Codon usage bias predicts the functional MYB10 gene in Populus.

Area of Science:

• Plant molecular biology
• Genomics
• Bioinformatics

Background:

• Codon usage bias (CUB) analysis reveals genetic information transfer patterns.
• MYB10 is a key regulator of anthocyanin biosynthesis.
• Identifying functional genes in complex plant genomes is challenging.

Purpose of the Study:

• To analyze CUB of MYB10 genes across species.
• To identify the functional MYB10 gene in Populus among two candidates.
• To validate the effectiveness of CUB analysis for gene identification in plants.

Main Methods:

• Analysis of MYB10 coding sequences from 10 plant species using Codon W, CHIPS, CUSP, and CAI.
• Comparative CUB analysis to identify gene similarity.
• Gene cloning and transient transformation in Populus seedlings.
• Phenotypic and anthocyanin content analysis.

Main Results:

• Optimal MYB10 codons predominantly end in A/U; GGA, UCA, GCA, AGA, and CCA codons are over-represented.
• Potri.17G125700 showed higher codon usage similarity to other plant MYB10 genes.
• Transient transformation confirmed Potri.17G125700 as the functional MYB10 gene, positively regulating anthocyanin.
• CUB analysis successfully selected a MYB12 candidate in Malus sp.

Conclusions:

• CUB analysis is effective for identifying functional genes in long-living plants.
• Potri.17G125700 is the functional MYB10 gene in Populus, regulating anthocyanin accumulation.
• This study validates CUB as a tool for gene discovery in complex plant genetics.