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Codon usage patterns across seven Rosales species.

Yao Zhang1,2, Zenan Shen3, Xiangrui Meng1,2

  • 1College of Life Science, Hebei Agricultural University, Baoding, China.

BMC Plant Biology
|February 6, 2022
PubMed
Summary
This summary is machine-generated.

Codon usage bias analysis in Rosales species reveals natural selection drives evolutionary relationships. This study extends codon usage bias analysis to distantly related species, offering new insights into genetic connections.

Keywords:
Codon usage biasEvolutionary relationshipsNatural selectionRosales

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Codon usage bias (CUB) analysis is crucial for understanding species specificity, evolution, and gene discovery.
  • Previous CUB studies focused on closely related species, limiting insights into distantly related taxa.
  • This study investigates CUB in seven economically important Rosales species.

Purpose of the Study:

  • To analyze codon usage patterns in Rosales species.
  • To determine the factors influencing CUB in this order.
  • To explore the utility of CUB analysis for revealing evolutionary relationships among distantly related species.

Main Methods:

  • Analysis of codon usage bias (CUB) in seven Rosales species.
  • GC content analysis (GC1, GC2, GC3).
  • Neutrality plot and ENc plot analysis.
  • Biclustering heat map analysis.

Main Results:

  • Rosales species exhibit a preference for A/T as the final codon, with average GC3 content at 43.12%.
  • Natural selection was identified as the primary driver of CUB in Rosales evolution.
  • High-frequency codons (AGA, GTT, TTG) were conserved, but codon pairs and GC3 distribution varied among species.
  • CUB analysis effectively revealed evolutionary relationships at the family/order level, consistent with genome data.

Conclusions:

  • Natural selection significantly shapes codon usage patterns in Rosales.
  • This research pioneers CUB analysis in Rosales, providing a novel approach for studying broad evolutionary relationships.