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Related Concept Videos

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A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material...
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The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
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John H. Renwick first coined the term “synteny” in 1971, which refers to the genes present on the same chromosomes, even if they are not genetically linked. The species with common ancestry tend to show conserved syntenic regions. Therefore, the concept of synteny is nowadays used to describe the evolutionary relationship between species.
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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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In a population that is not at Hardy-Weinberg equilibrium, the frequency of alleles changes over time. Therefore, any deviations from the five conditions of Hardy-Weinberg equilibrium can alter the genetic variation of a given population. Conditions that change the genetic variability of a population include mutations, natural selection, non-random mating, gene flow, and genetic drift (small population size).
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During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
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Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example
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Non-adaptive evolution in codon usage of human-origin monkeypox virus.

Xu Guo1, Junwei Zou1, Kankan Yang2

  • 1College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China.

Comparative Immunology, Microbiology and Infectious Diseases
|July 24, 2023
PubMed
Summary

Monkeypox virus (Mpox) evolution shows Clade-IIb-B underwent non-adaptive changes, reducing host adaptation compared to Clade-I. Codon usage shifts may influence Mpox virulence and host gene expression.

Keywords:
Codon adaptation indexCodon usageEvolutionMonkeypox virusNon-adaptiveRelative codon deoptimization indexVirulence

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Area of Science:

  • Virology
  • Genomics
  • Evolutionary Biology

Background:

  • Monkeypox virus (Mpox) is a zoonotic pathogen causing significant human and animal health concerns.
  • The 2022 global outbreak highlighted the need to understand Mpox evolution and host adaptation.

Purpose of the Study:

  • To analyze codon usage differences between Mpox Clade-I and Clade-IIb-B.
  • To investigate the evolutionary mechanisms driving host adaptation in Mpox.

Main Methods:

  • Comparative analysis of Mpox genome codon usage between Clade-I and Clade-IIb-B.
  • Identification of adaptive and non-adaptive mutations in individual genes.
  • Assessment of codon usage similarity to host genes (up-regulated and down-regulated).

Main Results:

  • Mpox Clade-IIb-B exhibited non-adaptive evolution, indicating reduced host adaptation compared to Clade-I.
  • 48 genes showed non-adaptive mutations, while 38 displayed adaptive mutations.
  • Mpox codon usage correlated with down-regulated host genes post-infection, suggesting an impact on host gene expression.

Conclusions:

  • Non-adaptive codon usage changes may contribute to variations in Mpox virulence.
  • Understanding these evolutionary patterns offers insights into Mpox pathogenicity and host adaptation.
  • The study reveals potential mechanisms influencing Mpox-host interactions.