Transcription, mRNA export and immune evasion shape the codon usage of viruses
Christine Mordstein,Laura Cano,Atahualpa Castillo Morales,Bethan Young,Bethan Young,Alexander T Ho,Alan M. Rice,Michael Liss,Laurence D. Hurst,Grzegorz Kudla +9 more
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TLDR
This paper analyzed the patterns of codon usage in 1,520 vertebrate-infecting viruses, focusing on parameters known to be under selection and associated with gene regulation, and found that GC content, dinucleotide content, and splicing and m6A modification-related sequence motifs are associated with the type of genetic material (DNA or RNA), strandedness, and replication compartment of viruses.Abstract:
The nucleotide composition, dinucleotide composition, and codon usage of many viruses differs from their hosts. These differences arise because viruses are subject to unique mutation and selection pressures that do not apply to host genomes; however, the molecular mechanisms that underlie these evolutionary forces are unclear. Here, we analysed the patterns of codon usage in 1,520 vertebrate-infecting viruses, focusing on parameters known to be under selection and associated with gene regulation. We find that GC content, dinucleotide content, and splicing and m6A modification-related sequence motifs are associated with the type of genetic material (DNA or RNA), strandedness, and replication compartment of viruses. In an experimental follow-up, we find that the effects of GC content on gene expression depend on whether the genetic material is delivered to the cell as DNA or mRNA, whether it is transcribed by endogenous or exogenous RNA polymerase, and whether transcription takes place in the nucleus or cytoplasm. Our results suggest that viral codon usage cannot be explained by a simple adaptation to the codon usage of the host - instead, it reflects the combination of multiple selective and mutational pressures, including the need for efficient transcription, export, and immune evasion.read more
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Causes and consequences of purifying selection on SARS-CoV-2.
Atahualpa Castillo Morales,Alan M. Rice,Alexander T Ho,Christine Mordstein,Christine Mordstein,Christine Mordstein,Stefanie Mühlhausen,Samir F Watson,Laura Cano,Bethan Young,Bethan Young,Grzegorz Kudla,Laurence D. Hurst +12 more
TL;DR: In this article, it was shown that the SARS-CoV-2 mutation rate is at least 49-67% higher than would be estimated based on the rate of appearance of variants in sampled genomes.
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Evolutionary Signatures Governing the Codon Usage Bias in Coronaviruses and Their Implications for Viruses Infecting Various Bat Species.
Naveen Kumar,Rahul Kaushik,Chandana Tennakoon,Vladimir N. Uversky,Vladimir N. Uversky,Anamika Mishra,Richa Sood,Pratiksha Srivastava,Meghna Tripathi,Kam Y. J. Zhang,Sandeep Bhatia +10 more
TL;DR: In this paper, the authors used a variety of genetic methods to identify the ancestor of SARS-CoV-2 and showed that trends in codon usage across chiroptera-hosted CoVs are collaboratively driven by geographically different host-species and temporal-spatial distribution.
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Study on the Characteristic Codon Usage Pattern in Porcine Epidemic Diarrhea Virus Genomes and Its Host Adaptation Phenotype
TL;DR: In this paper, a comprehensive investigation was carried out to reveal the systematic evolutionary processes of synonymous codon usage and host-adapted evolution phenotype of PEDV genome, and the authors found a low codon use bias (CUB) in PEDVs genome.
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Evolution and host adaptability of plant RNA viruses: Research insights on compositional biases
TL;DR: In this article , a mini-review of the evolution of plant RNA viruses in view of compositional biases and explore how they adapt to the host is presented, and it appears that adenine rich (A-rich) coding sequences, low CpG and UpA dinucleotide frequencies and lower codon usage patterns were found in the vast majority of plant IR viruses.
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Deep decoding of codon usage strategies and host adaption preferences of soybean mosaic virus.
TL;DR: In this article , a systemic analysis of 107 SMV strains was performed to explore the genome-wide codon usage profile and the various factors influencing the codon use patterns of SMV, which provides insight into its molecular evolution and elucidates its unknown host adaptation pattern.
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