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Selective modes determine evolutionary rates, gene compactness and expression patterns in Brassica.

Yue Guo1, Jing Liu1, Jiefu Zhang2

  • 1Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.

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Summary

Positively selected genes (PSGs) and negatively selected genes (NSGs) exhibit distinct evolutionary, structural, and functional properties. Selective pressures significantly influence gene evolution, compactness, and expression patterns in Brassica species.

Keywords:
Brassicanonsynonymous substitutionpositive selectionpurifying selectionsynonymous substitution

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Area of Science:

  • Evolutionary genomics
  • Molecular evolution
  • Plant genetics

Background:

  • Nuclear protein-coding genes are broadly classified into positively selected genes (PSGs) and negatively selected genes (NSGs).
  • The distinct characteristics and evolutionary trajectories of PSGs and NSGs remain incompletely understood.

Purpose of the Study:

  • To investigate and compare the evolutionary rates, gene structures, expression patterns, and codon bias between PSGs and NSGs in Brassica species.
  • To determine if selective pressure (Ka/Ks) influences other gene properties.

Main Methods:

  • Comparative analysis of orthologous genes between Brassica rapa and Brassica oleracea.
  • Quantification of nonsynonymous (Ka) and synonymous (Ks) substitution rates.
  • Comparison of gene length, exon number, functional specificity, expression levels, tissue specificity, and codon bias between PSGs and NSGs.

Main Results:

  • PSGs exhibit higher protein evolutionary rates (Ka), lower synonymous substitution rates (Ks), shorter gene length, and fewer exons compared to NSGs.
  • PSGs demonstrate higher functional specificity, lower overall expression levels, increased tissue-specific expression, and stronger codon bias than NSGs.
  • These relative differences were also observed in the model species Arabidopsis, supporting the findings.

Conclusions:

  • PSGs and NSGs are distinguishable not only by selective pressure (Ka/Ks) but also by their evolutionary, structural, and functional attributes.
  • Selective modes appear to be a key determinant of evolutionary rates, gene compactness, and expression patterns in Brassica.