scholarly journals A Comprehensive Classification of Coronaviruses and Inferred Cross-Host Transmissions

2020 ◽  
Author(s):  
Yiran Fu ◽  
Marco Pistolozzi ◽  
Xiaofeng Yang ◽  
Zhanglin Lin
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Classification Scheme ◽  
Gene Trees ◽  
Robust Classification ◽  
Protein Clusters ◽  
Comprehensive Classification

AbstractIn this work, we present a unified and robust classification scheme for coronaviruses based on concatenated protein clusters. This subsequently allowed us to infer the apparent “horizontal gene transfer” events via reconciliation with the corresponding gene trees, which we argue can serve as a marker for cross-host transmissions. The cases of SARS-CoV, MERS-CoV, and SARS-CoV-2 are discussed. Our study provides a possible technical route to understand how coronaviruses evolve and are transmitted to humans.

scholarly journals Proposal of a new classification scheme for periocular injuries

2017 ◽  
Vol 50 (01) ◽  
pp. 021-028 ◽  
Author(s):  
Devi Prasad Mohapatra ◽  
Friji Meethale Thiruvoth ◽  
Ravi Kumar Chittoria ◽  
S. Dinesh Kumar ◽  
Sudhanva Hemant Kumar ◽  
...  
Keyword(s):  
Soft Tissue ◽  
Classification Scheme ◽  
Soft Tissue Injuries ◽  
Classification Systems ◽  
Lateral Canthus ◽  
Aesthetic Appearance ◽  
Adjacent Structures ◽  
Tissue Injuries ◽  
Comprehensive Classification

ABSTRACT Background: Eyelids are important structures and play a role in protecting the globe from trauma, brightness, in maintaining the integrity of tear films and moving the tears towards the lacrimal drainage system and contribute to aesthetic appearance of the face. Ophthalmic trauma is an important cause of morbidity among individuals and has also been responsible for additional cost of healthcare. Periocular trauma involving eyelids and adjacent structures has been found to have increased recently probably due to increased pace of life and increased dependence on machinery. A comprehensive classification of periocular trauma would help in stratifying these injuries as well as study outcomes. Material and Methods: This study was carried out at our institute from June 2015 to Dec 2015. We searched multiple English language databases for existing classification systems for periocular trauma. We designed a system of classification of periocular soft tissue injuries based on clinico-anatomical presentations. This classification was applied prospectively to patients presenting with periocular soft tissue injuries to our department. Results: A comprehensive classification scheme was designed consisting of five types of periocular injuries. A total of 38 eyelid injuries in 34 patients were evaluated in this study. According to the System for Peri-Ocular Trauma (SPOT) classification, Type V injuries were most common. SPOT Type II injuries were more common isolated injuries among all zones. Discussion: Classification systems are necessary in order to provide a framework in which to scientifically study the etiology, pathogenesis, and treatment of diseases in an orderly fashion. The SPOT classification has taken into account the periocular soft tissue injuries i.e., upper eyelid, lower eyelid, medial and lateral canthus injuries., based on observed clinico-anatomical patterns of eyelid injuries. Conclusion: The SPOT classification seems to be a reliable system to address eyelid injuries. This classification scheme would guide the ophthalmic and facial reconstructive surgeons to provide optimal outcomes in eyelid injuries. Based on the classification scheme and review of existing literature, an algorithm is presented to facilitate repair and reconstruction.

scholarly journals Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life

2009 ◽  
Vol 364 (1527) ◽  
pp. 2229-2239 ◽  
Author(s):  
Gregory P. Fournier ◽  
Jinling Huang ◽  
J. Peter Gogarten
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Evolutionary History ◽  
Phylogenetic Reconstruction ◽  
Gene Trees ◽  
Individual Gene ◽  
Evolution Of Life ◽  
Domains Of Life ◽  
Life On Earth ◽  
Simple Tree

Horizontal gene transfer (HGT) is often considered to be a source of error in phylogenetic reconstruction, causing individual gene trees within an organismal lineage to be incongruent, obfuscating the ‘true’ evolutionary history. However, when identified as such, HGTs between divergent organismal lineages are useful, phylogenetically informative characters that can provide insight into evolutionary history. Here, we discuss several distinct HGT events involving all three domains of life, illustrating the selective advantages that can be conveyed via HGT, and the utility of HGT in aiding phylogenetic reconstruction and in dating the relative sequence of speciation events. We also discuss the role of HGT from extinct lineages, and its impact on our understanding of the evolution of life on Earth. Organismal phylogeny needs to incorporate reticulations; a simple tree does not provide an accurate depiction of the processes that have shaped life's history.

scholarly journals Horizontal gene transfer: essentiality and evolvability in prokaryotes, and roles in evolutionary transitions

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 1805 ◽  
Author(s):  
Eugene V. Koonin
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Phylogenetic Trees ◽  
Point Mutations ◽  
Theoretical Models ◽  
Microbial Evolution ◽  
Gene Gain ◽  
Gene Trees ◽  
Ratchet Effect ◽  
Evolutionary Transitions

The wide spread of gene exchange and loss in the prokaryotic world has prompted the concept of ‘lateral genomics’ to the point of an outright denial of the relevance of phylogenetic trees for evolution. However, the pronounced coherence congruence of the topologies of numerous gene trees, particularly those for (nearly) universal genes, translates into the notion of a statistical tree of life (STOL), which reflects a central trend of vertical evolution. The STOL can be employed as a framework for reconstruction of the evolutionary processes in the prokaryotic world. Quantitatively, however, horizontal gene transfer (HGT) dominates microbial evolution, with the rate of gene gain and loss being comparable to the rate of point mutations and much greater than the duplication rate. Theoretical models of evolution suggest that HGT is essential for the survival of microbial populations that otherwise deteriorate due to the Muller’s ratchet effect. Apparently, at least some bacteria and archaea evolved dedicated vehicles for gene transfer that evolved from selfish elements such as plasmids and viruses. Recent phylogenomic analyses suggest that episodes of massive HGT were pivotal for the emergence of major groups of organisms such as multiple archaeal phyla as well as eukaryotes. Similar analyses appear to indicate that, in addition to donating hundreds of genes to the emerging eukaryotic lineage, mitochondrial endosymbiosis severely curtailed HGT. These results shed new light on the routes of evolutionary transitions, but caution is due given the inherent uncertainty of deep phylogenies.

scholarly journals Horizontal gene transfer and recombination analysis of SARS-CoV-2 genes helps discover its close relatives and shed light on its origin

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Vladimir Makarenkov ◽  
Bogdan Mazoure ◽  
Guillaume Rabusseau ◽  
Pierre Legendre
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Intermediate Host ◽  
Close Relative ◽  
Intragenic Recombination ◽  
Recombination Analysis ◽  
Gene Trees ◽  
Intermediate Hosts ◽  
Evolutionary Patterns ◽  
Close Relatives

Abstract Background The SARS-CoV-2 pandemic is one of  the greatest  global medical and social challenges that have emerged in recent history. Human coronavirus strains discovered during previous SARS outbreaks have been hypothesized to pass from bats to humans using intermediate hosts, e.g. civets for SARS-CoV and camels for MERS-CoV. The discovery of an intermediate host of SARS-CoV-2 and the identification of specific mechanism of its emergence in humans are topics of primary evolutionary importance. In this study we investigate the evolutionary patterns of 11 main genes of SARS-CoV-2. Previous studies suggested that the genome of SARS-CoV-2 is highly similar to the horseshoe bat coronavirus RaTG13 for most of the genes and to some Malayan pangolin coronavirus (CoV) strains for the receptor binding (RB) domain of the spike protein. Results We provide a detailed list of statistically significant horizontal gene transfer and recombination events (both intergenic and intragenic) inferred for each of 11 main genes of the SARS-CoV-2 genome. Our analysis reveals that two continuous regions of genes S and N of SARS-CoV-2 may result from intragenic recombination between RaTG13 and Guangdong (GD) Pangolin CoVs. Statistically significant gene transfer-recombination events between RaTG13 and GD Pangolin CoV have been identified in region [1215–1425] of gene S and region [534–727] of gene N. Moreover, some statistically significant recombination events between the ancestors of SARS-CoV-2, RaTG13, GD Pangolin CoV and bat CoV ZC45-ZXC21 coronaviruses have been identified in genes ORF1ab, S, ORF3a, ORF7a, ORF8 and N. Furthermore, topology-based clustering of gene trees inferred for 25 CoV organisms revealed a three-way evolution of coronavirus genes, with gene phylogenies of ORF1ab, S and N forming the first cluster, gene phylogenies of ORF3a, E, M, ORF6, ORF7a, ORF7b and ORF8 forming the second cluster, and phylogeny of gene ORF10 forming the third cluster. Conclusions The results of our horizontal gene transfer and recombination analysis suggest that SARS-CoV-2 could not only be a chimera virus resulting from recombination of the bat RaTG13 and Guangdong pangolin coronaviruses but also a close relative of the bat CoV ZC45 and ZXC21 strains. They also indicate that a GD pangolin may be an intermediate host of this dangerous virus. 

scholarly journals Horizontal gene transfer and recombination analysis of SARS-CoV-2 genes helps discover its close relatives and shed light on its origin

2020 ◽  
Author(s):  
Vladimir Makarenkov ◽  
Bogdan Mazoure ◽  
Guillaume Rabusseau ◽  
Pierre Legendre
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Intermediate Host ◽  
Close Relative ◽  
Intragenic Recombination ◽  
Recombination Analysis ◽  
Gene Trees ◽  
Intermediate Hosts ◽  
Evolutionary Patterns ◽  
Close Relatives

AbstractBackgroundThe SARS-CoV-2 pandemic is among the most dangerous infectious diseases that have emerged in recent history. Human CoV strains discovered during previous SARS outbreaks have been hypothesized to pass from bats to humans using intermediate hosts, e.g. civets for SARS-CoV and camels for MERS-CoV. The discovery of an intermediate host of SARS-CoV-2 and the identification of specific mechanism of its emergence in humans are topics of primary evolutionary importance. In this study we investigate the evolutionary patterns of 11 main genes of SARS-CoV-2. Previous studies suggested that the genome of SARS-CoV-2 is highly similar to the horseshoe bat coronavirus RaTG13 for most of the genes and to some Malayan pangolin coronavirus (CoV) strains for the receptor binding (RB) domain of the spike protein.ResultsWe provide a detailed list of statistically significant horizontal gene transfer and recombination events (both intergenic and intragenic) inferred for each of 11 main genes of the SARS-Cov-2 genome. Our analysis reveals that two continuous regions of genes S and N of SARS-CoV-2 may result from intragenic recombination between RaTG13 and Guangdong (GD) Pangolin CoVs. Statistically significant gene transfer-recombination events between RaTG13 and GD Pangolin CoV have been identified in region [1215-1425] of gene S and region [534-727] of gene N. Moreover, some significant recombination events between the ancestors of SARS-CoV-2, RaTG13, GD Pangolin CoV and bat CoV ZC45-ZXC21 coronaviruses have been identified in genes ORF1ab, S, ORF3a, ORF7a, ORF8 and N. Furthermore, topology-based clustering of gene trees inferred for 25 CoV organisms revealed a three-way evolution of coronavirus genes, with gene phylogenies of ORF1ab, S and N forming the first cluster, gene phylogenies of ORF3a, E, M, ORF6, ORF7a, ORF7b and ORF8 forming the second cluster, and phylogeny of gene ORF10 forming the third cluster.ConclusionsThe results of our horizontal gene transfer and recombination analysis suggest that SARS-Cov-2 could not only be a chimera resulting from recombination of the bat RaTG13 and Guangdong pangolin coronaviruses but also a close relative of the bat CoV ZC45 and ZXC21 strains. They also indicate that a GD pangolin may be an intermediate host of SARS-CoV-2.

scholarly journals Reflection as an Applied Problem in Psychology

2016 ◽  
Vol 12 (3) ◽  
pp. 208-225 ◽  
Author(s):  
V.K. Vasilev
Keyword(s):  
Theoretical Analysis ◽  
Theoretical Basis ◽  
Classification Scheme ◽  
Applied Problem ◽  
Complex Phenomenon ◽  
Practical Application ◽  
Methodological Procedures ◽  
Comprehensive Classification ◽  
Application Programs

The article presents some of the procedures and the results of a detailed study on reflection: analysis of the previous philosophical ideas and views, basic psychological concepts for reflection, classification of its types and species. Through specially selected and developed methodological procedures for the theoretical analysis the author has synthesized a thorough understanding of the nature of reflection as a complex phenomenon manifested in different modes — types and species. Proposed is a comprehensive classification scheme of reflection in which are divided it’s four types. Specifically addressed are the opportunities, the approaches and some achievements in converting theoretical ideas into practical application-programs, methodologies and technologies based on our knowledge of reflection. Analysis of the theoretical basis for the formation of a new, independent type of reflection — praxeological and its peculiarities. The author presents the basic guidelines and some results from the study of this fascinating human phenomenon — reflection.

scholarly journals Indications for Acquisition of Reductive Dehalogenase Genes through Horizontal Gene Transfer by Dehalococcoides ethenogenes Strain 195

2005 ◽  
Vol 71 (6) ◽  
pp. 2955-2961 ◽  
Author(s):  
Christophe Regeard ◽  
Julien Maillard ◽  
Christine Dufraigne ◽  
Patrick Deschavanne ◽  
Christof Holliger
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Gc Content ◽  
Hierarchical Classification ◽  
Reductive Dehalogenase ◽  
Dehalococcoides Ethenogenes ◽  
Bioinformatic Tool ◽  
Key Enzyme ◽  
Reductive Dehalogenase Genes

ABSTRACT The genome of Dehalococcoides ethenogenes strain 195, an anaerobic dehalorespiring bacterium, contains 18 copies of putative reductive dehalogenase genes, including the well-characterized tceA gene, whose gene product functions as the key enzyme in the environmentally important dehalorespiration process. The genome of D. ethenogenes was analyzed using a bioinformatic tool based on the frequency of oligonucleotides. The results in the form of a genomic signature revealed several local disruptions of the host signature along the genome sequence. These fractures represent DNA segments of potentially foreign origin, so-called atypical regions, which may have been acquired by an ancestor through horizontal gene transfer. Most interestingly, 15 of the 18 reductive dehalogenase genes, including the tceA gene, were found to be located in these regions, strongly indicating the foreign nature of the dehalorespiration activity. The GC content and the presence of recombinase genes within some of these regions corroborate this hypothesis. A hierarchical classification of the atypical regions containing the reductive dehalogenase genes indicated that these regions were probably acquired by several gene transfer events.

scholarly journals Phylogenomic fingerprinting of tempo and functions of horizontal gene transfer within ochrophytes

2021 ◽  
Vol 118 (4) ◽  
pp. e2009974118
Author(s):  
Richard G. Dorrell ◽  
Adrien Villain ◽  
Benoît Perez-Lamarque ◽  
Guillemette Audren de Kerdrel ◽  
Giselle McCallum ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Large Scale ◽  
Single Gene ◽  
Gene Trees ◽  
Reference Tree ◽  
In Silico Modeling ◽  
Genes Encoding ◽  
Eukaryotic Genomes ◽  
Algal Evolution

Horizontal gene transfer (HGT) is an important source of novelty in eukaryotic genomes. This is particularly true for the ochrophytes, a diverse and important group of algae. Previous studies have shown that ochrophytes possess a mosaic of genes derived from bacteria and eukaryotic algae, acquired through chloroplast endosymbiosis and from HGTs, although understanding of the time points and mechanisms underpinning these transfers has been restricted by the depth of taxonomic sampling possible. We harness an expanded set of ochrophyte sequence libraries, alongside automated and manual phylogenetic annotation, in silico modeling, and experimental techniques, to assess the frequency and functions of HGT across this lineage. Through manual annotation of thousands of single-gene trees, we identify continuous bacterial HGT as the predominant source of recently arrived genes in the model diatom Phaeodactylum tricornutum. Using a large-scale automated dataset, a multigene ochrophyte reference tree, and mathematical reconciliation of gene trees, we note a probable elevation of bacterial HGTs at foundational points in diatom evolution, following their divergence from other ochrophytes. Finally, we demonstrate that throughout ochrophyte evolutionary history, bacterial HGTs have been enriched in genes encoding secreted proteins. Our study provides insights into the sources and frequency of HGTs, and functional contributions that HGT has made to algal evolution.

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