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Evolution of Codon Usage Bias in Diatoms.

Marc Krasovec1, Dmitry A Filatov1

  • 1Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK.

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Marine phytoplankton, like diatoms, show surprisingly modest codon usage bias (CUB) despite large populations. This may be due to frequent shifts in preferred codons rather than weak selection, limiting the development of strong CUB.

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codon biascodon usagediatomseffective population sizephytoplankton evolution

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Area of Science:

  • Marine biology
  • Genomics
  • Evolutionary biology

Background:

  • Codon usage bias (CUB) is the preferential use of synonymous codons, influenced by selection for translational efficiency.
  • Marine phytoplankton, particularly diatoms, have vast populations, suggesting strong CUB should exist.
  • Previous studies on CUB have not included marine phytoplankton.

Purpose of the Study:

  • To investigate codon usage bias patterns in a diverse range of diatom species.
  • To test the prediction that large population sizes in marine plankton lead to strong CUB.
  • To explore potential drivers of CUB in diatoms, considering selection and population dynamics.

Main Methods:

  • Genome-wide analysis of codon usage patterns across 35 diatom genera.
  • Calculation of the Effective Number of Codons (ENC) to quantify CUB.
  • Analysis of genetic diversity and GC3 content to infer population size and codon usage shifts.

Main Results:

  • Most studied diatom species exhibit modest CUB (mean ENC = 56), with some exceptions (ENC = 44).
  • Modest CUB may result from a large disparity between census and effective population sizes, or frequent shifts in optimal codons.
  • Significant shifts in GC3 content were observed within genera, indicating dynamic codon usage.

Conclusions:

  • Diatoms display unexpectedly low CUB, challenging the direct correlation with large population sizes.
  • Frequent changes in preferred codons, rather than weak selection, are proposed as the primary reason for modest CUB.
  • Variation in selection intensity and mutation spectrum likely contribute to observed CUB patterns in diatoms.