratory secretions and feces. A better understanding of the susceptibility of animal species to SARS-CoV-2 may help to elucidate transmission mechanisms and identify potential reservoirs and sources of infection that are important in both animal and human health.


Asunto(s)
Animales de Zoológico/virología , Betacoronavirus/fisiología , Infecciones por Coronavirus/transmisión , Infecciones por Coronavirus/veterinaria , Pandemias/veterinaria , Panthera/virología , Neumonía Viral/transmisión , Neumonía Viral/veterinaria , Animales , Betacoronavirus/clasificación , Betacoronavirus/genética , Betacoronavirus/aislamiento & purificación , Infecciones por Coronavirus/diagnóstico , Infecciones por Coronavirus/virología , Genoma Viral/genética , Haplotipos , Humanos , Ciudad de Nueva York/epidemiología , Salud Única , Filogenia , Neumonía Viral/diagnóstico , Neumonía Viral/virología , Zoonosis/epidemiología , Zoonosis/transmisión , Zoonosis/virología
13.
Nat Commun ; 11(1): 5238, 2020 10 16.
Artículo en Inglés | MEDLINE | ID: mdl-33067439

RESUMEN

In heterozygous genomes, allele-specific measurements can reveal biologically significant differences in DNA methylation between homologous alleles associated with local changes in genetic sequence. Current approaches for detecting such events from whole-genome bisulfite sequencing (WGBS) data perform statistically independent marginal analysis at individual cytosine-phosphate-guanine (CpG) sites, thus ignoring correlations in the methylation state, or carry-out a joint statistical analysis of methylation patterns at four CpG sites producing unreliable statistical evidence. Here, we employ the one-dimensional Ising model of statistical physics and develop a method for detecting allele-specific methylation (ASM) events within segments of DNA containing clusters of linked single-nucleotide polymorphisms (SNPs), called haplotypes. Comparisons with existing approaches using simulated and real WGBS data show that our method provides an improved fit to data, especially when considering large haplotypes. Importantly, the method employs robust hypothesis testing for detecting statistically significant imbalances in mean methylation level and methylation entropy, as well as for identifying haplotypes for which the genetic variant carries significant information about the methylation state. As such, our ASM analysis approach can potentially lead to biological discoveries with important implications for the genetics of complex human diseases.


Asunto(s)
Metilación de ADN , Enfermedad/genética , Alelos , Islas de CpG , Haplotipos , Humanos , Polimorfismo de Nucleótido Simple , Especificidad de la Especie , Secuenciación Completa del Genoma
14.
PLoS One ; 15(10): e0230763, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-33002022

RESUMEN

Scalloped Hammerhead shark (Sphyrna lewini) is an endangered species which its populations have been declining globally including in Indonesia, the world's top shark fishing country. However, there is a lack of information on the recent population structure of this species to promote proper management and its conservation status. This study aimed to investigate the genetic diversity, population structure, and connectivity of the S. lewini population, in three major shark landing sites: Aceh (n = 41), Balikpapan (n = 30), and Lombok (n = 29). Meanwhile, additional sequences were retrieved from West Papua (n = 14) and the Western Indian Ocean (n = 65) populations. From the analyses of the mitochondrial CO1 gene, a total of 179 sequences of S. lewini, with an average size of 594 bp, and 40 polymorphic loci in four and eight haplotypes for the Indonesian population and the Western Indian Ocean population were identified. The overall values of genetic diversity were high (h = 0.717; π = 0.013), with the highest values recorded in Aceh (h = 0.668; π = 0.002) and the lowest in Papua (h = 0.143; π = 0.000). On the contrary, the overall value was fairly low in the Western Indian Ocean (h = 0.232; π = 0.001). Furthermore, AMOVA and FST showed three significant subdivisions in Indonesia (FST = 0.442; P < 0.001), with separated populations for Aceh and West Papua, and mixed between Balikpapan and Lombok (FST = 0.044; P = 0.091). In contrast, genetic homogeneity was observed within the population of the Western Indian Ocean (FST = -0.013; P = 0.612). The establishment of a haplotype network provided evidence of a significantly different population and a limited genetic distribution between the Indonesian and the Western Indian Ocean populations (FST = 0.740; P < 0.001). This study showed the presence of a complex population of S. lewini with limited connectivity only in Indonesia separated from the Western Indian Ocean and requiring specific management measures based on the population structure at the regional level.


Asunto(s)
Especies en Peligro de Extinción , Tiburones/genética , Animales , ADN Mitocondrial/genética , Complejo IV de Transporte de Electrones/genética , Genética de Población , Haplotipos , Océano Índico , Indonesia , Océanos y Mares
15.
BMC Bioinformatics ; 21(1): 461, 2020 Oct 16.
Artículo en Inglés | MEDLINE | ID: mdl-33066733

RESUMEN

BACKGROUND: Linkage disequilibrium (LD) analysis is broadly utilized in genetics to understand the evolutionary and demographic history and helps geneticists identify genes associated with interested inherited traits, such as diseases. There are some tools for linkage disequilibrium analysis either in a local or online way; however, there has been no such tool supporting both graphical user interface (GUI) and parallel computing. RESULTS: We developed a GUI software called LDkit for LD analysis, which supports parallel computing. The LDkit supports both variant call format (VCF) and PLINK 'ped + map' format. At the same time, users could also just analyze a subset of individuals from the whole population. The LDkit reads the data by block and then paralleled the computation process by monitoring the usage of processes. Assessment on the Human 1000 genome data showed that when paralleled with 32 threads, the running time was reduced to less than 6 minutes from ~77 minutes using the chromosome 22 dataset with 1,103,547 SNPs and 2504 individuals. CONCLUSIONS: The software LDkit can be effectively used to calculate and plot LD decay, LD block, and linkage disequilibrium analysis between a site and a given region. Most importantly, both graphical user interface (GUI) and stand-alone packages are available for users' convenience. LDkit was written in JAVA language under cross-platform support.


Asunto(s)
Desequilibrio de Ligamiento/genética , Programas Informáticos , Haplotipos/genética , Humanos , Complejo Mayor de Histocompatibilidad/genética , Polimorfismo de Nucleótido Simple/genética , Interfaz Usuario-Computador
16.
BMC Bioinformatics ; 21(1): 475, 2020 Oct 22.
Artículo en Inglés | MEDLINE | ID: mdl-33092523

RESUMEN

BACKGROUND: Single individual haplotype problem refers to reconstructing haplotypes of an individual based on several input fragments sequenced from a specified chromosome. Solving this problem is an important task in computational biology and has many applications in the pharmaceutical industry, clinical decision-making, and genetic diseases. It is known that solving the problem is NP-hard. Although several methods have been proposed to solve the problem, it is found that most of them have low performances in dealing with noisy input fragments. Therefore, proposing a method which is accurate and scalable, is a challenging task. RESULTS: In this paper, we introduced a method, named NCMHap, which utilizes the Neutrosophic c-means (NCM) clustering algorithm. The NCM algorithm can effectively detect the noise and outliers in the input data. In addition, it can reduce their effects in the clustering process. The proposed method has been evaluated by several benchmark datasets. Comparing with existing methods indicates when NCM is tuned by suitable parameters, the results are encouraging. In particular, when the amount of noise increases, it outperforms the comparing methods. CONCLUSION: The proposed method is validated using simulated and real datasets. The achieved results recommend the application of NCMHap on the datasets which involve the fragments with a huge amount of gaps and noise.


Asunto(s)
Algoritmos , Biología Computacional/métodos , Haplotipos/genética , Secuencia de Bases , Análisis por Conglomerados , Simulación por Computador , Bases de Datos Genéticas , Humanos , Polimorfismo de Nucleótido Simple/genética
17.
PLoS One ; 15(10): e0241405, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-33119657

RESUMEN

BACKGROUND: The first cases of COVID-19 caused by the SARS-CoV-2 virus were reported in China in December 2019. The disease has since spread globally. Many countries have instated measures to slow the spread of the virus. Information about the spread of the virus in a country can inform the gradual reopening of a country and help to avoid a second wave of infections. Our study focuses on Denmark, which is opening up when this study is performed (end-May 2020) after a lockdown in mid-March. METHODS: We perform a phylogenetic analysis of 742 publicly available Danish SARS-CoV-2 genome sequences and put them into context using sequences from other countries. RESULTS: Our findings are consistent with several introductions of the virus to Denmark from independent sources. We identify several chains of mutations that occurred in Denmark. In at least one case we find evidence that the virus spread from Denmark to other countries. A number of the mutations found in Denmark are non-synonymous, and in general there is a considerable variety of strains. The proportions of the most common haplotypes remain stable after lockdown. CONCLUSION: Employing phylogenetic methods on Danish genome sequences of SARS-CoV-2, we exemplify how genetic data can be used to trace the introduction of a virus to a country. This provides alternative means for verifying existing assumptions. For example, our analysis supports the hypothesis that the virus was brought to Denmark by skiers returning from Ischgl. On the other hand, we identify transmission routes which suggest that Denmark was part of a network of countries among which the virus was being transmitted. This challenges the common narrative that Denmark only got infected from abroad. Our analysis concerning the ratio of haplotypes does not indicate that the major haplotypes appearing in Denmark have a different degree of virality.


Asunto(s)
Betacoronavirus/genética , Infecciones por Coronavirus/transmisión , Genoma Viral , Mutación , Neumonía Viral/transmisión , Infecciones por Coronavirus/epidemiología , Dinamarca/epidemiología , Haplotipos , Humanos , Pandemias , Filogenia , Neumonía Viral/epidemiología
18.
Fa Yi Xue Za Zhi ; 36(4): 538-544, 2020 Aug.
Artículo en Inglés, Chino | MEDLINE | ID: mdl-33047540

RESUMEN

Abstract: Objective To provide a theoretical basis for building a Y chromosome database in specific regions by analyzing the pedigree specific core haplogroup and region specific genetic structure in Changshu. Methods One thousand seven hundred and two samples from unrelated Han male individuals in Changshu were collected. Then 27 Y-STR were genotyped through YfilerTM Plus PCR Amplification Kit, Y-SNP haplogroup of each sample was speculated using Y-Predictor software and some samples were verified by amplification refractory mutation system-polymerase chain reaction (ARMS-PCR). Results A total of 1 556 haplotypes were found on the 27 Y-STR genetic markers of the 1 702 samples. The haplotype diversity (HD) value was 0.999 827. DYS385 (0.933) had the highest gene diversity (GD) value while DYS438 (0.409) had the lowest. By the Y-Predictor software, all samples were confirmed to be from 162 sub-haplogroups of C, D, N, O, Q and R. Samples were randomly selected to verify the prediction results by the software and the prediction accuracy of Y-Predictor software was as high as 95.74%. Conclusion This study found that 27 Y-STR genetic markers have relatively high polymorphisms in the Changshu population, and have good forensic individual identification and paternity testing ability.


Asunto(s)
Cromosomas Humanos Y , Genética de Población , Cromosomas Humanos Y/genética , Frecuencia de los Genes , Haplotipos , Humanos , Masculino , Repeticiones de Microsatélite , Polimorfismo Genético
19.
PLoS One ; 15(9): e0238255, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32936832

RESUMEN

It was shown that the human Angiotensin-converting enzyme 2 (ACE2) is the receptor of recent coronavirus SARS-CoV-2, and variation in this gene may affect the susceptibility of a population. Therefore, we have analysed the sequence data of ACE2 among 393 samples worldwide, focusing on South Asia. Genetically, South Asians are more related to West Eurasian populations rather than to East Eurasians. In the present analyses of ACE2, we observed that the majority of South Asian haplotypes are closer to East Eurasians rather than to West Eurasians. The phylogenetic analysis suggested that the South Asian haplotypes shared with East Eurasians involved two unique event polymorphisms (rs4646120 and rs2285666). In contrast with the European/American populations, both of the SNPs have largely similar frequencies for East Eurasians and South Asians, Therefore, it is likely that among the South Asians, host susceptibility to the novel coronavirus SARS-CoV-2 will be more similar to that of East Eurasians rather than to that of Europeans.


Asunto(s)
Grupo de Ascendencia Continental Asiática/genética , Infecciones por Coronavirus/genética , Peptidil-Dipeptidasa A/genética , Neumonía Viral/genética , Polimorfismo de Nucleótido Simple , Receptores Virales/genética , Asia/epidemiología , Betacoronavirus/fisiología , Infecciones por Coronavirus/etnología , Grupo de Ascendencia Continental Europea/genética , Haplotipos/genética , Migración Humana , Humanos , Desequilibrio de Ligamiento , Pandemias , Filogenia , Neumonía Viral/etnología
20.
PLoS One ; 15(9): e0237160, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32881879

RESUMEN

Pareiorhaphis hystrix is a widely distributed species, occurring in the upper and middle Uruguay River and in the Taquari River basin, Patos Lagoon system, southern Brazil. Morphological variation has been detected throughout the distribution of P. hystrix, and this work seeks to test the conspecific nature of populations in several occurrence areas. Specimens from six areas in the Uruguay River basin and three in the Taquari River basin were compared. Variance analysis (ANOVA) was performed for the meristic data, and Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA) were conducted for morphometric data. Molecular analyses used coI, cytb, 12S and 16S mitochondrial genes, examining nucleotide diversity, haplotype diversity, genetic distance, and delimitation of possible multiple species through the Generalized Mixed Yule Coalescent (GMYC) method. Phylogenetic relationships of studied populations were also investigated through Bayesian inference. While PCA indicated a tendency of overlap between areas, ANOVA and LDA detected a subtle differentiation between populations from the two hydrographic basins. Yet, both latter analyses recovered the population from Pelotas River, a tributary to Uruguay River, as more similar to populations from Taquari River, which is congruent to morphological observations of anterior abdominal plates. The molecular data indicated a nucleotide diversity lower than the haplotypic diversity, suggestive of recent expansion. The concatenated haplotype network points to slight differentiation between areas, with each locality presenting unique and non-shared haplotypes, although with few mutational steps in general. The species delimitation by coalescence analysis suggested the presence of a variable number of OTUs depending on the inclusion or exclusion of an outgroup. In general, the morphological data suggest a subtle variation by river basin, while the genetic data indicates a weak population structuration by hydrographic areas, especially the Chapecó and Passo Fundo rivers. However, there is still not enough differentiation between the specimens to suggest multiple species. The iterative analyses indicate that Pareiorhaphis hystrix is composed of a single, although variable, species.


Asunto(s)
Bagres/anatomía & histología , Bagres/clasificación , Animales , Teorema de Bayes , Brasil , Bagres/genética , Análisis Discriminante , Femenino , Genes Mitocondriales , Geografía , Haplotipos/genética , Masculino , Fenotipo , Filogenia , Pigmentación , Análisis de Componente Principal , Ríos , Especificidad de la Especie
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