Scaled codon usage similarity index: A comprehensive resource for crop plants.

Area of Science:

• Molecular Biology
• Bioinformatics
• Genomics

Background:

• Species-specific codon usage bias optimizes heterologous gene expression.
• High costs of synthesizing codon-optimized genes for multiple species limit applications.

Purpose of the Study:

• To develop a method for grouping species with similar codon usage to reduce gene synthesis costs.
• To facilitate the development of multi-species expression systems for efficient gene expression.

Main Methods:

• Introduced the Scaled Codon Usage Similarity (SCUS) index for standardizing species similarity assessments.
• Analyzed the SCUS index across 77 plant nuclear genomes from 13 families.
• Developed an online SCUS index database and a Consensus Relative Synonymous Codon Usage (CRSCU) calculator.

Main Results:

• Identified codon usage patterns and similarities among plant species using the SCUS index.
• The CRSCU calculator provides a tool to determine suitable codon usage patterns for multiple species.
• Established an accessible online resource (https://pcud.plantcodon.info) for codon usage analysis.

Conclusions:

• The SCUS index and CRSCU calculator enable cost-effective, multi-species gene expression.
• This approach facilitates the efficient expression of single synthetic genes across diverse crop species.
• Innovations pave the way for efficient heterologous gene expression in various plant species.