Patterns of Ancestral Green Plants Codon Usage Bias Revealed through Rhodophyta

Rhodophyta is one of the closest known relatives of green plants. Studying the codons of their genomes can provide us with a new understanding of how plants evolved from their unicellular and multicellular ancestors. Codon usage bias has been widely studied in some green plants. However, little is known about the characteristics of codon usage for green plant ancestors. Here, we have studied the codon usage patterns of all close ancestors for green plants, including four unicellular red algae and four multicellular red algae. Codon usage in almost all species is conservative. High-bias genes prefer codons ending with GC, but limited analysis indicates that it is likely to be caused by local mutation pressure. Our analysis proves that natural selection is the dominant factor for the codon usage bias of red algae in terms of translation accuracy and efficiency. It is worth noting that the selection of translation accuracy even can be found in the low-bias genes of individual species. The high-frequency codons are proven to evolve with tRNA together. Optimal codons are found to be complementary and bound to the tRNA genes with the highest copy number. Additionally, tRNA modification is found in the highly degenerate amino acids of all multicellular red algae and individual unicellular red algae. It seems that highly biased genes tend to use modified tRNA in translation. Determining optimal codons will help to design and carry out transgenic work in some economic red algae in the future, by maximizing the corresponding protein yield.