scholarly journals Conservation analysis of SARS-CoV-2 spike suggests complicated viral adaptation history from bat to human

2020 ◽  
Vol 2020 (1) ◽  
pp. 290-303
Author(s):  
Kuan Cheok Lei ◽  
Xiaohua Douglas Zhang
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Mutation Analysis ◽  
Evolutionary History ◽  
Sequence Similarity ◽  
Similarity Analysis ◽  
Current Form ◽  
Conservation Analysis ◽  
Spike Sequences ◽  
History Of ◽  
Spike Sequence

Abstract Background The current coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome (SARS)-CoV-2, has become the most devastating public health emergency in the 21st century and one of the most influential plagues in history. Studies on the origin of SARS-CoV-2 have generally agreed that the virus probably comes from bat, closely related to a bat CoV named BCoV-RaTG13 taken from horseshoe bat (Rhinolophus affinis), with Malayan pangolin (Manis javanica) being a plausible intermediate host. However, due to the relatively low number of SARS-CoV-2-related strains available in public domain, the evolutionary history remains unclear. Methodology Nine hundred ninety-five coronavirus sequences from NCBI Genbank and GISAID were obtained and multiple sequence alignment was carried out to categorize SARS-CoV-2 related groups. Spike sequences were analyzed using similarity analysis and conservation analyses. Mutation analysis was used to identify variations within receptor-binding domain (RBD) in spike for SARS-CoV-2-related strains. Results We identified a family of SARS-CoV-2-related strains, including the closest relatives, bat CoV RaTG13 and pangolin CoV strains. Sequence similarity analysis and conservation analysis on spike sequence identified that N-terminal domain, RBD and S2 subunit display different degrees of conservation with several coronavirus strains. Mutation analysis on contact sites in SARS-CoV-2 RBD reveals that human-susceptibility probably emerges in pangolin. Conclusion and implication We conclude that the spike sequence of SARS-CoV-2 is the result of multiple recombination events during its transmission from bat to human, and we propose a framework of evolutionary history that resolve the relationship of BCoV-RaTG13 and pangolin coronaviruses with SARS-CoV-2. Lay Summary This study analyses whole-genome and spike sequences of coronavirus from NCBI using phylogenetic and conservation analyses to reconstruct the evolutionary history of severe acute respiratory syndrome (SARS)-CoV-2 and proposes an evolutionary history of spike in the progenitors of SARS-CoV-2 from bat to human through mammal hosts before they recombine into the current form.

scholarly journals Phylogenetic analysis of the betacoronavirus S1 subunit

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 1389
Author(s):  
Irina Zyrianova
Keyword(s):  
Phylogenetic Analysis ◽  
Middle East ◽  
Severe Acute Respiratory Syndrome ◽  
Evolutionary History ◽  
Protein Sequences ◽  
Cell Receptor ◽  
Receptor Binding Domain ◽  
Host Cell Receptor ◽  
History Of ◽  
The Many

The ongoing pandemic outbreak of coronavirus disease 2019 (COVID-19) has been caused by the new betacoronavirus (BetaCoV) severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2). Together with other epidemic outbreaks of BetaCoV infectious diseases (Severe Acute Respiratory Syndrome (SARS) in 2002-2003 in China and Middle East Respiratory Syndrome (MERS) in 2012 in the Middle East, which have been caused by SARS-CoV and MERS-CoV, respectively), these events have generated interest in the coronaviruses (CoVs). Although many phylogenetic analyzes have been reported at a gene or protein level, there is no study as yet encompassing the many sequences publicly available for BetaCoVs, including those that have been manipulated in the lab. In this study, the phylogenetic analysis of 679 different S1 protein sequences of BetaCoVs from a total of 1595, which are publicly available in GenBank from the beginning of the pandemic event to April 2020, has been carried out. The S1 subunit is one part of the S (spike) protein, one of three CoV envelope proteins. The S1 subunit contains a host cell receptor binding domain. This domain is essential in the initiation of the infectious process. Therefore, its phylogenetic analysis is very important for studying CoV evolution. The phylogenetic analysis of BetaCoV S1 protein presented herein shows the evolutionary history of BetaCoVs from bovine CoV to SARS-CoV-2.

scholarly journals Inferring the Evolutionary History of Vibrios by Means of Multilocus Sequence Analysis

2007 ◽  
Vol 189 (21) ◽  
pp. 7932-7936 ◽  
Author(s):  
Tomoo Sawabe ◽  
Kumiko Kita-Tsukamoto ◽  
Fabiano L. Thompson
Keyword(s):  
Sequence Analysis ◽  
Evolutionary History ◽  
Gene Sequence ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
Amino Acid Identity ◽  
Multilocus Sequence Analysis ◽  
Protein Coding ◽  
History Of

ABSTRACT We performed the first broad study aiming at the reconstruction of the evolutionary history of vibrios by means of multilocus sequence analysis of nine genes. Overall, 14 distinct clades were recognized using the SplitsTree decomposition method. Some of these clades may correspond to families, e.g., the clades Salinivibrio and Photobacteria, while other clades, e.g., Splendidus and Harveyi, correspond to genera. The common ancestor of all vibrios was estimated to have been present 600 million years ago. We can define species of vibrios as groups of strains that share >95% gene sequence similarity and >99.4% amino acid identity based on the eight protein-coding housekeeping genes. The gene sequence data were used to refine the standard online electronic taxonomic scheme for vibrios (http://www.taxvibrio.lncc.br ).

Phylogenetic roots of Alu-mediated rearrangements leading to cancer

Genome ◽  
2005 ◽  
Vol 48 (1) ◽  
pp. 160-167 ◽  
Author(s):  
Rosaleen Gibbons ◽  
Achilles Dugaiczyk
Keyword(s):  
Phylogenetic Analysis ◽  
Evolutionary History ◽  
Sequence Similarity ◽  
Dna Recombination ◽  
Splice Sites ◽  
Alu Repeats ◽  
Alu Sequence ◽  
History Of ◽  
High Level ◽  
Genomic Locations

There are over a million Alu repetitive elements dispersed throughout the human genome, and a high level of Alu-sequence similarity ensures a strong propensity for unequal crossover events, some of which have lead to deleterious oncogenic rearrangements. Furthermore, Alu insertions introduce consensus 3' splice sites, which potentially facilitate alternative splicing. Not surprisingly, Alu-mediated defective splicing has also been associated with cancer. To investigate a possible correlation between the expansion of Alu repeats associated with primate divergence and predisposition to cancer, 4 Alu-mediated rearrangements — known to be the basis of cancer — were selected for phylogenetic analysis of the necessary genotype. In these 4 cases, it was determined that the different phylogenetic age of the oncogenic recombination-prone genotype reflected the evolutionary history of Alu repeats spreading to new genomic sites. Our data implies that the evolutionary expansion of Alu repeats to new genomic locations establishes new predispositions to cancer in various primate species.Key words: Alu repeats, evolution, cancer, primates, splicing, DNA recombination.

scholarly journals A phylogenetic perspective on the association between ants (Hymenoptera: Formicidae) and black yeasts (Ascomycota: Chaetothyriales)

2017 ◽  
Vol 284 (1850) ◽  
pp. 20162519 ◽  
Author(s):  
Marie Vasse ◽  
Hermann Voglmayr ◽  
Veronika Mayer ◽  
Cécile Gueidan ◽  
Maximilian Nepel ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Internal Transcribed Spacer ◽  
Evolutionary History ◽  
Geographical Origin ◽  
Sequence Similarity ◽  
Black Yeasts ◽  
Symbiotic Associations ◽  
Operational Taxonomic Units ◽  
History Of ◽  
Phylogenetic Perspective

The frequency and the geographical extent of symbiotic associations between ants and fungi of the order Chaetothyriales have been highlighted only recently. Using a phylogenetic approach based on seven molecular markers, we showed that ant-associated Chaetothyriales are scattered through the phylogeny of this order. There was no clustering according to geographical origin or to the taxonomy of the ant host. However, strains tended to be clustered according to the type of association with ants: strains from ant-made carton and strains from plant cavities occupied by ants (‘domatia’) rarely clustered together. Defining molecular operational taxonomic units (MOTUs) with an internal transcribed spacer sequence similarity cut-off of 99% revealed that a single MOTU could be composed of strains collected from various ant species and from several continents. Some ant-associated MOTUs also contained strains isolated from habitats other than ant-associated structures. Altogether, our results suggest that the degree of specialization of the interactions between ants and their fungal partners is highly variable. A better knowledge of the ecology of these interactions and a more comprehensive sampling of the fungal order are needed to elucidate the evolutionary history of mutualistic symbioses between ants and Chaetothyriales.

scholarly journals Nanopore sequencing and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization

2019 ◽  
Author(s):  
Alex N. Salazar ◽  
Arthur R. Gorter de Vries ◽  
Marcel van den Broek ◽  
Nick Brouwers ◽  
Pilar de la Torre Cortès ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Sequence Similarity ◽  
Brewing Yeast ◽  
Linear Evolution ◽  
Pure Cultures ◽  
History Of ◽  
Evolutionary Trajectories ◽  
Group 2 ◽  
Genome Assemblies ◽  
Group 1

AbstractBackgroundThe lager brewing yeast,S. pastorianus, is a hybrid betweenS. cerevisiaeandS. eubayanuswith extensive chromosome aneuploidy.S. pastorianusis subdivided into Group 1 and Group 2 strains, where Group 2 strains have higher copy number and a larger degree of heterozygosity forS. cerevisiaechromosomes. As a result, Group 2 strains were hypothesized to have emerged from a hybridization event distinct from Group 1 strains. Current genome assemblies ofS. pastorianusstrains are incomplete and highly fragmented, limiting our ability to investigate their evolutionary history.ResultsTo fill this gap, we generated a chromosome-level genome assembly of theS. pastorianusstrain CBS 1483 using MinION sequencing and analysed the newly assembled subtelomeric regions and chromosome heterozygosity. To analyse the evolutionary history ofS. pastorianusstrains, we developed Alpaca: a method to compute sequence similarity between genomes without assuming linear evolution. Alpaca revealed high similarities between theS. cerevisiaesubgenomes of Group 1 and 2 strains, and marked differences from sequencedS. cerevisiae strains.ConclusionsOur findings suggest that Group 1 and Group 2 strains originated from a single hybridization involving a heterozygousS. cerevisiaestrain, followed by different evolutionary trajectories. The clear differences between both groups may originate from a severe population bottleneck caused by the isolation of the first pure cultures. Alpaca provides a computationally inexpensive method to analyse evolutionary relationships while considering non-linear evolution such as horizontal gene transfer and sexual reproduction, providing a complementary viewpoint beyond traditional phylogenetic approaches.

Elaborating the role of reflection and individual differences in the study of folk-economic beliefs

2018 ◽  
Vol 41 ◽  
Author(s):  
Kevin Arceneaux
Keyword(s):  
Decision Making ◽  
Individual Differences ◽  
Cognitive Processes ◽  
Evolutionary History ◽  
Behavioral Responses ◽  
History Of ◽  
Economic Beliefs

AbstractIntuitions guide decision-making, and looking to the evolutionary history of humans illuminates why some behavioral responses are more intuitive than others. Yet a place remains for cognitive processes to second-guess intuitive responses – that is, to be reflective – and individual differences abound in automatic, intuitive processing as well.

The Art of Chinese Philosophy

2020 ◽  
Author(s):  
Paul Goldin
Keyword(s):  
Chinese Philosophy ◽  
Philosophical Tradition ◽  
Current Form ◽  
Han Feizi ◽  
Textual History ◽  
Classical Chinese ◽  
History Of ◽  
Crucial Characteristic ◽  
The Way

This book provides an unmatched introduction to eight of the most important works of classical Chinese philosophy—the Analects of Confucius, Mozi, Mencius, Laozi, Zhuangzi, Sunzi, Xunzi, and Han Feizi. The book places these works in rich context that explains the origin and meaning of their compelling ideas. Because none of these classics was written in its current form by the author to whom it is attributed, the book begins by asking, “What are we reading?” and showing that understanding the textual history of the works enriches our appreciation of them. A chapter is devoted to each of the eight works, and the chapters are organized into three sections: “Philosophy of Heaven,” which looks at how the Analects, Mozi, and Mencius discuss, often skeptically, Heaven (tian) as a source of philosophical values; “Philosophy of the Way,” which addresses how Laozi, Zhuangzi, and Sunzi introduce the new concept of the Way (dao) to transcend the older paradigms; and “Two Titans at the End of an Age,” which examines how Xunzi and Han Feizi adapt the best ideas of the earlier thinkers for a coming imperial age. In addition, the book presents explanations of the protean and frequently misunderstood concept of qi—and of a crucial characteristic of Chinese philosophy, nondeductive reasoning. The result is an invaluable account of an endlessly fascinating and influential philosophical tradition.

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