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Analysis of codon usage patterns in Morus notabilis based on genome and transcriptome data.

Yan Wen1,1, Ziliang Zou1,1, Hongshun Li1,1

  • 1State Key Laboratory of Silkworm Genome Biology, Southwest University, Tiansheng Road, Beibei, Chongqing 400715, China.

Genome
|February 9, 2017
PubMed
Summary

This study reveals genome-wide codon bias in mulberry trees (Morus notabilis), showing that gene expression levels are influenced by nucleotide composition, mutation pressure, and natural selection. Optimal codons are favored in highly expressed genes.

Keywords:
Morus notabiliscodon usagegène domestiquehousekeeping genesélection transcriptionnelletranscriptional selectionusage des codons

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Codon usage significantly impacts gene expression regulation and mRNA stability.
  • Research on codon bias in multicellular organisms, like the mulberry tree (Morus notabilis), is less advanced compared to unicellular organisms.

Purpose of the Study:

  • To characterize genome-wide codon bias patterns in Morus notabilis.
  • To analyze codon usage across 12 species within the Rosales order.
  • To investigate factors influencing codon usage and identify optimal codons in M. notabilis.

Main Methods:

  • Genome-wide analysis of codon usage patterns.
  • Comparative analysis across multiple species in the Rosales order.
  • Investigation of correlations between codon bias and factors like nucleotide composition, mutation pressure, natural selection, and gene expression levels.

Main Results:

  • Codon usage in M. notabilis is shaped by nucleotide composition, mutation pressure, natural selection, and gene expression.
  • Optimal codons were identified, and highly expressed genes preferentially utilize these codons.
  • Genes with higher expression exhibit shorter coding regions and reduced amino acid complexity.
  • Housekeeping genes demonstrate stronger translational selection, independent of expression level differences.

Conclusions:

  • Codon bias is a significant regulatory mechanism in Morus notabilis.
  • Translational selection plays a crucial role in optimizing gene expression in highly expressed genes.
  • Understanding codon usage patterns provides insights into gene regulation and evolution in plants.