ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models

Darriba, Diego; Posada, David; Kozlov, Alexey M; Stamatakis, Alexandros; Morel, Benoît; Flouri, Tomáš

doi:10.1093/molbev/msz189

Cited by 1,247 publications

(836 citation statements)

References 23 publications

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“…The analysis used an automatic bootstrapping option using a general timereversible substitution model with a gamma-shape parameter (GTR+ G). The model was selected as the best-fit model under the Akaike information criterion using ModelTest-NG (Darriba et al, 2020). Phylogenetic trees were viewed using FigTree v1.4 (http://tree.bio.ed.ac.uk/ software/figtree/).…”

Section: Methodsmentioning

confidence: 99%

Nonstructural proteins NS7b and NS8 are likely to be phylogenetically associated with evolution of 2019-nCoV

Fahmi

Kubota

Ito

2020

Infection, Genetics and Evolution

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The seventh novel human infecting Betacoronavirus that causes pneumonia (2019 novel coronavirus, 2019-nCoV) originated in Wuhan, China. The evolutionary relationship between 2019-nCoV and the other human respiratory illness-causing coronavirus is not closely related. We sought to characterize the relationship of the translated proteins of 2019-nCoV with other species of Orthocoronavirinae. A phylogenetic tree was constructed from the genome sequences. A cluster tree was developed from the profiles retrieved from the presence and absence of homologs of ten 2019-nCoV proteins. The combined data were used to characterize the relationship of the translated proteins of 2019-nCoV to other species of Orthocoronavirinae. Our analysis reliably suggests that 2019-nCoV is most closely related to BatCoV RaTG13 and belongs to subgenus Sarbecovirus of Betacoronavirus, together with SARS coronavirus and Bat-SARS-like coronavirus. The phylogenetic profiling cluster of homolog proteins of one annotated 2019-nCoV protein against other genome sequences revealed two clades of ten 2019-nCoV proteins. Clade 1 consisted of a group of conserved proteins in Orthocoronavirinae comprising Orf1ab polyprotein, Nucleocapsid protein, Spike glycoprotein, and Membrane protein. Clade 2 comprised six proteins exclusive to Sarbecovirus and Hibecovirus. Two of six Clade 2 nonstructural proteins, NS7b and NS8, were exclusively conserved among 2019-nCoV, BetaCoV_RaTG, and BatSARS-like Cov. NS7b and NS8 have previously been shown to affect immune response signaling in the SARS-CoV experimental model. Thus, we speculated that knowledge of the functional changes in the NS7b and NS8 proteins during evolution may provide important information to explore the human infective property of 2019-nCoV.

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Section: Methodsmentioning

confidence: 99%

Nonstructural proteins NS7b and NS8 are likely to be phylogenetically associated with evolution of 2019-nCoV

Fahmi

Kubota

Ito

2020

Infection, Genetics and Evolution

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“…1 [15]. ModelTest-NG [6] was used to select the best-fit evolutionary model of nucleotide substitution, that is, GTR + G + I. Bootstrap analysis (100 pseudo-replicates) was conducted in order to evaluate the statistical significance of the inferred trees.…”

Section: Phylogenetic Analysismentioning

confidence: 99%

Codon usage and evolutionary rates of the 2019-nCoV genes

Dilucca

Forcelloni

Pavlopoulou

et al. 2020

Preprint

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Severe acute respiratory syndrome coronavirus 2 (2019-nCoV), which first broke out in 1 Wuhan (China) in December of 2019, causes a severe acute respiratory illness with a mortality 2 ranging from 3% to 6%. To better understand the evolution of the newly emerging 2019-nCoV, in this 3 paper, we analyze the codon usage pattern of 2019-nCoV. For this purpose, we compare the codon 4 usage of 2019-nCoV with that of other 30 viruses belonging to the subfamily of orthocoronavirinae. 5 We found that 2019-nCoV shows a rich composition of AT nucleotides that strongly influences its 6 codon usage, which appears to be not optimized to human host. Then, we study the evolutionary 7 pressures influencing the codon usage and evolutionary rates of the sequences of five conserved 8 genes that encode the corresponding proteins (viral replicase, spike, envelope, membrane and 9 nucleocapsid) characteristic of coronaviruses. We found different patterns of both mutational bias 10 and nature selection that affect the codon usage of these genes at different extents. Moreover, we 11 show that the two integral membrane proteins proteins (matrix and envelope) tend to evolve slowly 12 by accumulating nucleotide mutations on their genes. Conversely, genes encoding nucleocapsid 13 (N), viral replicase and spike proteins are important targets for the development of vaccines and 14 antiviral drugs, tend to evolve faster as compared to other ones. Taken together, our results suggest 15 that the higher evolutionary rate observed for these two genes could represent a major barrier in the 16 development of antiviral therapeutics 2019-nCoV.

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“…Divergent and ambiguously aligned blocks were removed using Gblocks. Substitution model was selected using ModelTest-NG v0.1.6 (Darriba et al, 2020) by the AIC criterium. Bayesian phylogenetic reconstruction was conducted with MrBayes as described above by running chains for 300,000 generations and checking for convergence.…”

Section: Phylogenetic and Recombination Analysesmentioning

confidence: 99%

The protector within: Comparative genomics of APSE phages across aphids reveals rampant recombination and diverse toxin arsenals

Rouïl

Jousselin

d’Acier

et al. 2020

Preprint

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ABSTRACTPhages can fundamentally alter the physiology and metabolism of their hosts. While ubiquitous in the bacterial world, they have seldom been described among endosymbiotic bacteria. One notable exception in the APSE phage that is found associated with the gammaproteobacterial Hamiltonella defensa, hosted by several insect species. This secondary facultative endosymbiont is not necessary for the survival of its hosts but can infect certain individuals or even whole populations. Its infection in aphids is often associated with protection against parasitoid wasps. This protective phenotype has actually been linked to the infection of the symbiont strain with an APSE, which carries a toxin cassette that varies among so-called ”types”. In the present work, we seek to expand our understanding of the diversity of APSE phages as well as the relations of their Hamiltonella hosts. For this, we assembled and annotated the full genomes of 16 APSE phages infecting Hamiltonella symbionts across 10 insect species. Molecular and phylogenetic analyses suggest that recombination has occurred repeatedly among lineages. Comparative genomics of the phage genomes revealed two variable regions that are useful for phage typing. Additionally, we find that mobile elements could play a role in the acquisition of new genes in the toxin cassette. Altogether, we provide an unprecedented view of APSE diversity and their genome evolution across aphids. This genomic investigation will provide a valuable resource for the design and interpretation of experiments aiming at understanding the protective phenotype these phages confer to their insect hosts.

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ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models

Cited by 1,247 publications

References 23 publications

Nonstructural proteins NS7b and NS8 are likely to be phylogenetically associated with evolution of 2019-nCoV

Nonstructural proteins NS7b and NS8 are likely to be phylogenetically associated with evolution of 2019-nCoV

Codon usage and evolutionary rates of the 2019-nCoV genes

The protector within: Comparative genomics of APSE phages across aphids reveals rampant recombination and diverse toxin arsenals

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