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When the fitness of a trait is influenced by how common it is (i.e., its frequency) relative to different traits within a population, this is referred to as frequency-dependent selection. Frequency-dependent selection may occur between species or within a single species. This type of selection can either be positive—with more common phenotypes having higher fitness—or negative, with rarer phenotypes conferring increased fitness.
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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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ACT1-CUP1 Assays Determine the Substrate-Specific Sensitivities of Spliceosomal Mutants in Budding Yeast
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Selection constraints determine preference for A/U-ending codons in Taxus contorta.

Aasim Majeed1,1, Harpreet Kaur1,1, Pankaj Bhardwaj1,1

  • 1Molecular Genetics Laboratory, Department of Botany, Central University of Punjab, City Campus, Mansa Road, Bathinda-151001, India.

Genome
|January 28, 2020
PubMed
Summary

Codon usage bias in the endangered Himalayan gymnosperm *Taxus contorta* is not strong. Natural selection predominantly shapes codon bias, with mutational pressure and other factors having minor influences.

Keywords:
RNA-seqRNAseqTaxus contortabiais dans l’usage des codonscodon usage biasmutationselectionsélection

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Molecular Biology

Background:

  • Unequal synonymous codon usage, known as codon usage bias (CUB), is crucial for translation accuracy and efficiency in organisms.
  • Gymnosperms, particularly endangered species like *Taxus contorta*, have been understudied concerning CUB.
  • Investigating CUB in *Taxus contorta* offers insights into its evolutionary characteristics.

Purpose of the Study:

  • To determine the extent of codon usage bias in *Taxus contorta*.
  • To identify the primary evolutionary forces driving CUB in this endangered gymnosperm.
  • To interpret the evolutionary significance of CUB for *Taxus contorta*.

Main Methods:

  • RNA sequencing data was used to assemble transcripts and identify unigenes.
  • Full-length sequences (13,061) were analyzed for codon usage bias.
  • Analysis included compositional properties (GC-content), effective number of codons (ENC), P2 index, Mutation Responsive Index (MRI), neutrality plots, and parity plots.

Main Results:

  • The genome of *T. contorta* is AT-rich (average GC-content 44.28%).
  • Codon usage bias is not strong in *T. contorta* (mean ENC value indicates this).
  • Preferred codons are A/U-ending, while G/C-ending codons are avoided.
  • Natural selection is the predominant force shaping CUB, supported by P2, MRI, neutrality, and parity plots.
  • Mutational pressure, gene length, hydropathicity, aromaticity, and nucleotide composition have weak influences on CUB.

Conclusions:

  • Natural selection is the main driver of codon usage bias in *Taxus contorta*.
  • While other factors weakly influence CUB, their impact is secondary to natural selection.
  • Understanding CUB in *T. contorta* enhances our knowledge of evolutionary processes in endangered gymnosperms.