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1.
Science ; 370(6512): 34-35, 2020 10 02.
Artigo em Inglês | MEDLINE | ID: mdl-33004501
2.
Plant Genome ; 13(1): e20002, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-33016638

RESUMO

Genomic selection (GS) is a marker-based selection initially suggested for livestock breeding and is being encouraged for crop breeding. Several statistical models are used to implement GS; however, none have been tested for use in lentil (Lens culinaris Medik.) breeding. This study was conducted to compare the accuracy of different GS models and prediction scenarios based on empirical data and to make recommendations for designing genomic selection strategies for lentil breeding. We evaluated nine single-trait (ST) models, two multiple-trait (MT) models, and a model that incorporates genotype × environment interaction (GEI) using populations from a lentil diversity panel and two recombinant inbred lines (RILs). The lines in all populations were phenotyped for five phenological traits and genotyped using a custom exome capture assay. Within-population, across-population, and across-environment genomic predictions were made. Prediction accuracy varied among the evaluated models, populations, prediction scenarios, and traits. Single-trait models showed similar accuracy in the absence of large effect quantitative trait loci (QTL) but BayesB outperformed all models when there were QTL with relatively large effects. Models that accounted for GEI and MT-GS models increased prediction accuracy for a low heritability trait by up to 66 and 14%, respectively. Moderate to high accuracies were obtained for within-population (range of .36-.85) and across-environment (range of .19-.89) predictions but across-population prediction accuracy was very low. Results suggest that GS can be implemented in lentil breeding to make predictions within populations and across environments, but across-population prediction should not be considered when the population size is small.


Assuntos
Lens (Planta) , Cruzamento , Genômica , Lens (Planta)/genética , Modelos Genéticos , Seleção Genética
3.
Proc Biol Sci ; 287(1931): 20200975, 2020 07 29.
Artigo em Inglês | MEDLINE | ID: mdl-33043864

RESUMO

Alternative mating strategies are widespread among animal taxa, with strategies controlled by a genetic polymorphism (Mendelian strategy) being rarer in nature than condition-dependent developmental strategies. Mendelian strategies are predicted to have equal average fitnesses and the proportion of offspring produced by a strategy should equal the equilibrium proportion of individuals representing the strategy in a population. Developmental strategies are not expected to produce offspring in equilibrium proportions; however, whether the alternative phenotypes should have equal average fitness is debated. The Wellington tree weta (Hemideina crassidens) (Orthoptera: Anostostomatidae) is a harem polygynous insect in which intense sexual competition has favoured the evolution of three alternative mating strategies that differ in weapon size and the ability to fight for control of harems. Here, we use molecular genotyping to test the hypothesis that the alternative strategies in this species are maintained by having equal relative fitness and that morphs produce offspring in equilibrium proportions. As expected, the average relative fitness of the three strategies did not significantly differ and the proportion of offspring produced by each morph is equal to the frequency of that morph in the population. Our results support the hypothesis that the alternative male morphs in H. crassidens represent Mendelian strategies.


Assuntos
Insetos/fisiologia , Comportamento Sexual Animal , Animais , Feminino , Masculino , Ortópteros , Fenótipo , Polimorfismo Genético , Seleção Genética
4.
Biomed Res Int ; 2020: 9089768, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32923488

RESUMO

Purpose: We investigated sequences of the feline coronaviruses (FCoV), which include feline enteric coronavirus (FECV) and feline infectious peritonitis virus (FIPV), from China and other countries to gain insight into the adaptive evolution of this virus. Methods: Ascites samples from 31 cats with suspected FIP and feces samples from 8 healthy cats were screened for the presence of FCoV. Partial viral genome sequences, including parts of the nsp12-nsp14, S, N, and 7b genes, were obtained and aligned with additional sequences obtained from the GenBank database. Bayesian phylogenetic analysis was conducted, and the possibility of recombination within these sequences was assessed. Analysis of the levels of selection pressure experienced by these sequences was assessed using methods on both the PAML and Datamonkey platforms. Results: Of the 31 cats investigated, two suspected FIP cats and one healthy cat tested positive for FCoV. Phylogenetic analysis showed that all of the sequences from mainland China cluster together with a few sequences from the Netherlands as a distinct clade when analyzed with FCoV sequences from other countries. Fewer than 3 recombination breakpoints were detected in the nsp12-nsp14, S, N, and 7b genes, suggesting that analyses for positive selection could be conducted. A total of 4, 12, 4, and 4 positively selected sites were detected in the nsp12-nsp14, S, N, and 7b genes, respectively, with the previously described site 245 of the S gene, which distinguishes FIPV from FECV, being a positive selection site. Conversely, 106, 168, 25, and 17 negative selection sites in the nsp12-14, S, N, and 7b genes, respectively, were identified. Conclusion: Our study provides evidence that the FCoV genes encoding replicative, entry, and virulence proteins potentially experienced adaptive evolution. A greater number of sites in each gene experienced negative rather than positive selection, which suggests that most of the protein sequence must be conservatively maintained for virus survival. A few of the sites showing evidence of positive selection might be associated with the more severe pathology of FIPV or help these viruses survive other harmful conditions.


Assuntos
Adaptação Biológica/genética , Coronavirus Felino/genética , Peritonite Infecciosa Felina/virologia , Panleucopenia Felina/virologia , Genoma Viral/genética , Animais , Teorema de Bayes , Gatos , China , Coronavirus Felino/fisiologia , Evolução Molecular , Fezes/virologia , Peritonite Infecciosa Felina/patologia , Panleucopenia Felina/patologia , Mutação , Filogenia , Recombinação Genética , Seleção Genética , Proteínas Virais/genética
5.
Rev Esp Salud Publica ; 942020 Sep 30.
Artigo em Espanhol | MEDLINE | ID: mdl-32994390

RESUMO

In the midst of the SARS-CoV-2 public-health pandemic emergency, it is important to understand its zoonotic origin and how an animal virus finally infects humans. Identifying the circumstances in which a virus jumps species boundaries to infect humans so productively is objective of this work and will help us to determine the epidemiology and pathogenisis of this agent. Nowadays, it is known that bats serve as reservoir hosts for virus progenitor, but determine the possibility of a potential intermediate host of SARS-CoV-2 is still a challenge. Scientific investigations stablish the natural selection theory as the most probable (natural selection in an animal host before zoonotic transfer or acquired mutations in humans following crossing species barrier). It is necessary to find out how SARS-CoV-2 emerged, its rapidly spreads within a community and the optimal context in which this virus binds to human receptor. One Health is a multisectoral, collaborative and transdisciplinary approach which allows a cooperative working between animal and human health that will help us to introduce some possible control measures that might reduce the spread of the virus; improving sanitary management, identifying new outbreaks and preventing future zoonotic and pandemic events.


Assuntos
Betacoronavirus , Quirópteros/virologia , Doenças Transmissíveis Emergentes/transmissão , Infecções por Coronavirus/transmissão , Reservatórios de Doenças/virologia , Pandemias , Pneumonia Viral/transmissão , Zoonoses/transmissão , Animais , Betacoronavirus/genética , Betacoronavirus/patogenicidade , Doenças Transmissíveis Emergentes/epidemiologia , Doenças Transmissíveis Emergentes/virologia , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/virologia , Saúde Global , Humanos , Pneumonia Viral/epidemiologia , Pneumonia Viral/virologia , Seleção Genética , Zoonoses/epidemiologia , Zoonoses/virologia
6.
Proc Natl Acad Sci U S A ; 117(38): 23652-23662, 2020 09 22.
Artigo em Inglês | MEDLINE | ID: mdl-32868447

RESUMO

The magnitude of the COVID-19 pandemic underscores the urgency for a safe and effective vaccine. Many vaccine candidates focus on the Spike protein, as it is targeted by neutralizing antibodies and plays a key role in viral entry. Here we investigate the diversity seen in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequences and compare it to the sequence on which most vaccine candidates are based. Using 18,514 sequences, we perform phylogenetic, population genetics, and structural bioinformatics analyses. We find limited diversity across SARS-CoV-2 genomes: Only 11 sites show polymorphisms in >5% of sequences; yet two mutations, including the D614G mutation in Spike, have already become consensus. Because SARS-CoV-2 is being transmitted more rapidly than it evolves, the viral population is becoming more homogeneous, with a median of seven nucleotide substitutions between genomes. There is evidence of purifying selection but little evidence of diversifying selection, with substitution rates comparable across structural versus nonstructural genes. Finally, the Wuhan-Hu-1 reference sequence for the Spike protein, which is the basis for different vaccine candidates, matches optimized vaccine inserts, being identical to an ancestral sequence and one mutation away from the consensus. While the rapid spread of the D614G mutation warrants further study, our results indicate that drift and bottleneck events can explain the minimal diversity found among SARS-CoV-2 sequences. These findings suggest that a single vaccine candidate should be efficacious against currently circulating lineages.


Assuntos
Betacoronavirus/genética , Genoma Viral , Vacinas Virais/genética , Betacoronavirus/imunologia , Infecções por Coronavirus/genética , Infecções por Coronavirus/prevenção & controle , Variação Genética , Humanos , Pandemias/prevenção & controle , Pneumonia Viral/prevenção & controle , Mutação Puntual , Seleção Genética
7.
PLoS One ; 15(8): e0236186, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32866164

RESUMO

AIM: To establish a gene co-expression network for identifying principal modules and hub genes that are associated with drought resistance mechanisms, analyzing their mechanisms, and exploring candidate genes. METHODS AND FINDINGS: 42 data sets including PRJNA380841 and PRJNA369686 were used to construct the co-expression network through weighted gene co-expression network analysis (WGCNA). A total of 1,896,897,901 (284.30 Gb) clean reads and 35,021 differentially expressed genes (DEGs) were obtained from 42 samples. Functional enrichment analysis indicated that photosynthesis, DNA replication, glycolysis/gluconeogenesis, starch and sucrose metabolism, arginine and proline metabolism, and cell cycle were significantly influenced by drought stress. Furthermore, the DEGs with similar expression patterns, detected by K-means clustering, were grouped into 29 clusters. Genes involved in the modules, such as dark turquoise, yellow, and brown, were found to be appreciably linked with drought resistance. Twelve central, greatly correlated genes in stage-specific modules were subsequently confirmed and validated at the transcription levels, including TraesCS7D01G417600.1 (PP2C), TraesCS5B01G565300.1 (ERF), TraesCS4A01G068200.1 (HSP), TraesCS2D01G033200.1 (HSP90), TraesCS6B01G425300.1 (RBD), TraesCS7A01G499200.1 (P450), TraesCS4A01G118400.1 (MYB), TraesCS2B01G415500.1 (STK), TraesCS1A01G129300.1 (MYB), TraesCS2D01G326900.1 (ALDH), TraesCS3D01G227400.1 (WRKY), and TraesCS3B01G144800.1 (GT). CONCLUSIONS: Analyzing the response of wheat to drought stress during different growth stages, we have detected three modules and 12 hub genes that are associated with drought resistance mechanisms, and five of those genes are newly identified for drought resistance. The references provided by these modules will promote the understanding of the drought-resistance mechanism. In addition, the candidate genes can be used as a basis of transgenic or molecular marker-assisted selection for improving the drought resistance and increasing the yields of wheat.


Assuntos
Aclimatação/genética , Regulação da Expressão Gênica de Plantas , Redes Reguladoras de Genes , Estresse Fisiológico/genética , Triticum/genética , China , Análise por Conglomerados , Conjuntos de Dados como Assunto , Secas , Perfilação da Expressão Gênica , Genes de Plantas , Melhoramento Vegetal/métodos , RNA-Seq , Seleção Genética
8.
Infez Med ; 28(3): 302-311, 2020 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-32920565

RESUMO

SARS-CoV-2 has created a global disaster by infecting millions of people and causing thousands of deaths across hundreds of countries. Currently, the infection is in its exponential phase in several countries and there is no sign of immediate relief from this deadly virus. At the same time, some "conspiracy theories" have arisen on the origin of this virus due to the lack of a "definite origin". To understand if this controversy is also reflected in scientific publications, here, we reviewed the key articles published at initial stages of the COVID-19 pandemic (January 01, 2020 to April 30, 2020) related to the zoonotic origin of SARS-CoV-2 and the articles opposing the "conspiracy theories". We also provide an overview on the current knowledge on SARS-CoV-2 Spike as well as the Coronavirus research domain. Furthermore, a few important points related to the "conspiracy theories" such as "laboratory engineering" or "bioweapon" aspects of SARS-CoV-2 are also reviewed. In this article, we have only considered the peer-reviewed publications that are indexed in PubMed and other official publications, and we have directly quoted the authors' statements from their respective articles to avoid any controversy.


Assuntos
Betacoronavirus/genética , Infecções por Coronavirus/virologia , Engenharia Genética/métodos , Pneumonia Viral/virologia , Seleção Genética , Animais , Derramamento de Material Biológico , Armas Biológicas , Quirópteros/virologia , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/transmissão , Dissidências e Disputas , Eutérios/classificação , Eutérios/virologia , Saúde Global/estatística & dados numéricos , Humanos , Pandemias , Pneumonia Viral/epidemiologia , Pneumonia Viral/transmissão , Recombinação Genética , Alinhamento de Sequência , Zoonoses/virologia
9.
Viruses ; 12(9)2020 09 14.
Artigo em Inglês | MEDLINE | ID: mdl-32937868

RESUMO

BACKGROUND: During the COVID-19 pandemic, the virus evolved, and we therefore aimed to provide an insight into which genetic variants were enriched, and how they spread in Sweden. METHODS: We analyzed 348 Swedish SARS-CoV-2 sequences freely available from GISAID obtained from 7 February 2020 until 14 May 2020. RESULTS: We identified 14 variant sites ≥5% frequency in the population. Among those sites, the D936Y substitution in the viral Spike protein was under positive selection. The variant sites can distinguish 11 mutational profiles in Sweden. Nine of the profiles appeared in Stockholm in March 2020. Mutational profiles 3 (B.1.1) and 6 (B.1), which contain the D936Y mutation, became the predominant profiles over time, spreading from Stockholm to other Swedish regions during April and the beginning of May. Furthermore, Bayesian phylogenetic analysis indicated that SARS-CoV-2 could have emerged in Sweden on 27 December 2019, and community transmission started on February 1st with an evolutionary rate of 1.5425 × 10-3 substitutions per year. CONCLUSIONS: Our study provides novel knowledge on the spatio-temporal dynamics of Swedish SARS-CoV-2 variants during the early pandemic. Characterization of these viral variants can provide precious insights on viral pathogenesis and can be valuable for diagnostic and drug development approaches.


Assuntos
Betacoronavirus/genética , Infecções por Coronavirus/virologia , Mutação , Pandemias , Pneumonia Viral/virologia , Adulto , Idoso , Teorema de Bayes , Betacoronavirus/isolamento & purificação , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/transmissão , Conjuntos de Dados como Assunto , Evolução Molecular , Feminino , Variação Genética , Genoma Viral , Humanos , Masculino , Pessoa de Meia-Idade , Filogenia , Pneumonia Viral/epidemiologia , Pneumonia Viral/transmissão , RNA Viral/genética , Recombinação Genética , Seleção Genética , Alinhamento de Sequência , Homologia de Sequência do Ácido Nucleico , Suécia/epidemiologia
10.
Proc Biol Sci ; 287(1935): 20201752, 2020 09 30.
Artigo em Inglês | MEDLINE | ID: mdl-32993472

RESUMO

Group living is a common strategy used by fishes to improve their fitness. While sociality is associated with many benefits in natural environments, including predator avoidance, this behaviour may be maladaptive in the Anthropocene. Humans have become the dominant predator in many marine systems, with modern fishing gear developed to specifically target groups of schooling species. Therefore, ironically, behavioural strategies which evolved to avoid non-human predators may now actually make certain fish more vulnerable to predation by humans. Here, we use an individual-based model to explore the evolution of fish schooling behaviour in a range of environments, including natural and human-dominated predation conditions. In our model, individual fish may leave or join groups depending on their group-size preferences, but their experienced group size is also a function of the preferences of others in the population. Our model predicts that industrial fishing selects against individual-level behaviours that produce large groups. However, the relationship between fishing pressure and sociality is nonlinear, and we observe discontinuities and hysteresis as fishing pressure is increased or decreased. Our results suggest that industrial fishing practices could be altering fishes' tendency to school, and that social behaviour should be added to the list of traits subject to fishery-induced evolution.


Assuntos
Pesqueiros , Peixes/fisiologia , Comportamento Social , Animais , Conservação dos Recursos Naturais , Seleção Genética
11.
Proc Biol Sci ; 287(1934): 20201111, 2020 09 09.
Artigo em Inglês | MEDLINE | ID: mdl-32873205

RESUMO

How genetic variation arises and persists over evolutionary time despite the depleting effects of natural selection remains a long-standing question. Here, we investigate the impacts of two extreme forms of population regulation-at the level of the total, mixed population (hard selection) and at the level of local, spatially distinct patches (soft selection)-on the emergence and fate of diversity under strong divergent selection. We find that while the form of population regulation has little effect on rates of diversification, it can modulate the long-term fate of genetic variation, diversity being more readily maintained under soft selection compared to hard selection. The mechanism responsible for coexistence is negative frequency-dependent selection which, while present initially under both forms of population regulation, persists over the long-term only under soft selection. Importantly, coexistence is robust to continued evolution of niche specialist types under soft selection but not hard selection. These results suggest that soft selection could be a general mechanism for the maintenance of ecological diversity over evolutionary time scales.


Assuntos
Evolução Biológica , Seleção Genética , Animais , Ecossistema , Variação Genética , Densidade Demográfica
12.
Proc Biol Sci ; 287(1934): 20201377, 2020 09 09.
Artigo em Inglês | MEDLINE | ID: mdl-32900311

RESUMO

Ever since Darwin's discovery of natural selection, we expect traits to evolve to increase organisms' fitness. As a result, we can use optimization models to make a priori predictions of phenotypic variation, even when selection is frequency-dependent. A notable example is the prediction of female-biased sex ratios resulting from local mate competition (LMC) and inbreeding. LMC models incorporate the effects of LMC and inbreeding. Fig wasp sex ratio adjustments fit LMC predictions well. However, the appropriateness of LMC models to fig wasps has been questioned, and the role that a coincidental by-product plays in creating the apparent fit has been clearly illustrated. Here, we show that the sex ratio adjustments of a fig wasp are the result of a dual mechanism. It consists of a standard facultative LMC response favoured by natural selection, as well as a mechanism that may be the result of selection, but that could also be a coincidental by-product. If it is a by-product, the fitness increase is coincidental and natural selection's role was limited to fine-tuning it for higher fitness returns. We further document a case of an apparent fitness-reducing sex ratio adjustment. We conclude that the use of the adaptationist approach demands that our understanding of traits must be remodelled continually to rectify spurious assumptions.


Assuntos
Seleção Genética , Comportamento Sexual Animal/fisiologia , Vespas/fisiologia , Animais , Feminino , Masculino , Razão de Masculinidade
13.
Nat Commun ; 11(1): 4488, 2020 09 08.
Artigo em Inglês | MEDLINE | ID: mdl-32901040

RESUMO

Sustainable food production in the context of climate change necessitates diversification of agriculture and a more efficient utilization of plant genetic resources. Fonio millet (Digitaria exilis) is an orphan African cereal crop with a great potential for dryland agriculture. Here, we establish high-quality genomic resources to facilitate fonio improvement through molecular breeding. These include a chromosome-scale reference assembly and deep re-sequencing of 183 cultivated and wild Digitaria accessions, enabling insights into genetic diversity, population structure, and domestication. Fonio diversity is shaped by climatic, geographic, and ethnolinguistic factors. Two genes associated with seed size and shattering showed signatures of selection. Most known domestication genes from other cereal models however have not experienced strong selection in fonio, providing direct targets to rapidly improve this crop for agriculture in hot and dry environments.


Assuntos
Digitaria/genética , Grão Comestível/genética , África , Agricultura/métodos , Mudança Climática , Digitaria/classificação , Domesticação , Grão Comestível/classificação , Evolução Molecular , Variação Genética , Genoma de Planta , Anotação de Sequência Molecular , Seleção Genética , Especificidade da Espécie
14.
Virol J ; 17(1): 138, 2020 09 14.
Artigo em Inglês | MEDLINE | ID: mdl-32928234

RESUMO

The outbreak of coronavirus disease 2019 (COVID-19) due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed significant threats to international health. The genetic traits as well as evolutionary processes in this novel coronavirus are not fully characterized, and their roles in viral pathogenesis are yet largely unknown. To get a better picture of the codon architecture of this newly emerging coronavirus, in this study we perform bioinformatic analysis, based on publicly available nucleotide sequences of SARS-CoV-2 along with those of other members of human coronaviruses as well as non-human coronaviruses in different hosts, to take a snapshot of the genome-wide codon usage pattern of SARS-CoV-2 and uncover that all over-represented codons end with A/U and this newly emerging coronavirus has a relatively low codon usage bias, which is shaped by both mutation pressure and natural selection. Additionally, there is slight variation in the codon usage pattern among the SARS-CoV-2 isolates from different geo-locations. Furthermore, the overall codon usage pattern of SARS-CoV-2 is generally similar to that of its phylogenetic relatives among non-human betacoronaviruses such as RaTG13. Taken together, we comprehensively analyze the characteristics of codon usage pattern in SARS-CoV-2 via bioinformatic approaches. The information from this research may not only be helpful to get new insights into the evolution of SARS-CoV-2, but also have potential value for developing coronavirus vaccines.


Assuntos
Betacoronavirus/genética , Uso do Códon , Infecções por Coronavirus/virologia , Genoma Viral , Pneumonia Viral/virologia , Animais , Sequência de Bases , Análise por Conglomerados , Códon , Biologia Computacional , Evolução Molecular , Humanos , Mutação , Pandemias , Filogenia , Seleção Genética , Proteínas Virais/genética , Sequenciamento Completo do Genoma
15.
Nat Commun ; 11(1): 4603, 2020 09 14.
Artigo em Inglês | MEDLINE | ID: mdl-32929079

RESUMO

Amino acid propensities at a site change in the course of protein evolution. This may happen for two reasons. Changes may be triggered by substitutions at epistatically interacting sites elsewhere in the genome. Alternatively, they may arise due to environmental changes that are external to the genome. Here, we design a framework for distinguishing between these alternatives. Using analytical modelling and simulations, we show that they cause opposite dynamics of the fitness of the allele currently occupying the site: it tends to increase with the time since its origin due to epistasis ("entrenchment"), but to decrease due to random environmental fluctuations ("senescence"). By analysing the genomes of vertebrates and insects, we show that the amino acids originating at negatively selected sites experience strong entrenchment. By contrast, the amino acids originating at positively selected sites experience senescence. We propose that senescence of the current allele is a cause of adaptive evolution.


Assuntos
Aminoácidos/genética , Evolução Molecular , Alelos , Sequência de Aminoácidos , Animais , Simulação por Computador , Meio Ambiente , Genes Mitocondriais , Aptidão Genética , Heterogeneidade Genética , Insetos/genética , Seleção Genética , Vertebrados/genética
16.
Nat Commun ; 11(1): 4740, 2020 09 21.
Artigo em Inglês | MEDLINE | ID: mdl-32958755

RESUMO

The immune system can recognize and attack cancer cells, especially those with a high load of mutation-induced neoantigens. Such neoantigens are abundant in DNA mismatch repair (MMR)-deficient, microsatellite-unstable (MSI) cancers. MMR deficiency leads to insertion/deletion (indel) mutations at coding microsatellites (cMS) and to neoantigen-inducing translational frameshifts. Here, we develop a tool to quantify frameshift mutations in MSI colorectal and endometrial cancer. Our results show that frameshift mutation frequency is negatively correlated to the predicted immunogenicity of the resulting peptides, suggesting counterselection of cell clones with highly immunogenic frameshift peptides. This correlation is absent in tumors with Beta-2-microglobulin mutations, and HLA-A*02:01 status is related to cMS mutation patterns. Importantly, certain outlier mutations are common in MSI cancers despite being related to frameshift peptides with functionally confirmed immunogenicity, suggesting a possible driver role during MSI tumor evolution. Neoantigens resulting from shared mutations represent promising vaccine candidates for prevention of MSI cancers.


Assuntos
Mutação da Fase de Leitura , Repetições de Microssatélites/genética , Neoplasias/genética , Neoplasias/imunologia , Antígenos de Neoplasias/genética , Antígenos de Neoplasias/imunologia , Antígenos HLA/genética , Humanos , Mutação INDEL , Vigilância Imunológica , Instabilidade de Microssatélites , Taxa de Mutação , Seleção Genética , Microglobulina beta-2/genética
17.
Nat Commun ; 11(1): 4739, 2020 09 21.
Artigo em Inglês | MEDLINE | ID: mdl-32958756

RESUMO

More people globally depend on the water buffalo than any other domesticated species, and as the most closely related domesticated species to cattle they can provide important insights into the shared evolutionary basis of domestication. Here, we sequence the genomes of 79 water buffalo across seven breeds and compare patterns of between breed selective sweeps with those seen for 294 cattle genomes representing 13 global breeds. The genomic regions under selection between cattle breeds significantly overlap regions linked to stature in human genetic studies, with a disproportionate number of these loci also shown to be under selection between water buffalo breeds. Investigation of potential functional variants in the water buffalo genome identifies a rare example of convergent domestication down to the same mutation having independently occurred and been selected for across domesticated species. Cross-species comparisons of recent selective sweeps can consequently help identify and refine important loci linked to domestication.


Assuntos
Búfalos/genética , Bovinos/genética , Domesticação , Genoma/genética , Animais , Cruzamento , Búfalos/classificação , Bovinos/classificação , Evolução Molecular , Loci Gênicos/genética , Variação Genética , Fenótipo , Filogeografia , Seleção Genética
18.
Curr Biol ; 30(15): R849-R857, 2020 08 03.
Artigo em Inglês | MEDLINE | ID: mdl-32750338

RESUMO

There is no doubt that the novel coronavirus SARS-CoV-2 that causes COVID-19 is mutating and thus has the potential to adapt during the current pandemic. Whether this evolution will lead to changes in the transmission, the duration, or the severity of the disease is not clear. This has led to considerable scientific and media debate, from raising alarms about evolutionary change to dismissing it. Here we review what little is currently known about the evolution of SARS-CoV-2 and extend existing evolutionary theory to consider how selection might be acting upon the virus during the COVID-19 pandemic. Although there is currently no definitive evidence that SARS-CoV-2 is undergoing further adaptation, continued evidence-based analysis of evolutionary change is important so that public health measures can be adjusted in response to substantive changes in the infectivity or severity of COVID-19.


Assuntos
Betacoronavirus/fisiologia , Evolução Biológica , Infecções por Coronavirus/epidemiologia , Pneumonia Viral/epidemiologia , Adaptação Biológica/genética , Animais , Infecções Assintomáticas , Betacoronavirus/genética , Betacoronavirus/patogenicidade , Infecções por Coronavirus/transmissão , Pleiotropia Genética , Variação Genética , Humanos , Mutação , Pandemias , Pneumonia Viral/transmissão , Crescimento Demográfico , Seleção Genética , Distância Social , Zoonoses
19.
PLoS Pathog ; 16(8): e1008718, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32797103

RESUMO

APOBEC3 enzymes are innate immune effectors that introduce mutations into viral genomes. These enzymes are cytidine deaminases which transform cytosine into uracil. They preferentially mutate cytidine preceded by thymidine making the 5'TC motif their favored target. Viruses have evolved different strategies to evade APOBEC3 restriction. Certain viruses actively encode viral proteins antagonizing the APOBEC3s, others passively face the APOBEC3 selection pressure thanks to a depleted genome for APOBEC3-targeted motifs. Hence, the APOBEC3s left on the genome of certain viruses an evolutionary footprint. The aim of our study is the identification of these viruses having a genome shaped by the APOBEC3s. We analyzed the genome of 33,400 human viruses for the depletion of APOBEC3-favored motifs. We demonstrate that the APOBEC3 selection pressure impacts at least 22% of all currently annotated human viral species. The papillomaviridae and polyomaviridae are the most intensively footprinted families; evidencing a selection pressure acting genome-wide and on both strands. Members of the parvoviridae family are differentially targeted in term of both magnitude and localization of the footprint. Interestingly, a massive APOBEC3 footprint is present on both strands of the B19 erythroparvovirus; making this viral genome one of the most cleaned sequences for APOBEC3-favored motifs. We also identified the endemic coronaviridae as significantly footprinted. Interestingly, no such footprint has been detected on the zoonotic MERS-CoV, SARS-CoV-1 and SARS-CoV-2 coronaviruses. In addition to viruses that are footprinted genome-wide, certain viruses are footprinted only on very short sections of their genome. That is the case for the gamma-herpesviridae and adenoviridae where the footprint is localized on the lytic origins of replication. A mild footprint can also be detected on the negative strand of the reverse transcribing HIV-1, HIV-2, HTLV-1 and HBV viruses. Together, our data illustrate the extent of the APOBEC3 selection pressure on the human viruses and identify new putatively APOBEC3-targeted viruses.


Assuntos
Citidina Desaminase/metabolismo , Genoma Viral/genética , Interações Hospedeiro-Patógeno/genética , Seleção Genética/genética , Replicação Viral/genética , Coronaviridae/genética , Humanos , Imunidade Inata/imunologia , Papillomaviridae/genética , Parvoviridae/genética , Polyomaviridae/genética , Proteínas Virais/genética
20.
BMC Res Notes ; 13(1): 398, 2020 Aug 27.
Artigo em Inglês | MEDLINE | ID: mdl-32854762

RESUMO

OBJECTIVE: In December 2019 a novel coronavirus (SARS-CoV-2) that is causing the current COVID-19 pandemic was identified in Wuhan, China. Many questions have been raised about its origin and adaptation to humans. In the present work we performed a genetic analysis of the Spike glycoprotein (S) of SARS-CoV-2 and other related coronaviruses (CoVs) isolated from different hosts in order to trace the evolutionary history of this protein and the adaptation of SARS-CoV-2 to humans. RESULTS: Based on the sequence analysis of the S gene, we suggest that the origin of SARS-CoV-2 is the result of recombination events between bat and pangolin CoVs. The hybrid SARS-CoV-2 ancestor jumped to humans and has been maintained by natural selection. Although the S protein of RaTG13 bat CoV has a high nucleotide identity with the S protein of SARS-CoV-2, the phylogenetic tree and the haplotype network suggest a non-direct parental relationship between these CoVs. Moreover, it is likely that the basic function of the receptor-binding domain (RBD) of S protein was acquired by the SARS-CoV-2 from the MP789 pangolin CoV by recombination and it has been highly conserved.


Assuntos
Betacoronavirus/genética , Coronaviridae/genética , Recombinação Genética , Glicoproteína da Espícula de Coronavírus/genética , Adaptação Biológica/genética , Animais , Sítios de Ligação/genética , Quirópteros/virologia , Eutérios/virologia , Evolução Molecular , Furina/metabolismo , Especificidade de Hospedeiro , Humanos , Peptidil Dipeptidase A/metabolismo , Filogenia , Seleção Genética , Glicoproteína da Espícula de Coronavírus/metabolismo
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