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Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers
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Analysis of codon usage patterns in Haloxylon ammodendron based on genomic and transcriptomic data.

Xiang Huang1, Yalin Jiao1, Jiaxing Guo1

  • 1College of Agriculture, Shihezi University, Shihezi, Xinjiang 832003, PR China.

Gene
|August 29, 2022
PubMed
Summary

This study reveals codon usage bias in Haloxylon ammodendron, a desert shrub. Natural selection, not mutation pressure, is the primary driver, influencing gene expression and function for drought and salt tolerance.

Keywords:
Codon usage bias (CUB)Mutation pressureNatural selectionNucleotide compositionOptimal codon

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Area of Science:

  • Plant genomics
  • Molecular evolution
  • Bioinformatics

Background:

  • Haloxylon ammodendron is a crucial xero-halophytic shrub in desert ecosystems, vital for sand fixation due to its drought and salt tolerance.
  • The codon usage bias (CUB) in H. ammodendron, a key factor in gene expression and protein synthesis, remains largely uncharacterized.

Purpose of the Study:

  • To investigate and compare codon usage patterns in H. ammodendron using both whole-genome and transcriptome data.
  • To identify the primary factors influencing CUB in H. ammodendron, including natural selection and mutation pressure.
  • To explore the relationship between CUB, gene expression levels, gene function, and salt tolerance in this species.

Main Methods:

  • Comparative analysis of codon usage patterns across 38,657 genomic and 3,948 transcriptomic coding sequences (CDSs) of H. ammodendron.
  • Analysis using neutrality plots, effective number of codons (ENC) plots, and parity rule 2 (PR2) bias plots.
  • Examination of the influence of gene expression levels, gene function, and protein length on CUB.

Main Results:

  • H. ammodendron exhibits codon usage bias towards A- and U-ending codons, with guanine-and-cytosine (GC) content predominantly between 40-45%.
  • Natural selection was identified as the most significant determinant of CUB, surpassing mutation pressure.
  • Salt-tolerant unigenes showed similar codon usage, while highly expressed genes utilized optimal codons more frequently and had lower GC content compared to lowly expressed genes.

Conclusions:

  • This study elucidates the primary mechanisms driving codon usage bias in H. ammodendron, highlighting the dominant role of natural selection.
  • The findings provide insights into gene expression regulation and adaptation to arid and saline environments.
  • The results contribute to gene identification and genetic engineering strategies for H. ammodendron.