Comprehensive analysis of coding sequence architecture features and gene expression in Arachis duranensis

Area of Science:

• Plant molecular biology
• Bioinformatics
• Genomics

Background:

• Coding sequence (CDS) architecture significantly impacts gene expression levels across organisms.
• Codon optimization is a key strategy for enhancing gene expression, making codon usage patterns crucial for genetic engineering.
• While codon usage in many model plants is understood, the relationship between CDS architecture and gene expression in *Arachis duranensis* is largely unexplored.

Purpose of the Study:

• To investigate the relationship between coding sequence (CDS) architecture and gene expression in *Arachis duranensis* under normal and stress conditions.
• To identify specific codon usage patterns and their correlation with gene expression, particularly for differentially expressed genes (DEGs).

Main Methods:

• Bioinformatic analysis of *Arachis duranensis* CDS architectures, including frequency of optimal codon (Fop), polypeptide length, and GC content at the first (GC1), second (GC2), and third (GC3) codon positions.
• Utilized *Arachis* RNA-seq datasets from PeanutBase to assess relationships between gene expression and CDS architecture.
• Compared gene expression and CDS architecture under normal growth, nematode stress, and drought stress conditions.

Main Results:

• Identified 26 high-frequency codons in *A. duranensis* CDSs, preferentially ending in A or T, across all tested conditions.
• Observed similar CDS architectures in DEGs under nematode and drought stresses.
• Found differences in GC1 content between DEGs and non-differentially expressed genes (NDEGs) under both drought and nematode stresses, with DEGs' expression levels affected by CDS architecture under drought stress.

Conclusions:

• Specific CDS architectures, particularly GC1 content, are associated with differential gene expression in *Arachis duranensis* under stress conditions, especially drought.
• While some CDS architectural features correlate with gene expression under stress, no overall correlation was found between differential gene expression and CDS architecture under nematode or drought stress.
• These findings contribute to understanding gene expression regulation in *Arachis duranensis*, with implications for improving cultivated peanut through genetic engineering.