EasyCodeML: A visual tool for analysis of selection using CodeML

The SARS-CoV-2 epidemic started in late December 2019 in Wuhan, China, and has since impacted a large portion of China and raised major global concern. Herein, we investigated the extent of molecular divergence between SARS-CoV-2 and other related coronaviruses.Although we found only 4% variability in genomic nucleotides between SARS-CoV-2 and a bat SARS-related coronavirus (SARSr-CoV; RaTG13), the difference at neutral sites was 17%, suggesting the divergence between the two viruses is much larger than previously estimated. Our results suggest that the development of new variations in functional sites in the receptor-binding domain (RBD) of the spike seen in SARS-CoV-2 and viruses from pangolin SARSr-CoVs are likely caused by mutations and natural selection besides recombination.Population genetic analyses of 103 SARS-CoV-2 genomes indicated that these viruses evolved into two major types (designated L and S), that are well defined by two different SNPs that show nearly complete linkage across the viral strains sequenced to date. Although the L type (~70%) is more prevalent than the S type (~30%), the S type was found to be the ancestral version. Whereas the L type was more prevalent in the early stages of the outbreak in Wuhan, the frequency of the L type decreased after early January 2020. Human intervention may have placed more severe selective pressure on the L type, which might be more aggressive and spread more quickly. On the other hand, the S type, which is evolutionarily older and less aggressive, might have increased in relative frequency due to relatively weaker selective pressure. These findings strongly support an urgent need for further immediate, comprehensive studies that combine genomic data, epidemiological data, and chart records of the clinical symptoms of patients with coronavirus disease 2019 .

show abstract

“…Positive selection was detected using EasyCodeML [42], a recently published wrapper of CODEML [20]. The M7 and M8 models were compared.…”

Section: Positively Selected Amino Acidsmentioning

confidence: 99%

On the origin and continuing evolution of SARS-CoV-2

Tang

et al. 2020

National Science Review

1,554

1,622

View full text Add to dashboard Cite

show abstract

“…The positively selected sites were evaluated using maximum-likelihood (ML) method implemented in MEGA. A site model was selected for the positively selected sites, and the parameters under seven different codon substitution models and their performances were evaluated using likelihood ratio tests (LRTs) implemented in EasyCodeML 1.2 [13] . The animal experiments were carried out according to the Animal Experiment Committee of Henan Academy of Agricultural Sciences (Approval number SYXK 2014-0007).…”

Section: Methodsmentioning

confidence: 99%

Orta Çin’de Sığır Koronavirusun Tam Uzunlukta Spike Genine Dayalı Tespiti ve Moleküler Karakterizasyonu

Shi¹,

Wang²,

Xu³

et al. 2019

Kafkas Univ Vet Fak Derg

View full text Add to dashboard Cite

Bovine coronavirus (BCoV) is prevalent throughout the world and is an important aetiological agent of diarrhoea in new-born calves. However, little is known about the genetic diversity and molecular epidemiology of BCoV in China. In this study, a total of 127 faecal samples from diarrhoeic dairy calves from nine cities in Henan Province, Central China, were collected between 2017 and 2018 and evaluated by RT-PCR for the N gene. BCoV was detected in 15% (19/127) of calves. In addition, the full-length sequence of the S gene from 13 representative BCoV strains was obtained and analysed. Sequencing results for the full-length S gene showed 97.3-97.5% nucleotide (nt) identity and 96.3-96.8% amino acid (aa) identity with the classical Mebus strain. Phylogenetic analysis based on the full-length S gene showed that the BCoV strains in this study clustered with Vietnamese and Cuban BCoV strains on a large branch of the tree. These results enrich the molecular characterization of the Chinese BCoV strains and provide the first large-scale epidemiological examination of the prevalence of BCoV in diarrhoeic calves in Henan Province, Central China. ÖzSığır koronavirüs (BCoV) tüm dünyada yaygındır ve yeni doğmuş buzağılarda ishal olgularının etiyolojisinde önemli rol oynar. Bununla birlikte, Çin'de BCoV'nin genetik çeşitliliği ve moleküler epidemiyolojisi hakkında çok az şey bilinmektedir. Bu çalışmada, 2017 ile 2018 yılları arasında Orta Çin'in Henan eyaletindeki dokuz ilden ishalli süt buzağılarından toplam 127 adet dışkı örneği toplandı ve N geni için RT-PCR ile değerlendirildi. Buzağıların %15'inde (19/127) BCoV tespit edildi. Ek olarak, 13 temsilci BCoV suşundan S geninin tam uzunluktaki dizisi elde edildi ve analiz edildi. Tam uzunluktaki S geni için sıralama sonuçları, klasik Mebus suşu ile %97.3-97.5 nükleotit (nt) özdeşliği ve %96.3-96.8 amino asit (aa) özdeşliği gösterdi. Tam uzunluktaki S genine dayanan filogenetik analiz, bu çalışmada BCoV suşlarının, ağacın büyük bir dalında Vietnam ve Küba BCoV suşları ile kümelendiğini gösterdi. Bu sonuçlar, Orta Çin'in Henan Eyaletindeki ishalli buzağılarda BCoV suşlarının moleküler karakterizasyonunu zenginleştirerek BCoV prevalansının ilk büyük ölçekli epidemiyolojik incelenmesini sağlamış oldu.

show abstract

“…The program EasyCodeML (Gao et al, 2019) was used to analyze the selective pressure on mitogenomes; this is an interactive visual tool for detecting selection in a molecular evolutionary analysis based on CodeML (Yang, 2007). The ω ratio is the rate of nonsynonymous (dN ) versus synonymous (dS) substitution (dN /dS) and can indicate natural selection acting on the proteins.…”

Section: Analysis Of Positive Selectionmentioning

confidence: 99%

Characterization of the mitochondrial genomes of two toads, Anaxyrus americanus (Anura: Bufonidae) and Bufotes pewzowi (Anura: Bufonidae), with phylogenetic and selection pressure analyses

Cai

Qin

Zhang

et al. 2020

PeerJ

View full text Add to dashboard Cite

Mitogenomes are useful in analyzing phylogenetic relationships and also appear to influence energy metabolism, thermoregulation and osmoregulation. Much evidence has accumulated for positive selection acting on mitochondrial genes associated with environmental adaptation. Hence, the mitogenome is a likely target for environmental selection. The family Bufonidae (true toads) has only nine complete and four partial mitogenomes published compared to the 610 known species of this family. More mitogenomes are needed in order to obtain a clearer understanding of the phylogenetic relationships within Bufonidae that are currently controversial. To date, no mitogenomes have been reported from the genera Anaxyrus and Bufotes. Anaxyrus americanus can live in low temperature environments and Bufotes pewzowi can live in high salinity environments. We sequenced the mitogenomes of these two species to discuss the phylogenetic relationships within Bufonidae and the selection pressures experienced by specimens living in low temperature or saline environments. Like other toads, the circular mitogenomes of both species contained the typical 37 genes. Anaxyrus americanus had the highest A+T content of the complete mitogenome among the Bufonidae. In addition, A. americanus showed a negative AT-skew in the control region, whereas Bufotes pewzowi showed a positive AT-skew. Additionally, both toad species had unique molecular features in common: an ND1 gene that uses TTG as the start codon, an extra unpaired adenine (A) in the anticodon arm of trnS (AGY), and the loss of the DHU loop in trnC. The monophyly of Bufonidae was corroborated by both BI and ML trees. An analysis of selective pressure based on the 13 protein coding genes was conducted using the EasyCodeML program. In the branch model analysis, we found two branches of A. americanus and Bufotes pewzowi that were under negative selection. Additionally, we found two positively selected sites (at positions 115 and 119, BEB value > 0.90) in the ND6 protein in the site model analysis. The residue D (119) was located only in A. americanus and may be related to adaptive evolution in low temperature environments. However, there was no evidence of a positively selected site in Bufotes pewzowi in this study.

show abstract

EasyCodeML: A visual tool for analysis of selection using CodeML

Cited by 323 publications

References 27 publications

On the origin and continuing evolution of SARS-CoV-2

On the origin and continuing evolution of SARS-CoV-2

Orta Çin’de Sığır Koronavirusun Tam Uzunlukta Spike Genine Dayalı Tespiti ve Moleküler Karakterizasyonu

Characterization of the mitochondrial genomes of two toads, Anaxyrus americanus (Anura: Bufonidae) and Bufotes pewzowi (Anura: Bufonidae), with phylogenetic and selection pressure analyses

Contact Info

Product

Resources

About