scholarly journals Adaptation and Codon-Usage Preference of Apple and Pear-Infecting Apple Stem Grooving Viruses

2021 ◽  
Vol 9 (6) ◽  
pp. 1111
Author(s):  
Jaedeok Kim ◽  
Aamir Lal ◽  
Eui-Joon Kil ◽  
Hae-Ryun Kwak ◽  
Hwan-Su Yoon ◽  
...  
Keyword(s):  
Codon Usage ◽  
Host Adaptation ◽  
Agricultural Fields ◽  
Cp Gene ◽  
Apple Stem Grooving Virus ◽  
Apple Stem ◽  
Pyrus Communis L ◽  
Positive Sense ◽  
Codon Usage Preference ◽  
Usage Preference

Apple stem grooving virus (ASGV; genus Capillovirus) is an economically important virus. It has an approx. 6.5 kb, monopartite, linear, positive-sense, single-stranded RNA genome. The present study includes identification of 24 isolates—13 isolates from apple (Pyrus malus L.) and 11 isolates from pear (Pyrus communis L.)—from different agricultural fields in South Korea. The coat protein (CP) gene of the corresponding 23 isolates were amplified, sequenced, and analyzed. The CP sequences showed phylogenetic separation based on their host species, and not on the geography, indicating host adaptation. Further analysis showed that the ASGV isolated in this study followed host adaptation influenced and preferred by the host codon-usage.

scholarly journals Analysis of codon usage preference in hemagglutinin genes of the swine-origin influenza A (H1N1) virus

2016 ◽  
Vol 49 (4) ◽  
pp. 477-486 ◽  
Author(s):  
Sheng-Fan Wang ◽  
Ming-Wei Su ◽  
Sung-Pin Tseng ◽  
Ming-Chun Li ◽  
Ching-Han Tsao ◽  
...  
Keyword(s):  
Codon Usage ◽  
Influenza A ◽  
H1n1 Virus ◽  
Influenza A H1n1 ◽  
Codon Usage Preference ◽  
Usage Preference

scholarly journals Evolutionary and codon usage preference insights into spike glycoprotein of SARS-CoV-2

2020 ◽  
Author(s):  
Yashpal Singh Malik ◽  
Mohd Ikram Ansari ◽  
Jobin Jose Kattoor ◽  
Rahul Kaushik ◽  
Shubhankar Sircar ◽  
...  
Keyword(s):  
Codon Usage ◽  
Vaccine Development ◽  
Genetic Material ◽  
Cell Receptor ◽  
Spike Glycoprotein ◽  
Mutation Pressure ◽  
Virus Attachment ◽  
Codon Usage Preference ◽  
Usage Preference ◽  
S Genes

Abstract Interaction of SARS-CoV-2 spike glycoprotein with the ACE2 cell receptor is very crucial for virus attachment to human cells. Selected mutations in SARS-CoV-2 S-protein are reported to strengthen its binding affinity to mammalian ACE2. The N501T mutation in SARS-CoV-2-CTD furnishes better support to hotspot 353 in comparison with SARS-CoV and shows higher affinity for receptor binding. Recombination analysis exhibited higher recombination events in SARS-CoV-2 strains, irrespective of their geographical origin or hosts. Investigation further supports a common origin among SARS-CoV-2 and its predecessors, SARS-CoV and bat-SARS-like-CoV. The recombination events suggest a constant exchange of genetic material among the co-infecting viruses in possible reservoirs and human hosts before SARS-CoV-2 emerged. Furthermore, a comprehensive analysis of codon usage bias (CUB) in SARS-CoV-2 revealed significant CUB among the S-genes of different beta-coronaviruses governed majorly by natural selection and mutation pressure. Various indices of codon usage of S-genes helped in quantifying its adaptability in other animal hosts. These findings might help in identifying potential experimental animal models for investigating pathogenicity for drugs and vaccine development experiments.

Usage Patterns of Codons Versus Complementary Codons Among Cellular Organisms and Organelles

2003 ◽  
Vol 11 (04) ◽  
pp. 407-418
Author(s):  
Fei Ma ◽  
Yonglong Zhuang ◽  
Yanda Li ◽  
Xiaofeng Xu ◽  
Xueping Chen
Keyword(s):  
Codon Usage ◽  
Optimum Combination ◽  
Translation Efficiency ◽  
Evolutionary Mechanisms ◽  
Evolutionary Selection ◽  
Synonymous Codons ◽  
Usage Patterns ◽  
Pair Number ◽  
Codon Usage Preference ◽  
Usage Preference

Genetic code is one of the most important biological languages in communications between DNA and protein, so peoples have been paying a great attention to the usage bias of synonymous codons. Based on Grosjean and Ikemura's "optimum combination of codon-anticodon complex" and "translation efficiency" hypotheses, in this paper, we put forward that a biased codon usage is identical to its corresponding complementary codon usage preference. To testify the hypothesis and reveal usage patterns between codons and corresponding complementary codons among different cellular organisms and organelles, the usage data of both codons and corresponding complementary ones from 28 cellular organisms and 20 organelles were analyzed. The results showed that: (1) there is a significantly positive correlation between codons and their complementary ones in most cellular organisms, chloroplasts and mitochondria; (2) all 32 single pairs codon versus complementary codon shared the likely usage correlation patterns, with the significantly positive, unrelated and significantly negative pair number of 18, 12 and 2 within 28 cellular organisms as well as 11, 17 and 4 within 20 organelles respectively, and some usage patterns of 32 single pairs codon versus complementary codon of cellular organisms are highly consistency with two kinds of organelles, which strongly implied that their codon usage has undergone the similar evolutionary selection in their wobbling and modification; (3) the codon-frequency tree agreed fairly well with the traditional one. These results demonstrated the validity of our hypothesis, and indicated the usefulness of correlation between codon and complementary codon in elucidating molecular evolutionary mechanisms.

scholarly journals The Insights of Genomic Synteny and Codon Usage Preference on Genera Demarcation of Iridoviridae Family

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhaobin Deng ◽  
Jun Wang ◽  
Wenjie Zhang ◽  
Yi Geng ◽  
Mingde Zhao ◽  
...  
Keyword(s):  
Codon Usage ◽  
Synonymous Codon ◽  
Phylogenetic Analyses ◽  
Synonymous Codon Usage ◽  
Amino Acid Sequences ◽  
Dna Viruses ◽  
Family Based ◽  
Codon Usage Preference ◽  
Usage Preference ◽  
Core Genes

The members of the family Iridoviridae are large, double-stranded DNA viruses that infect various hosts, including both vertebrates and invertebrates. Although great progress has been made in genomic and phylogenetic analyses, the adequacy of the existing criteria for classification within the Iridoviridae family remains unknown. In this study, we redetermined 23 Iridoviridae core genes by re-annotation, core-pan analysis and local BLASTN search. The phylogenetic tree based on the 23 re-annotated core genes (Maximum Likelihood, ML-Tree) and amino acid sequences (composition vector, CV-Tree) were found to be consistent with previous reports. Furthermore, the information provided by synteny analysis and codon usage preference (relative synonymous codon usage, correspondence analysis, ENC-plot and Neutrality plot) also supports the phylogenetic relationship. Collectively, our results will be conducive to understanding the genera demarcation within the Iridoviridae family based on genomic synteny and component (codon usage preference) and contribute to the existing taxonomy methods for the Iridoviridae family.

scholarly journals Guapiaçu virus, a new insect-specific flavivirus isolated from two species of Aedes mosquitoes from Brazil

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Geovani de Oliveira Ribeiro ◽  
Antonio Charlys da Costa ◽  
Danielle Elise Gill ◽  
Edcelha Soares D’Athaide Ribeiro ◽  
Marlisson Octavio da S. Rego ◽  
...  
Keyword(s):  
Codon Usage ◽  
Mammalian Cells ◽  
Plasma Sample ◽  
Genetic Characterization ◽  
Secondary Structures ◽  
Host Adaptation ◽  
Major Group ◽  
Aedes Mosquitoes ◽  
Evolutionary Relatedness

AbstractClassical insect-flaviviruses (cISFVs) and dual host-related insect-specific flavivirus (dISFV) are within the major group of insect-specific flavivirus. Remarkably dISFV are evolutionarily related to some of the pathogenic flavivirus, such as Zika and dengue viruses. The Evolutionary relatedness of dISFV to flavivirus allowed us to investigate the evolutionary principle of host adaptation. Additionally, dISFV can be used for the development of flavivirus vaccines and to explore underlying principles of mammalian pathogenicity. Here we describe the genetic characterization of a novel putative dISFV, termed Guapiaçu virus (GUAPV). Distinct strains of GUAPV were isolated from pools of Aedes terrens and Aedes scapularis mosquitoes. Additionally, we also detected viral GUAPV RNA in a plasma sample of an individual febrile from the Amazon region (North of Brazil). Although GUAPV did not replicate in tested mammalian cells, 3′UTR secondary structures duplication and codon usage index were similar to pathogenic flavivirus.

Optimization of tissue and time for rapid serological and molecular detection of Apple stem pitting virus and Apple stem grooving virus in apple’

2018 ◽  
Vol 46 (5) ◽  
pp. 705-713 ◽  
Author(s):  
Sajad Un Nabi ◽  
Javid Iqbal Mir ◽  
Om Chand Sharma ◽  
Desh Beer Singh ◽  
Shafia Zaffer ◽  
...  
Keyword(s):  
Molecular Detection ◽  
Apple Stem Grooving Virus ◽  
Apple Stem ◽  
Apple Stem Pitting Virus ◽  
Stem Pitting

scholarly journals Survey of Apple Chlorotic Leaf Spot Virus and Apple Stem Grooving Virus Occurrence in Korea and Frequency of Mixed Infections in Apple

2015 ◽  
Vol 60 (2) ◽  
pp. 323-329 ◽  
Author(s):  
Jae-Yeong Han ◽  
Jung-Kyu Kim ◽  
Jin–Soo Cheong ◽  
Eun–Yeong Seo ◽  
Chan–Hwan Park ◽  
...  
Keyword(s):  
Leaf Spot ◽  
Mixed Infections ◽  
Spot Virus ◽  
Apple Stem Grooving Virus ◽  
Apple Stem ◽  
Chlorotic Leaf

Characterization of Apple stem grooving virus infecting Actinidia deliciosa (Kiwi) in India

2014 ◽  
Vol 176 ◽  
pp. 105-111 ◽  
Author(s):  
Pooja Bhardwaj ◽  
Raja Ram ◽  
Aijaz A. Zaidi ◽  
Vipin Hallan
Keyword(s):  
Actinidia Deliciosa ◽  
Apple Stem Grooving Virus ◽  
Apple Stem

Host Adaptation of Codon Usage in SARS-CoV-2 From Mammals Indicate Natural Selection

2021 ◽  
Author(s):  
Yanan Fu ◽  
Yanping Huang ◽  
Jingjing Rao ◽  
Feng Zeng ◽  
Ruiping Yang ◽  
...  
Keyword(s):  
Natural Selection ◽  
Codon Usage ◽  
Binding Affinity ◽  
Codon Bias ◽  
Synonymous Codon ◽  
Host Adaptation ◽  
Synonymous Codon Usage ◽  
Mutation Pressure ◽  
Usage Analysis ◽  
Human Receptor

Abstract The outbreak of COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, spread across hosts from humans to animals, transmitting particularly effectively in mink. How SARS-CoV-2 selects and evolves in the host, and the differences in the evolution of different animals are still unclear. To analysis the mutation and codon usage bias of SARS-CoV-2 in infected humans and animals. The SARS-CoV-2 sequence in mink (Mink-SARS2) and binding energy with receptor were calculated compared with human. The relative synonymous codon usage of viral encoded gene was analyzed to characterize the differences and the evolutionary characteristics. A synonymous codon usage analysis showed that SARS-CoV-2 is optimized to adapt in the animals in which it is currently reported, and all of the animals showed decreased adaptability relative to that of humans, except for mink. The neutrality plot showed that the effect of natural selection on different SARS-CoV-2 sequences is stronger than mutation pressure. A binding affinity analysis indicated that the spike protein of the SARS-CoV-2 variant in mink showed a greater preference for binding with the mink receptor ACE2 than with the human receptor, especially as the mutation Y453F and N501T in Mink-SARS2 lead to improvement of binding affinity for mink receptor. In summary, mutations Y453F and N501T in Mink-SARS2 lead to improvement of binding affinity with mink receptor, indicating possible natural selection and current host adaptation. Monitoring the variation and codon bias of SARS-CoV-2 provides a theoretical basis for tracing the epidemic, evolution and cross-species spread of SARS-CoV-2.

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