Alteration of synonymous codon usage bias accompanies polyploidization in wheat.

Area of Science:

• Genomics
• Molecular Biology
• Evolutionary Biology

Background:

• Polyploid genomes undergo variation, including synonymous nucleotide substitutions, leading to synonymous codon usage bias (SCUB).
• SCUB's role in polyploid formation is not well understood, despite its potential to reflect plant evolutionary specialization.
• Hexaploid wheat and its progenitors provide a model system to study SCUB during polyploidization.

Purpose of the Study:

• To investigate the effect of synonymous codon usage bias (SCUB) on polyploid formation in wheat.
• To analyze SCUB patterns in hexaploid wheat and its progenitors in relation to ploidy level and genomic features.
• To explore the link between SCUB, DNA methylation, and epigenetic variation during wheat polyploidization.

Main Methods:

• Comparative analysis of synonymous codon usage bias (SCUB) across different ploidy levels in wheat and its progenitors.
• Examination of SCUB patterns in relation to gene introns and exon positions.
• Investigation of DNA methylation changes and their correlation with SCUB alterations during polyploidization.

Main Results:

• Synonymous codons (SCs) ending in cytosine (NNC) or guanine (NNG) were more frequent than those ending in adenosine (NNA) or thymine (NNT), with preference increasing with genome ploidy.
• SCUB ratios (NNC/G vs. NNA/T) decreased with more introns and diminished between wheat and progenitors as ploidy increased.
• SCUB was homogeneous across subgenomes (A, B, D) of hexaploid wheat, and DNA methylation-mediated C-to-T conversion weakened with ploidy, correlating with stronger NNC/G bias.

Conclusions:

• Synonymous codon usage bias (SCUB) patterns mirror the formation of hexaploid wheat, providing insights into genome shock-induced genetic variation during polyploidization.
• SCUB contributes to epigenetic variation in hexaploid wheat, with DNA methylation changes playing a role.
• Understanding SCUB in polyploids can aid in genetic dissection and improvement of agricultural traits in wheat and other polyploid crops.